Table of contents :

Thousands of different commensal microbial species populate Homo sapiens outer and inner body surfaces :

• in saliva 10⁸ bacteria/ mL
• in stomach 10³-10⁵ bacteria per gram or mL of luminal contents in mice, consisting mainly of acid-tolerant species (e.g. Lactobacilli spp., Streptococcus spp., Helicobacter pylori) unless patient is treated with antiacids (H₂ antagonists, PPI), a risk factor for aspiration pneumonia
• Boas-Oppler bacillus / lactobacillus of Boas-Oppler : a microorganism, probably a species of Lactobacillus, first found in the gastric juice of patients with stomach carcinoma
• in gut 500-1,000 different species exist : their microbiome contains 100-fold more genes than human genome. Gut is colonized ~ 40 hrs after birth.
• in small bowel :
• in duodenum and jejunum : 10²-10⁵ bacteria/mL (Streptococcus spp., Lactobacillus spp., Enterobacter spp., Bacteroides spp.)
• in ileum : 10⁸-10⁹ bacteria per gram or mL (Lactobacillus spp., Streptococcus spp., Bacteroides spp., Enterobacter spp.)
• in colon : 10¹⁰-10¹⁴ bacteria/mL (> 400 species, each present at approximately 10⁹ per gram : Streptococcus spp., Enterococcus spp., Enterobacter spp., anaerobes (Bacteroides spp., Bifidobacterium spp., gram-positive cocci and Clostridium spp., Fusobacterium spp., Peptococcus spp., and Peptostreptococcus spp. (very likely to cause IAI)). By contrast, aerobes and facultative aerobes, including enterobacteria and lactobacilli, are present at only moderate densities (10⁶-10⁸ per gram)
• paracolon bacilli : microorganisms commonly found in the intestinal flora, distinguished by delayed (5–21 days) fermentation of lactose. Organisms of this type belong to the genera Escherichia, Citrobacter, or Klebsiella
• in stools : 10¹² bacteria / g (70% ^w/_w)
There are 2 main difficulties in understanding and measuring these complex flora.
• a comparison of 2 techniques used to assess faecal bacterial numbers - counting colonies of culturable bacteria and estimating numbers using smears - shows that < 50% of intestinal bacteria can be cultured. This is becaue of the precise oxygen requirements of some species and their fastidious (and largely unknown) nutrient requirements
• although most measurements have been made using faecal bacteria, the intestine is not a homogeneous environment - groups of bacteria can also exist on the surface of the mucus layer or deep within it
Fortunately, there are ways of overcoming the difficulties in culturing intestinal bacteria. The 1.5-kb gene encoding 16S ribosomal RNA is present in multiple copies in bacterial chromosomes, and it is highly polymorphic. Therefore, the nucleotide sequences of this gene (obtained after amplification by PCR) can be used to determine the species of each organism, and the gene can serve as a target (in species-specific in situ hybridization) for studying the spatial arrangement of each bacterial group.
Bacteroides spp. decorate their capsular polysaccharides and surface glycoproteins with L-fucose, also abundant on the surface of intestinal epithelial cells, and stimulates intestinal epithelial cells to express fucosylated molecules : this molecular mimicry allows Bacteroides to be tolerated by the host^ref.
The majority of 13,355 prokaryotic ribosomal RNA gene sequences from multiple colonic mucosal sites and feces of healthy subjects correspond to uncultivated species and novel microorganisms, with significant intersubject variability and differences between stool and mucosa community composition^ref.
• in vagina 10⁸ bacteria / mL : Döderlein's bacillus : one of the gram-positive rods commonly found in vaginal secretions that may consist of mixtures of Lactobacillus acidophilus, L. casei, L. cellobiosisus, L. fermentum, or Leuconostoc mesenteroides. Said by some to be identical with L. acidophilus
• in nose microbiota is dominated by Corynebacterium spp., Microbacterium spp., Rhodococcus spp., Staphylococcus epidermidis,Staphylococcus capitis, Staphylococcus hominis,Staphylococcus haemolyticus,Staphylococcus lugdunensis and Staphylococcus warneri. Under special circumstances, single species, including IgA₁ protease-producing bacteria, may become predominant in a restricted area of the nasal mucosa^ref.
• in skin commensals can be divided into
• permanent (e.g. Staphylococcus epidermidis)
• transient (Staphylococcus aureus, Pseudomonas aeruginosa, Enterobacter spp.) : they are a leading cause of nosocomial infections, being present on 31 % of physicians' hands (7^.10⁴ CFUs / hand) and 17 % of nurses' hands (4^.10⁴ CFUs / hand).

Taxonomic units

• phylum / class (-es / -ia / -eae)
• [ subclass (-dae) ]
• order (-ales)
• [ suborder (-ineae) ]
• family (-aceae)
• genus
• species

• Actinobacteria (high G+C Gram-positive Bacteria)
• Actinobacteridae
• Actinomycetales
• Actinomycineae (form branched hyphae).
• Actinomycetaceae
• Actinomyces (a.k.a. Pseudomycetes (~ Hyphomycetes); strictly or facultative anaerobes => endogenous infections)
=> actinomycosis
• Actinomyces gerencseriae
• Actinomyces israelii

=> gingivitis
=> actinomycotic mycetoma / maduromycosis (chronic granuloma with draining fistulae from which sulfur granules come out)
• cervicofacial : 15-20 days after tooth extraction, mandibular fracture or mucosal injuries
• thoracic or pulmonary : hematogenic or contiguity with a cervicofacial one
• abdominal or gastrointestinal (ileocecal > anorectal > gastric) : after abdominal wall or gut mucous membrane injuries. Rarely creating cutaneous fistulas^ref
• genital or pelvic : in IUD-using females or after trauma
• rare : cerebral, bone, hepatic and renal.
• Actinomyces meyeri
• Actinomyces naeslundii
• Actinomyces neuii
• Actinomyces odontolyticus (a.k.a. Bacillus acidophilus odontolyticus)
• Actinomyces viscosus (only 6-deoxytalose⁺ strains are pathogenic)

=> periodontitis, caries, gingivitis
• Arcanobacterium
• Arcanobacterium haemolyticum (a.k.a. Corynebacterium haemolyticum)
Epidemiology : 1st described in 1946 as the pathogenic agent causing pharyngitis and cutaneous infections among US servicemen and indigenous peoples of the South Pacific in 1946. As a result of its close resemblance to Corynebacterium pyogenes, some investigators believed the bacterium to be a mutant of this species and appended a subspecies name, C. pyogenes subsp. hominis. Based on its biochemical and nucleic acid characteristics, the bacterium was renamed and reclassified as the 1st member of the genus Arcanobacterium, which means secretive bacteria, in 1982. In 2005 an antibiotics-resistant strain was found in 142 students with cold symptoms in Guri, Gyeonggi province, South Korea, starting on 20 May 2005
Transmission : spread through an unknown route by human contact with people who are infected. The chronic carrier state appears to be rare
=> primarily causing an exudative pharyngitis with a rash that may look like scarlet fever, the spectrum of diseases caused by A. haemolyticum has been expanded to include invasive infections, including sepsis and osteomyelitis. The pathophysiology of the rash is unknown;
however, it is thought that the rash is caused by a bacterial exotoxin.
Therapy : despite being fully sensitive to penicillin in vitro, penicillin treatment failures of A. haemolyticum were frequent^ref. The ability of A. haemolyticum to survive intracellularly for 4 days, thus creating intracellular reservoirs of bacteria, might explain this dichotomy. Osterlund also showed that erythromycin, an antibiotic known to penetrate well intracellularly, efficiently killed these bacteria
• Arcanobacterium pyogenes (a.k.a. Actinomyces pyogenes)
• Mobiluncus
• Mobiluncus curtisii
• Mobiluncus curtisii subsp. curtisii
• Mobiluncus curtisii subsp. holmesii
• Mobiluncus mulieris
=> bacterial vaginosis
• Corynebacterineae
• Corynebacteriaceae (coryneform bacteria : Babes-Ernst metachromatic granules) at the pear-shaped end ; resist high [K₂TeO₃], reducing it to Te (gray-black precipitates; Chinese ideograms-shaped colonies)
• Corynebacterium (obliged or facultative aerobes)
• Corynebacterium accolens from human clinical specimens (wound drainage, endocervix, sputum, and throat swab specimens) collected over a 30-year period was first described by Neubauer et al. in 1991. It is a gram-positive bacillus and was originally characterized by its satellite growth around a Staphylococcus aureus streak on blood agar. C. accolens is considered an inhabitant of the upper respiratory tract. It is a lipophilic species that forms small, gray, transparent, nonhemolytic colonies on sheep blood agar after 48 h of incubation. Typically, C. accolens produces good growth in media enriched with a significant amount of lipids (e.g., 0.1 to 1% Tween 80), where it produces colonies like those of Corynebacterium diphtheriae or C. minutissimum.
=> breast abscessref
• Corynebacterium amycolatum
=> bacteremia^ref
• Corynebacterium afermentans
=> bacteremia^ref
• Corynebacterium bovis
=> endocarditis
=> CNS infections
• Corynebacterium diphtheriae (a.k.a. Klebs-Löffler bacillus)
Epidemiology : a diphtheria epidemic began in 1990 in Russia and spread to all of the remaining New Independent States (NIS) of the former Soviet Union by the end of 1994. > 150 000 cases and 5000 deaths have been reported from the NIS in 1990-1998. Widespread immunization campaigns since 1994 have largely controlled the epidemic, although over 2700 cases were still reported in 1998.
Biovars :
• gravis (g-hemolytic; doubling time : 60'; large, flat and grey colonies)
• intermedius (doubling time : 100')
• mitis (a-hemolytic; doubling time : 180'; small, convex and black colonies).
Also, if the kinetics of toxin production follow the kinetics of bacterial growth, the faster growing variety would achieve an effective level of toxin before the slow growing varieties.
Genomics : a single circular chromosome of nearly 2.5 Mb with no plasmids, including 13 regions of unusually high GC content indicative of recent gene acquisition containing pathogenicity islands encoding the majority of factors such as fimbriae and fimbriae-related genes, as well as iron uptake systems. The location and GC content of the tox gene, at the right-hand end of an integrated corynephage b, also suggests recent acquisition by horizontal gene transfer  It encodes a disulfide-bound p62^A-B protein (diphteria toxin) : repressor is chromosome-encoded DtxR, corepressor is inorganic iron (Fe^{2+ / 3+}). Trypsin-like proteases create 2 disulfide-bound subunits : p40^B subunit binds the diphteria toxin receptor (DTR / p160^{heparin-binding (HB) prepro-EGF-like growth factor} (ubiquitary => pantropic toxin) and creates a pseudopore that allows p22^A subunit to enter the cell and to ADP-ribosylate diphtamide residue (a His modified by at least 3 eukaryal enzymes) 715 in eEF2. ADP-ribosylation increase eEF2 ability to be phosphorylated and inactivated by CaMKIII / eEF2K. LD₅₀ = 60 pg in Cavia porcellus. Core regions containing cell wall components contributing to pathogenicity have been identified, including an arabinogalactan polymer involved in adhesion.
Transmission :
• oro-oral or (in tropical regions only) skin-oral contagion (homogeneous and homonymous transmission) or ingestion of at least 0,1 mg toxin/Kg weight => diphteria (a.k.a. "El garatillo" (the strangler") in Spain, "the gullet disease" in Italy) : gray pseudomembrane (fibrinous angioflogosis) marks nasopharyngitis, oropharyngitis (oedema => "bull-neck") and/or larynx (maximal vascularization => maximal toxin absorption => malignant angina) or tracheitis (croup : suffocating risk if detachment occurs !) with regional lymphadenitis. Complications : after 2÷3 weeks 20÷30% undergo bacteraemia =>
• neurological manifestations
• hypesthesia and local paralysis of the soft palate
• weakness of the posterior pharyngeal, laryngeal, and facial nerves, causing a nasal tone in the voice, difficulty in swallowing, and risk of death from aspiration
• cranial neuropathies that characteristically occur in the 5th week and lead to oculomotor nerve paralysis and ciliary nerve paralysis, which manifest as strabismus, blurred vision, or difficulty with accommodation
• glossopharyngeal (IX) nerve palsy
• other cranial/spinal nerve palsies
• Widowitz's sign : protrusion of the eyeballs and sluggish movements of the eyeballs and eyelids seen in diphtheritic paralysis.
• symmetric polyneuropathy that begins within 10 days to 3 months after oropharyngeal infection and principally causes motor function deficit with diminished deep tendon reflexes
• proximal muscle weakness of the extremities progressing distally and, more commonly, distal weakness progressing proximally. Clinical and cerebrospinal fluid (CSF) findings in distal weakness are indistinguishable from findings of polyneuropathy of Guillain-Barre syndrome (GBS). Paralysis of the diaphragm can ensue.
• acute serous tonsillitis
• early or late myocarditis
• acute renal failure
Total lethality is 10% (16% in babies, 5% in adults) : diphtheria is more severe for those under 5 and over 40 years of age. Individuals that have fully recovered from diphtheria (usually within 8-10 days) may continue to harbor the organisms in the throat or nose for weeks or even months.
• skin-skin or oral-skin contagium => chronic skin ulcers that don't undergo scaring
Direct diagnosis :
• examination of glass slides (Gram and metachromatic stainings)
• culturing on Löffler or McLeod media
Demonstration of a toxin-producing strain  :
• in vivo by injecting a culture into a footpad of a guinea pig (negative control with neutralizing antiserum on the controlateral footpad)
• in vitro
• Elek test (an agar immunodiffusion)
• PCR looking for tox gene
Therapy :
• administration of heterologous immune antiserum within 48 hours of onset (almost useless after day 4) after testing for sensitivity to antitoxin;
• procaine penicillin G 600,000 units IM bid for 14 days (150,000 units/kg/day IV for 10 days for pediatric patients) or erythromycin 500 mg parenterally or po qid
• bedrest and supportive care
• isolation until secretions are noncontagious
• intubation
Prevention : attenuated, toxoid or heterologous vaccine in newborns : diphteria is reemerging in countries which have stopped vaccination programmes. Concentration of neutralizing Abs may be evaluated by Schick test (1913):

Skin response after subcutaneous injection in a forearm of ...	1/50 LD50 diphteria toxin = 0.8 ng in 0.2 mL		12.4 ng diphteria toxoid in 0.2 mL in the counterlateral forearm		INTERPRETATION
	24-48 h (36 h)	4-7 days (lasts for a week)	24-48 h (36 h)	4-7days
positive reaction	-	+	-	-	nonimmune (antitoxin titre < 1/30 U =  [ ] < 0.01 UI/mL), nonsensitive
negative reaction	-	-	-	-	immune (antitoxin titre > 1/30 U =  [ ] > 0.01 UI/mL), nonsensitive
pseudoreaction	+	-	+	-	immune, type IV hypersensitivity against polluttants in the toxin preparation
combined reaction	+	+	+	-	nonimmune, type IV hypersensitivity against polluttants in the toxin preparation

• Corynebacterium genitalium
• Corynebacterium jeikeium (group JK Corynebacterium), a skin bacterium rod that is a strict aerobe and is predominantly present in the human axilla and involved in axillary odor formation. Under the influence of the active deodorant ingredient 4-hydroxy-3-methoxybenzyl alcohol, the skin bacterium Corynebacterium jeikeium moderately responds with differential gene expression^ref. Coryneform bacteria are in dynamic equilibrium with coagulase-negative staphylococci and they amount 4,7% of resident aerobic flora. On the base of biological and metabolic features 49 different biotypes were indicated. Biotypes of lipophilic rods were the basic part of coryneform flora existing for long period. The most frequently isolated taxa were C. jeikeium (31%), CDC group G2 (23,4%), next in order CDC group G1 (11%) and C. afermentans ssp. lipophiluni (7%)^ref.
=> infection of skin wound => bacteriemia^ref => sepsis^ref. In many patients with Hickman catheters, C. jeikeium bacteremia may be treated successfully with vancomycin and without removal of the catheter^ref
=> mechanical or biological prosthetic valve endocarditis. All 38 patients with C. jeikeium endocarditis reported in the literature had at least one predisposing condition for the development of infective endocarditis. 74% had involvement of a prosthetic heart valve. The mortality attributed to C. jeikeium endocarditis was 33% and was similar in patients who did and did not undergo valve replacement^ref.
=> otitis media^ref => meningitis^ref
=> osteomyelitis^ref
=> prosthetic joint infection are extremely rare^ref
=> exit-site/tunnel infection in CAPD^ref
=> discitis^ref
Therapy : vancomycin is generally required for treatment of this multidrug-resistant organism. Oral cephalosporin may be an alternative treatment regimen for exit-site infections if sensitive. A high resistance rate to ciprofloxacin and erythromycin was found in the 3 species. Telithromycin was much more active than erythromycin (MIC₉₀ of erythromycin >or=128 mg/l for all 3 species; MIC(90) of telithromycin: 4 mg/l for C. jeikeium, 64 mg/l for C. amycolatum and 1 mg/l for C. urealyticum). There were no teicoplanin-resistant (MIC₉₀ 1, 0.5 and 1 mg/l, respectively) or linezolid-resistant strains (MIC(90) 1, 0.2 and 0.5 mg/l, respectively). Quinupristin-dalfopristin was active against most strains with an activity similar to linezolid, but 3 C. jeikeium and 1 C. amycolatum showed MICs >or=4 mg/l. Telithromycin showed much better activity against corynebacteria than older macrolides^ref. Synercid and linezolid were active against most isolates tested, including multidrug resistant strains^ref.
• Corynebacterium matruchotii (a.k.a. Bacterionema matruchotii)
• Corynebacterium minutissimum
Pathogenesis : overgrowth of Corynebacterium minutissimum in the superficial stratum corneum of moist intertriginous and interdigital regions
Laboratory examinations : under examination with ultraviolet A light from a Wood's lamp, the rash exhibits coral-red fluorescence as a result of the production of coproporphyrin III. It helps to distinguish this disorder from dermatophytoses, candidal intertrigo, and psoriasis. Skin scrapings show gram-positive filamentous rods, which may be helpful in assessing for concurrent dermatophytic and candidal infection.
=> erythrasma
• Corynebacterium propinquum
=> bacteremia^ref
• Corynebacterium pseudodiphtheriticum (a.k.a. Hofmann's bacillus, Corynebacterium hoffmanii)
=> endocarditis
=> LRT infections
• Corynebacterium pseudogenitalium described in 1979 by Furness et al.^ref for lipophilic corynebacteria isolated from urinary tract and was not considered a pathogen, in contrast to C. genitalium. C. pseudogenitalium was divided into 5 types based on biochemical patterns, and strains of the type C-5 were differentiated from other types on the basis of urease production. The pathogenicity of this bacterium was associated with strong urease activity

=> urinary tract infections (UTI)^{ref1, ref2}
• Corynebacterium pseudotuberculosis (a.k.a. Preisz-Nocard bacillus, Corynebacterium ovis)
=> granulomatous suppurative lymphadenitis
• Corynebacterium renale
Transmission : Bos taurus
=> urinary tract infections and urolithiasis^ref
• Corynebacterium riegelii
=> urinary tract infections (UTI)
• Corynebacterium striatum
=> endocarditis
=> exit-site/tunnel infection in CAPD^ref
=> disseminated infections in immunocompromised individuals
• Corynebacterium tenuis
=> trichomycosis axillaris : a superficial infection of the axillary or pubic hair in which yellow, black, or red nodular concretions form around the hair shaft
• Corynebacterium ulcerans
=> diphteria-like syndrome (producer of DT) : pharyngitis
• Corynebacterium urealyticum (group D2 Corynebacterium)
=> can transform urea to ammonia, creating alkaline urine. This process can result in a predisposition to the precipitation of struvite and calcium phosphate crystals, which can lead to the formation of kidney stones and encrustation throughout the urinary tract. Pyelitis and incrusted alkaline cystitis result from chronic inflammation^ref
• Corynebacterium xerosis
=> endocarditis
=> disseminated infections in immunocompromised individuals
other opportunistic pathogens are named diphteroid or para- / pseudodiphteric species
• Gordonia (previously classified as a Rhodococcus species) are a recognized pathogen in immunocompromised as well as immunocompetent patients, causing bacteremia^{ref1, ref2, ref3, ref4, ref5}, endocarditis^ref, and central nervous system infections^{ref1, ref2}. Biochemically, G. bronchialis and G. terrae cannot always be distinguished conclusively; however, the 2 species can be separated by 16S rRNA gene sequence differences^ref. The inability to clear the infection in our case with prolonged antimicrobial therapy deserves special attention. The recurrence of infection with Gordonia species has been described previously^{ref1, ref2, ref3}, usually with subsequent clearance. More frequently, the infections were cleared only after prolonged antimicrobial treatment and surgical debridement where appropriate^{ref1, ref2, ref3, ref4, ref5, ref6,}
• Gordonia bronchialis
=> recurrent breast abscess in an immunocompetent patient^ref
=> bacteremia in a patient with a sequestrated lung^ref and in sternal wound infections after coronary artery bypass surgery^ref
• Gordonia terrae
=> granulomatous mastitis following nipple piercing^re
• Mycobacteriaceae (strictly aerobes; alcohol- and acid-fast; cord factor of virulent mycobacteria that prevents fusion of lysosomes with endosomal vacuoles and allows serpentine cord-like formation in vitro, while in vivo they occur as "swallow tail-shaped" ; produce exochelin-mycobactin system for Fe²⁺ uptake; colonies will normally grow in 2-3 weeks, but if a patient is on some kind of chemotherapy, then growth may take up to 8 weeks. At 37 °C, cultures have been found viable and virulent after 12 years of sctorage. After 2 hours of direct sunlight, organisms from cultures will die. If the bacillus is contained within the sputum, it will take 20 to 30 hours of direct sunlight before the organisms are killed. Tubercle bacilli can survive for several months in sputum if protected from direct sunlight.
• Mycobacterium
• Runyon classification : based on the pigmentation and growth condition
=> mycobacterioses
• Mycobacterium tuberculosis complex (MTC)
• Mycobacterium africanum
• Mycobacterium bovis
• Mycobacterium cannettii
• Mycobacterium microti
• Mycobacterium tuberculosis
• atypical mycobacteria / mycobacteria other than tuberculosis (MOTT) / nontuberculosis mycobacteria (NTM)
• Mycobacterium abscessus

Epidemiology : a total of 12 cases, all laboratory-confirmed, have been reported from residents of New York (5), Massachusetts (2), North Carolina (2), Rhode Island (2), and Puerto Rico (1). The patients underwent procedures in multiple surgical centers in Santo Domingo during May 2003-February 2004. 11 of the 12 patients were interviewed. All were women; median age was 32 years (range: 19-59 years). Surgical procedures consisted of 1 or more of the following: abdominoplasty (i.e., "tummy tuck") (10 patients), liposuction (5), breast lift (4), breast reduction (4), and breast implant (1). Symptoms of infection began a median of 5 weeks after surgery (range: 1-20 weeks) and included subcutaneous or deep-tissue abscesses requiring incision, drainage, and antibiotic therapy in all patients; 9 patients were hospitalized. Molecular typing using PFGE and randomly amplified polymorphic DNA PCR confirmed that M.abscessus isolates from 7 of 12 specimens were indistinguishable. Organisms with this common genetic pattern were recovered from patients who had surgery performed during Oct-Dec 2003 in the same surgical center in Santo Domingo.
=> skin and soft tissue infections that often results from inoculation with contaminated foreign material (e.g. material used for soft-tissue augmentation)
=> endophthalmitis and crystalline keratopathy : therapeutic lamellar keratectomy with flap removal can provide an effective treatment modality for the management of post-LASIK keratitis that is unresponsive to amikacin and ciprofoxacin given for 6 weeks
=> lung infection (bilateral small nodular opacities, bronchiectasis, and cavity formation). It is the most prevalent nontuberculous mycobacterium in respiratory samples from children with cystic fibrosis
Therapy : flomoxef, imipenem-cilastatin, panipenem, meropenem, clarithromycin and minocycline
• Mycobacterium asiaticum
• Mycobacterium avium complex (MAC) (a.k.a. Mycobacterium tuberculosis var. avium)

They usually are much more drug-resistant than MTC Mycobacteria.
• Mycobacterium avium (nonphotochromogen MOTTs; serovars 1-6, 8-11 and 21)
• Mycobacterium avium subsp. avium

=> rare pulmonary infections (sometimes cavitating) in patients with COPD or CF
=> carpal tunnel syndrome (CTS)
• Mycobacterium avium subsp. paratuberculosis (MAP) (a.k.a. Mycobacterium johnei)
=> Johne's disease / paratuberculosis in ruminants and other animals
Transmission : infected cows secrete the bacteria into their milk and on to their pastures. Survival for up to 55 weeks was observed in fecal material in a dry fully shaded environment (from soil and grass in pasture plots and boxes), with much shorter survival times in unshaded locations. Moisture and application of lime to soil did not affect survival. UV radiation was an unlikely factor, but IR wavelengths leading to diurnal temperature flux may be the significant detrimental component that is correlated with lack of shade. The organism survived for up to 24 weeks on grass that germinated through infected fecal material applied to the soil surface in completely shaded boxes and for up to 9 weeks on grass in 70% shade. The observed patterns of recovery in three of four experiments and changes in viable counts were indicative of dormancy : however, survival of MAP in the environment is finite, consistent with its taxonomic description as an obligate parasite of animals^ref. The findings of several milk surveys during which optimised sensitive detection methods were employed (chemical decontamination with 0.75% cetyl pyridinium chloride (CPC) for 5 h prior to culture and a novel immunomagnetic PCR technique) have revealed that detectable levels of MAP are present in bulked raw cows' milk in the UK at both the farm level and at dairy processing plants prior to pasteurisation. Furthermore, results of 3 different experimental approaches to assess the effect of pasteurisation time/temperature conditions on the viability of MAP (laboratory pasteurisation studies, a national survey of commercially pasteurised milk, and processing of naturally infected milk through commercial-scale pasteurising plant) provide firm evidence that this organism is capable of surviving commercial milk pasteurisation on occasion. Hence, both raw and pasteurised cows' milk are potential vehicles of transmission of MAP to humans^ref. Published pasteurization studies in which milk samples were decontaminated before culture will have underestimated the survival capability of MAP after high-temperature, short-time (HTST) pasteurization. CPC decontamination should not be applied to pasteurized milk in future studies^ref.
=> inflammatory bowel diseases (IBDs) : the involvement of MAP in Crohn's disease (CD) in humans has been uncertain because of the substantial difficulties in detecting this pathogen : in its Ziehl-Neelsen staining-negative form, MAP is highly resistant to chemical and enzymatic lysis. By using optimized sample processing and DNA extraction procedures, MAP is detected by nested PCR methodologies targeted at IS900 in 92% of fresh ileocolonic biopsy specimens from patients with CD vs. 26% of patients in a control group and by mycobacterial growth indicator tube (MGIT) cultures in 42% CD patients (60% when incubated for > 38 weeks) vs. 9% of controls^ref. Up to 55% of dairy herds in Western Europe and America are infected with the bacteria, which can survive the normal flesh method of pasteurisation (it involves heating milk to 72°C for 15", but to be sure of killing MAP milk would need to be heated to that level for 30") and MAP bacteria are present in 2% of retail pasteurised milk cartons : those individuals with CD or their close relatives, who may feel particularly at risk, should drink UHT milk. Water supplies become infected as the droppings from herds seep into the soil, down into natural aquifers. American studies have isolated MAP from the breast milk of women with Crohn's disease but not in women who do not have the illness.
=> irritable bowel syndrome (IBS) : MAP inflames the nerves of the gut in both animals and humans
Laboratory examinations : DTH is tested with the extract johnin.
Transmission : infects mainly birds and is found in the environment. The organism is shed in large numbers via bird droppings, making contaminated food or bedding a potent source of infection. Sus scrofa are rarely infected by M. bovis but are commonly infected via environmental contamination by the avian/intracellulare complex, which does not spread between pigs.
=> HIV-1-immunocompromised individuals may acquire Mycobacterium avium through the intestinal tract where it translocates across the mucosa to enter submucosal macrophages in the lamina propria : from the mucosa, dissemination may then occur to a variety of susceptible tissues. 90% of disseminated infections in individuals with AIDS arise from serovars 1, 4 and 8. In HIV-1^- individuals, susceptibility to pulmonary infections often occurs in the context of predisposing lung conditions (elderly women and smokers) : cutaneous manifestations of MAC in immunocompetent individuals also occur, expecially in children. All of these manifestations of MAC have in common infiltration by mononuclear cells and granuloma formation.
• Mycobacterium avium-intracellulare (a.k.a. Battey bacilli [Battey, a tuberculosis hospital in Rome, Georgia, where many strains of these mycobacteria were first recognized]; nonphotochromogen MOTTs; serovars 7, 12-20 and 25)
=> batteyin : a product prepared from Battey bacilli (Group III of the unclassified mycobacteria), comparable to tuberculin, used in a cutaneous test of hypersensitivity.
=> opportunistic disseminated infection in patients with AIDS
=> rare pneumonia (sometimes cavitating) in patients with COPDor CF
=> carpal tunnel syndrome (CTS)
• Mycobacterium scrofulaceum (scotochromogen MOTT)

=> scrofula / scrofulosis (monolateral cervical lymphadenitis) in children from ingestion of milk, fresh milk derivatives or mollusks => fibrosis, ulcer and fistulae
=> septic arthritis
=> bronchopneumopathies
=> Lady Windermere syndrome
=> hot tub lung is a recently described form of granulomatous interstitial pneumonia in immunocompetent hosts that appears to have some features of diffuse infections and some features of hypersensitivity pneumonia : at T > 84°F, where many tubs operate, chlorine loses its disinfectant properties, and MAC can flourish. The bubbles and steam arising from the tub create an aerosol through which MAC readily enters the lung by inhalation. . Discontinuation of hot tub use, without antimycobacterial therapy, leads to prompt improvement in symptoms, pulmonary function, and radiographic abnormalities, strongly supporting a diagnosis of hypersensitivity pneumonitis.
=> genital and urinary tract infections (UTI)
=> osteomyelitis
=> systemic infections
• Mycobacterium bohemicam
• Mycobacterium celatum
• Mycobacterium conspicuum
• Mycobacterium chelonae (a.k.a. Mycobacterium chelonei; rapid grower)

Epidemiology : infections associated with face lifts-New Jersey, 2002-2003^ref. During October 1996-March 1998, 9 patients in 8 hospitals in Caracas, Venezuela, acquired surgical-site infections (SSI) caused by rapidly growing mycobacteria (RGM)^ref
=> pneumonia, bones (carpal tunnel syndrome (CTS)), CNS, prosthetic heart valves, skin and soft tissues, including localized infections and abscesses at the site of puncture wounds
Therapy : doxycycline
• Mycobacterium cosmeticum (a.k.a. Mycobacterium oesypum)

Epidemiology : isolated from footbath drains and a sink at a nail salon located in Atlanta, GA, USA; the fourth was obtained from a granulomatous subdermal lesion of a female patient in Venezuela who was undergoing mesotherapy^ref
• Mycobacterium elephantis
• Mycobacterium flavescens
• Mycobacterium fortuitum (rapid grower)
• Mycobacterium fortuitum subsp. pseudoperegrinum
Epidemiology : in September 2000-2001 4 patients in California after pedicure (footbaths at a nail salon)^{ref1, ref2}; in Dec 2004-Feb 2005 143 cases from 33 salons
=> infections of the lungs, bones (carpal tunnel syndrome (CTS)), CNS, prosthetic heart valves, skin and soft tissues, including localized infections and abscesses at the site of puncture wounds
Therapy : doxycycline
• Mycobacterium gastri
• Mycobacterium genavense is a frequently missed agent of disseminated disease in AIDS patients with a lymphocyte count < 25 cells/mm^{3ref1, ref2}. It has unusual fastidious growth requirements and shows poor and variable growth in vitro. Molecular biology techniques are necessary for accurate diagnosis of infection^ref
• Mycobacterium goodii
• Mycobacterium gordonae (a.k.a.: tap-water bacillus; scotochromogen MOTT)

=> meningitis
=> peritonitis
• Mycobacterium haemophilum (nonphotochromogen MOTT)

Epidemiology : reports have originated from diverse geographic areas worldwide; poorly defined; there appears to be a genetic diversity between strains isolated from different regions.
Transmission : probably present in the environment, but recovery by sampling has not been successful. M. haemophilum has several unique traits, including predilection for lower temperatures (30-32°C) and requirement for iron supplementation (ferric ammonium citrate or hemin). These may in the past have compromised recovery in the laboratory.
=> reports of the association with disease in humans have greatly increased. At least 64 cases have now been reported, with symptoms ranging from focal lesions to widespread, systemic disease. The organism is now known to cause primarily cutaneous and subcutaneous infection (subcutaneous nodules, painful swelling, ulcers progressing into abscess), septic arthritis, osteomyelitis, and pneumonitis in patients who are immunologically compromised and submandibular lymphadenitis^{ref1, ref2, ref3, ref4, ref5, ref6} and draining fistulas in apparently immunocompetent children. Underlying conditions in the compromised patients have included AIDS; renal, bone marrow, and cardiac transplantation; lymphoma; rheumatoid arthritis; marrow hypoplasia; and Crohn's disease
Laboratory examinations : M. haemophilum requires special growth conditions^ref, and most of the diagnostic laboratories do not use these culture conditions. Therefore, M. haemophilum infection could be seriously underdiagnosed^{ref1, ref2, ref3, ref4}. A species-specific real-time PCR has been developed to detect it directly in clinical materials^ref
Therapy : not been well elucidated, and the outcome appears to be influenced by the patient's underlying immunosuppression. The organisms are most susceptible to ciprofloxacin, clarithromycin, rifabutin, and rifampin. Timely diagnosis and therapy require communication between clinician and the laboratory^ref
• Mycobacterium heckeshornense
• Mycobacterium kansasii (photochromogen MOTT : red b-carotenes)

=> sporotrichoid (~ infection by Sporothrix schenckii), a chronic pneumonia involving the upper lobes, with evidence of scarring. Rare disseminated infection in immunocompromised hosts.
=> septic arthritis (carpal tunnel syndrome (CTS), synovitis, tendinitis, osteomyelitis)
• Mycobacterium immunogenum
• Mycobacterium interjectum
• Mycobacterium lentiflavum was described as a nontuberculous mycobacterium in 1966^{ref1, ref2}. Most of the isolates represented fortuitous isolations, although recently its identification has posed concerns about its possible clinical importance. M. lentiflavum was mainly isolated from lymphadenitis in young European children, while isolations from other sites (lung specimens included) were described only in immunocompromised patients^{ref1, ref2, ref3, ref4, ref5, ref6, ref7} : anyway a chronic pulmonary M. lentiflavum infection in an elderly immunocompetent woman has been reported^ref
• Mycobacterium leprae (a.k.a. lepra or leprosy bacillus, Hansen's bacillus)
Epidemiology : it was the 1st bacterium to be associated with a disease. The Norwegian Armauer Hansen discovered the organism in 1874 just prior to Koch's discovery of the the tubercle bacillus. The inability to cultivate M. leprae on artificial media (which persists today) allowed Koch to be credited with the discovery opening the germ theory of disease. Incidence = 600,000 new cases  in 2002. The vast majority of the world's cases of leprosy occur in
• South Asia
• India contributed 79% to global case detection in 1998
• Bangladesh
• Nepal
• Myanmar
• China
• Indonesia
• Brazil
• Nigeria
• Madagascar
There is a highly uneven distribution within endemic regions: areas of high prevalence border areas with little or no disease. In endemic countries like Nepal, about half of leprosy patients have a history of intimate (eg, household) contact with an infected person. Africa, the Americas and South-East Asia each contributed about 30% (40 000 new cases each) when India is excluded. During 1994-2000, case detection did not decrease in these 3 WHO Regions. The 33 countries contributed 99% and 98% to global case detection in 1994 and 1998, respectively. Cumulative case detection for the top 33 minus India gradually increased, overall almost doubling. The contribution of the top 14 to case detection of the top 33 hardly changed over time, equalling 96% in 1998 (81% when India is excluded). In terms of annual case detection, Brazil was always ranked second after India; it accounted for 27% of 1998 case detection in the top 33 except India. In 1998, 7 of the top 14 countries--including India and Brazil--had CDRs above 2 per 10,000. The CDR did not exceed 1 per 10,000 for the other half. Decreasing tendencies in CDR, either for the whole period or in the 1990s, are observed for four of the top 14 countries (Guinea and 3 Western Pacific countries: China, Vietnam and the Philippines). The target to eliminate leprosy as a public health problem, defined as a prevalence < 1 per 10,000, is an inadequate yardstick for decision making on leprosy control.
• in USA there are 200 cases each year (93 cases in 2003 and 82 cases in 2004. The disease is not

reportable in all states, so there may be a few more). Anything sent to CDC is immediately forwarded to Baton Rouge. Of that "200," about 160 are infections acquired abroad by incomers or US citizens traveling abroad or expats returning home. Of the remainder, 6-8 are Louisianans and 32-34 or so are Texans ... people living along the Gulf Coast. In the USA, M. leprae is known to have been transmitted in several states: Louisiana, Texas, Hawaii, and possibly California. 2 cases have been reported, however, in residents of the eastern USA who had no obvious history of relevant travel or exposure^ref.
Where and how they acquired their infections is unknown, and none of them report knowing someone with the disease. Interestingly, these Gulf Coast cases are genetically related to the M. leprae infections found in armadillos in the region and are not found anywhere else in the world. In the affected region, some 30% of adult armadillos are infected; outside, the infection is rare and essentially limited to male armadillos adventuring out from the enzootic area. Logically, human and armadillo M. leprae infections in Mexico would be expected to be genetically similar, but, unfortunately, Hansen's disease has a very low priority in that country, and in Central America as well, and there is a virtual total absence of biological samples to test. The Gulf Coast human and armadillo organisms probably share a common parentage; the 9-banded armadillo is notorious for burrowing and will do it in graveyards (which is why they don't eat it in Brazil, they prefer the non-digging 7-banded armadillo). It is presumed that armadillos got infected in the past from scavenging around HD corpses. Evidence for an ongoing inter-species transfer of infection is missing, although there are anecdotal stories of Texan armadillo aficionados becoming infected, and cooked armadillo is not unknown in Acadiana. Many years ago, Richard's dissertation was on the development of an ELISA test for M. leprae infection, and for many years we successfully used this as a vehicle for training epidemiology graduate students in wild animal (armadillo) sampling, bleeding, tagging and release -- very straightforward with a hand-net. Armadillos are a recent introduction in Louisiana; they arrived in the mid-1950s with the building of interstate highways and bridges. So the "home" of armadillo M. leprae infection may well be in NE Mexico, if anyone were to go looking for it.
Genomics : this unculturable pathogen has undergone extensive reductive evolution, with half of its genome now occupied by pseudogenes. All extant cases of leprosy are attributable to a single clone whose dissemination worldwide can be retraced from analysis of very rare single-nucleotide polymorphisms. The disease seems to have originated in Eastern Africa or the Near East and spread with successive human migrations. Europeans or North Africans introduced leprosy into West Africa and the Americas within the past 500 years^ref
Susceptibility : variants in the regulatory region shared by the Parkinson's disease gene PARK2 and the co-regulated gene PACRG act as common risk factors for leprosy^ref
Transmission : inhalatory route from reservoirs (also used as model organisms) : Armadillo officinalis (prevalence : 7%; => lepromatous lepromatous leprosy), gibbons and Erinaceidae. Transmission of leprosy remains poorly understood, with nasal droplet infection, contact with infected soil and insect vectors thought to play a role. Not culturable in vitro : propagated by injection into the footpads of Mus musculus or Rattus norvegicus (lower T)
Pathogenesis : obliged ts intracellular pathogen. Leprosy enables investigation of mechanisms by which the innate immune system contributes to host defense against infection, because in 1 form, the disease progresses, and in the other, the infection is limited. Toll-like receptor (TLR) activation of human monocytes induces rapid differentiation into 2 distinct subsets: DC-SIGN⁺ CD16⁺ macrophages and CD1b⁺ DC-SIGN^- dendritic cells. DC-SIGN⁺ phagocytic macrophages were expanded by TLR-mediated upregulation of IL-15 and IL-15R. CD1b⁺ dendritic cells were expanded by TLR-mediated upregulation of GM-CSF and its receptor, promoted T cell activation and secreted proinflammatory cytokines. Whereas DC-SIGN⁺ macrophages were detected in lesions and after TLR activation in all leprosy patients, CD1b⁺ dendritic cells were not detected in lesions or after TLR activation of peripheral monocytes in individuals with the progressive lepromatous form, except during reversal reactions in which bacilli were cleared by T_h1 responses. In tuberculoid lepromatous lesions, DC-SIGN⁺ cells were positive for macrophage markers, but negative for dendritic cell markers. Thus, TLR-induced differentiation of monocytes into either macrophages or dendritic cells seems to crucially influence effective host defenses in human infectious disease^ref.
=> leprosy / Hansen's disease (HD) : infection of nasal epithelium (it exits from the phagosome before phagolysosome formation) => incubation ranges from 3 months to 40 years (average 2-5 years for tuberculoid form and 8-12 years for lepromatous form !) => type II hypersensitivity due to cross-reactivity between bacterial and skin Ags presented on HLA-DRB1*15 (in HLA-DR2 haplotype)
Laboratory examinations : RF in 25-50%. Serological status is controlled after lepromin subcutaneous injection :
• Fernandez early reaction : papuloerythematous eruption within 48 hrs (DTH in an immunized subject)
• Mitsuda-Rost late reaction : strong nodule after 3÷4 weeks (primary immune response)
Therapy : multi-drug is the current accepted standard for all types of leprosy, and for LL generally includes dapsone (side effects : diffuse skin hyperpigmentation, unaccepted by Hinduists), clofazamine and rifampin daily for at least 2-3 years until all biopsies are negative for acid-fast bacilli. Patients with undeterminated or tuberculoid leprosy may be treated with dapsone and rifampin as above for 6÷12 months, followed by dapsone alone for > 2 years. Type III hypersensitivity is treated with prednisone or thalidomide.
• lepra reaction : an acute or subacute hypersensitivity state occurring during the course of anti-leprosy treatment or in untreated leprosy categories, involving two types of immunological reactions, one a delayed hypersensitivity reaction and the other an immune complex reaction
• reversal reaction : a lepra reaction usually occurring during chemotherapy in borderline leprosy representing a type IV (delayed) hypersensitivity reaction with “upgrading” of cell-mediated immunity to Mycobacterium leprae, which tends to move the disease toward the tuberculoid pole. It is chiefly characterized by erythema, edema, and tenderness of preexisting quiescent lesions, the appearance of new lesions, neuritis with nerve damage, fever, adenopathy, and elevation of the leukocyte count
• downgrading reaction : a lepra reaction, similar in appearance to the reversal (“upgrading”) reaction, representing a deterioration in the immune response to Mycobacterium leprae with worsening of the clinical symptoms of leprosy and an increased index of M. leprae in the tissues; it may be seen during antileprosy treatment in those in whom M. leprae has become drug resistant or in those with poor compliance with the chemotherapeutic regimen
M. leprae–induced demyelination is a result of direct bacterial ligation to and activation of ErbB2 receptor tyrosine kinase (RTK) signaling without ErbB2-ErbB3 heterodimerization, a previously unknown mechanism that bypasses the neuregulin-ErbB3–mediated ErbB2 phosphorylation. MEK-dependent Erk1 and Erk2 (hereafter referred to as Erk1/2) signaling is identified as a downstream target of M. leprae–induced ErbB2 activation that mediates demyelination. Herceptin (trastuzumab), a therapeutic humanized ErbB2-specific antibody, inhibits M. leprae binding to and activation of ErbB2 and Erk1/2 in human primary Schwann cells, and the blockade of ErbB2 activity by the small molecule dual ErbB1-ErbB2 kinase inhibitor PKI-166 effectively abrogates M. leprae–induced myelin damage in in vitro and in vivo models. These results may have implications for the design of ErbB2 RTK–based therapies for both leprosy nerve damage and other demyelinating neurodegenerative diseases^ref.
Prevention : isolation is generally not used for patients with Hansen's disease in the USA. While there are differences of opinion with regard to the degree of contagiousness, most people have natural immunity, and the
institution of antimicrobial therapy quickly reduces the risk of transmission.
Web resources :
• Leprosy at WHO
• International Federation of Anti-Leprosy Associations (ILEP)
• Mycobacterium malmoense
=> carpal tunnel syndrome (CTS)
• Mycobacterium marinum (photochromogen MOTT)

It has been found in both fresh and salt water. This organism can also cause disease in birds, mammals, and other aquatic animals. Young infected fish (prevalence < 5% in the Chesapeake Bay, USA) do not display clinical signs. As the disease progresses and the fish ages, or if an older fish is infected, the fish may show evidence of emaciation and muscle wasting, exophthalmia, and skin ulceration. Fish may become bloated and anorexic. Internally, the liver, spleen, kidney, and heart may develop somewhat characteristic granulomatous lesions.  The granulomatous nodules cause edema within the body cavity, peritonitis develops, and the infection progresses systemically, even affecting the skeletal system. The fish may develop clearly visible skin ulcerations. The most common form of transmission is believed to be ingestion of infected material. This may occur when foodstuffs are tossed overboard, or when fish consume other decaying fish. It is also possible for this organism to pass from parent to offspring. The same species of Mycobacterium that causes fish diseases may cause skin lesions in people, which has been referred to as "fish handler's disease."  Generally this occurs at breaks in the skin, such as around the cuticles, or when there is contact with a very high number of organisms. The pustules, which ooze a white pus, resemble a rash where skin contacts the water. In healthy people this is usually a self-limiting situation, but severe localized infections have resulted in deep wounds. Immunologically compromised individuals are at risk of systemic infections. Infection rates range from 10 to 100%. There is no cure for Mycobacterium infections, but conditions in the environment that promote it should be identified and hopefully corrected. If the disease occurs in aquaculture conditions, destroying the stock, cleansing the area, and restocking may be the best options. However, the entire Chesapeake Bay may be infected, so identifying the conditions that promote mycobacteriosis and correcting it may be the only option
Transmission :
• cleaning fish tanks with any type of injury on the hands
• improper manipulation of infected fish
It grows best at temperatures below body temperature. Superinfecting M. marinum traffic rapidly into preexisting granulomas, including their caseous (necrotic) centers, through specific mycobacterium-directed and host cell–mediated processes, yet adapt quickly to persist long term therein, demonstrating a failure of established granulomas, concentrated foci of activated macrophages and antigen-specific immune effector cells, to eradicate newly deposited mycobacteria not previously exposed to host responses^ref
=> after 2-3 weeks incubation : papule => wart => aquarium fish or swimming pool granuloma, usually of the skin and soft tissues.
=> septic arthritis (carpal tunnel syndrome (CTS)), osteomyelitis, chronic laryngitis.
• Mycobacterium neoaurum
First described in 1972, belongs to the M. parafortuitum complex of the genus Mycobacterium^ref. M. neoaurum is a rapidly growing scotochromogen that is found in soil. 8 cases of human infection from M. neoaurum have been described in the English-language literature^{ref1, ref2, ref3, ref4, ref5} (McNally CF, Mangino JE. Mycobacterium neoaurum: a case report and review of the literature. Infect Dis Clin Prac 2000;9:273–5;
Becker ML, Suchak AA, Wolfe JN, Zarychanski R, Kabani A, Nicolle LE. Mycobacterium neoaurum bacteremia in a hemodialysis patient. Can J Infect Dis 2003;14:45–8). 6 of these cases were associated with central venous catheters, one was associated with intravenous drug use, and another involved urinary isolation of M. neoaurum during an investigation of a catheter-associated urinary tract infection. None of these cases was fatal. A fatal case rapidly progressive dementia was reported^ref but aetiology was doubtful^ref.
• Mycobacterium nonchromogenicum
• Mycobacterium palustre
• Mycobacterium parafortuitum
• Mycobacterium phlei (timothy bacillus; rapid grower)

=> ?
• Mycobacterium pseudoshottsi (prevalence 12% in the Chesapeake Bay, USA)^ref
• Mycobacterium septicum (a.k.a. Mycobacterium concordense, Mycobacterium genomospecies 3)
• Mycobacterium shottsi (only discovered in 2001 by the Virginia Institute of Marine Science while researching an outbreak of the disease in stripers that started in 1997; named after Emmett Shotts, retired fish microbiologist) (prevalence 57% in the Chesapeake Bay, USA)^ref
Transmission : striped bass
=> fish tuberculosis (was first discovered at the Philadelphia Aquarium in 1926 and has been seen sporadically in small numbers of fish since)
=> fish handler's disease : disease similar to that caused by Mycobacterium marinum. It doesn't thrive at temperatures > 86°, so it can only live on people's extremities as a persistent rash. There is no danger of getting the disease from eating a striper. One reason is that cooking the fish to 170° for 20' kills the mycobacteria. Even if they got inside you, mycobacteria would find your body temperature too high to survive.
Prevention : gloves, hand washing, and quick release or disposal of infected fish
• Mycobacterium simiae (a.k.a. Mycobacterium habana; photochromogen MOTT)

=> a zooanthroponosis from Macaca mulatta
• Mycobacterium smegmatis (a.k.a. smegma bacillus; rapid grower)

=> usually saprophitic in smegma (causes false positivity for urinary tuberculosis in urinalysis), sometimes involved in pulmonary, skin, soft-tissues and bone infections.
• Mycobacterium szulgai (scotochromogen MOTT)

=> a pneumonia similar to tubercular pneumonia
=> carpal tunnel syndrome (CTS)
• Mycobacterium terrae
• Mycobacterium thermoresistibile
• Mycobacterium tilburgii (identified in the city of Tilburg (Buiting A, Vos M, Bergmans A, Schouls L. A new mycobacterial species causing disseminated infection. 35th Interscience Conference on Antimicrobial Agents and Chemotherapy. San Francisco 1995; Abstract K45. Washington: American Society for Microbiology; 1995))
=> duodenitis in an AIDS patient^ref
=> pulmonary nodules in an AIDS patient^ref
=> granulomatous cystitis, gastritis and colitis in a 43-year-old immunocompentent woman^ref
=> duodenitis in a 34-year-old AIDS patient^ref
• Mycobacterium triviale
• Mycobacterium ulcerans (nonphotochromogen MOTT)

Epidemiology : the 3rd most common mycobacterial infection in healthy people, after tuberculosis and leprosy, and the most poorly understood of these 3 diseases. It was 1st detected in 1948 among farmers in Australia (where it is known as Bairnsdale ulcer). However, cases were described, as early as 1897, in Uganda, by Sir Albert Cook. Most patients are women and children who live in rural areas near rivers or wetlands. It has been reported in 30 countries worldwide^ref. It occurs principally in Uganda and Zaire but has also been seen elsewhere in Central Africa, in Southeast Asia, in Australia, and sometimes in Central and South America. In some countries, particularly in West Africa, the disease has displaced leprosy to become the 2nd most important mycobacterial infection of man. Buruli ulcer, named after an area of Uganda that was the site of many cases in the 1960s, is most common in West Africa. All countries along the Gulf of Guinea are now affected. In Cote d'Ivoire, approximately 15 000 cases have been recorded since 1978, where up to 16% of the population in some villages are affected. In Benin, 4000 cases have been recorded since 1989. In Ghana (6000 recorded cases in a national survey in 1999), up to 22% of villagers are affected in some areas. There is evidence of huge under reporting of the disease. It is found in marshy parts of the tropical and sub-tropical regions of Africa, Asia, Latin America, and the Western Pacific. Cases have been reported, or suspected, in Angola, Australia (Victoria's Bellarine  Peninsula), Benin, Bolivia, Burkina Faso, Cameroon, China, Congo, Cote d'Ivoire, Democratic Republic of Congo, Equatorial Guinea, French Guyana, Gabon, Ghana, Guinea, India, Indonesia, Japan, Liberia, Malaysia, Mexico, Papua New Guinea, Peru, Sierra Leone, Sri Lanka, Sudan, Suriname, Togo, and Uganda. A few cases have been reported in non-endemic areas in North America and Europe linked to international travel. Since 1980, emerged as an important cause of human suffering
Transmission : close relationship to stagnant or slowly moving water. The disease is not known to be contagious between humans, and epidemiological studies have not yet established natural reservoirs or modes of transmission, though abrasions of the dermis and minor skin trauma after contact with contaminated water, soil, or vegetation could be likely routes of entry. There are a few preliminary reports on possible transmission by insects, including the demonstration experimentally that M. ulcerans could survive and multiply exclusively within salivary glands of aquatic bugs (Naucoris spp. and Diplonychus spp.), which were able to transmit M. ulcerans to mice by their bites, suggesting a possible mechanism for human infection^ref. Another study reported a potential role for fish in transmission^ref. Fish were found positive for M. ulcerans DNA, and all appeared to feed on insects or plankton and were believed to concentrate M. ulcerans from this usual food source. Endemic foci exist throughout the world, predominantly in tropical rain forest areas. The peak incidence of the disease coincides with the rainfall pattern and farming season in endemic districts. This lends credence to speculation that disease onset is related to farming activities, which predispose to injury and pricks. Mycobacterium ulcerans has also been found in snails, spiders and crayfish. Other insects said to have been found infected are march flies, a confusing name that may be used for flies in the family Bibionidae or the large biting tabanid flies (2 common genera being Tabanus spp. and Chrysops spp.) : at a guess, it would seem that tabanids would be a better vehicle for transmission of M. ulcerans. A research topic  for "M. ulcerans in Victoria"^ref says that previous research has shown that M. ulcerans ingested by mosquito larvae can be passed to adults. Clearly if -- as it seems from the present post -- mosquitoes serve as vectors, it needs to be known whether transmission is mechanical (such as by infected mosquito mouthparts and/or by their feces being scratched into the skin or abrasions) or whether the salivary glands are infected. If transmission is mechanical, or mainly so, then it is likely that many mosquito species might be involved, as well as other hematophagous insects. A useful reference is a 22-page abstract (in English) of a PhD thesis of Timothy Stinear, which has 155 references^ref.
Pathogenesis : unlike other mycobacteria, it produces a cytotoxin that destroys the tissue and suppresses the immune system
=> Buruli ulcer / Bairnsdale ulcer: incubation is months to several years => chronic progressive disease which primarily involves subcutaneous fat (small, firm, painless, movable, sometimes pruritic nodule teeming with mycobacteria that enlarges and becomes fluctuant) with secondary skin ulceration, leaving an undermined edge. The 3 main clinical forms are : localized necrotizing skin ulcers; contiguous dissemination over extensive body surfaces; and metastatic spread of M. ulcerans to distant sites, usually skin and bone. Minor forms heal spontaneously, ordinarily in 3-6 months by a delayed-type hypersensitivity response, followed by scarring. Devastating sequelae (scarring or amputations) often ensue from tissue destruction and osteomyelitis. Untreated, massive areas of skin, and, sometimes bone, are destroyed causing gross deformities. When lesions heal, scarring may cause restricted movement of limbs and other permanent disabilities. One important feature of Buruli ulcer is the minimally painful nature of the disease, which may partly explain why those affected do not seek prompt treatment. .
Therapy :
• at the present time, the only treatment available is surgery to remove the lesion, followed by a skin graft, if necessary. This is both costly and dangerous, leading to the loss of large amounts of tissue or permanent disability. Early detection, and surgical removal, of small lesions could prevent many complications.
• treatment with antibiotics has been unsuccessful to date, although the organism is sensitive, in vitro, to some of the antibiotics used for treatment of tuberculosis (clarithromycin, rifampin, and fluoroquinolones). Current research findings indicate that a combination of an aminoglycoside (amikacin or streptomycin) and rifampicin cures Buruli ulcer in mice.
Prevention : BCG (Bacille Calmette-Guerin) vaccination appears to offer some short-term protection from the disease. At present, BCG vaccination is the only biomedical intervention that may help control Buruli ulcer in the highly affected areas. Access to health services is restricted in endemic areas. Patients often seek treatment late, causing frequent, and severe, complications, and, prolonging costly hospitalization. Treatment cost per patient far exceeds annual per capita health spending. In Ghana, the average cost of treatment is estimated at USD 780 per patient. Alternatively, treatment for early lesions could cost about USD 20-30 per patient, with very limited hospitalization. In some areas, about 20-25% of people with healed lesions are disabled. With an increasing number of cases, and associated complications, the long-term economic and social impact of Buruli ulcer on rural populations could be substantial
• Mycobacterium vaccae
• Mycobacterium wolinskyi
• Mycobacterium xenopi (nonphotochromogen MOTT; growth at 42 °C)

=> tuberculosis-like syndrome.
• Nocardiaceae (obliged anaerobes)
• Nocardia
• Nocardia asteroides
=> actinomycotic mycetoma / maduromycosis
• Nocardia brasiliensis

=> actinomycotic mycetoma / maduromycosis
• Nocardia farcinica (a.k.a. Nocardia paratuberculosis)
• Nocardia nova
=> aortitis^ref
• Nocardia otitidiscaviarum

=> actinomycotic mycetoma / maduromycosis
• Nocardia transvalensis
=> nocardiosis (opportunistic exogenous infections) from inhalatory route
opportunistic pleurisy in individuals with AIDS
lung abscess ==bacteraemia==> meningitis, acute nephritis
Chemotherapy : sulfadiazine
Rhodococcus
• Rhodococcus equi
=> necrotizing pneumonia and pleurisy in individuals with AIDS
• Williamsiaceae^ref (Goodfellow M, Isik K, Yates E. Actinomycete systematics: an unfinished synthesis. Nova Acta Leopold. 1999;312:47–82)
• Williamsia : mycolic acid–containing actinomycetes (Stackebrandt E, Rainey FA, Ward-Rainey NL. Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Bacteriol. 1997;47:479–491)
• Williamsia muralis, isolated from a daycare center^ref; the isolation of >1,000 CFU/mL of W. muralis from a protected specimen brush sample of an 80-year-old woman has been reported. The number of colonies obtained, as well as features of the source of the clinical sample and the chest radiograph (clearly pathologic) at the time the isolate was obtained, strongly suggest that this microorganism was associated with lung infiltrates and poor prognosis, resulting in the death of the patient^ref
• Williamsia maris, isolated from the Sea of Japan^ref
• Micrococcineae
• Dermacoccaceae
• Kytococcus
• Kytococcus schroeteri is a new micrococcal species resistant to penicillins^ref implicated in 2 cases of acute prosthetic valve endocarditis^{ref1, ref2}. Most micrococcal species, including K. sedentarius but not K. schroeteri, were isolated from human skin and mucosa (Szczerba I, Krzeminski Z. Occurrence and number of bacteria from the Micrococcus, Kocuria, Nesterenkonia, Kytococcus and Dermacoccus genera on skin and mucous membranes in humans. Med Dosw Mikrobiol 2002;55:67-74). As moxifloxacin was more rapidly microbicidal than vancomycin in an animal model of Staphylococcus aureus prosthetic valve endocarditis^ref, it might present a potential advantage against infections caused by K. schroeteri, especially when the oral route is favored.
• Kytococcus sedentarius
• Dermatophilaceae
• Dermatophilus
• Dermatophilus congolensis (a.k.a. Streptothrix bovis)

Transmission : reservoirs : Bos taurus, Ovis aries, Equus caballus, Canis familiaris, Capra hircus, Cervidae
=> in sheep (lumpy wool / proliferative dermatitis / strawberry foot rot) : exudative red scaling lesions that form pyramidal masses
=> dermatophilosis / dermatophiliasis / streptotrichosis
• Microbacteriaceae
• Leifsonia
• Leifsonia aquatica (a.k.a. Corynebacterium aquaticum)

=> endocarditis
=> disseminated infections in immunocompromised hosts
• Microbacterium (a.k.a. Aureobacterium)
• Microbacterium alconae (?)

=> 2.9% all acute otitis externa (AOE)
• Microbacterium otitidis (?)

=> 6.6% all acute otitis externa (AOE)
• Micrococcaceae (obliged aerobes, no Glc fermentation)
• Kocuria
• Kocuria rosea (a.k.a. Micrococcus roseus)
• Micrococcus
• Micrococcus luteus
• Rothia
• Rothia dentocariosa
• Propionibacterineae
• Propionibacteriaceae
• Propionibacterium (strictly or facultative anaerobes)
• Propionibacterium acnes (a.k.a. Corynebacterium parvum)

Coryneform / diphtheroid; synthesizes phosphatidylinositol; peptidoglycan contains a cross-linkage region of peptide chains with L,L-diaminopimelic acid and D-Ala in which 2 Gly residues combine with amino and carboxyl groups of 2 L,L-diaminopimelic acid residues.
It releases lipases, proteases and hyaluronidase / spreading factor which contribute to tissue injury and contributes to the inflammatory nature of acne by inducing monocytes to secrete proinflammatory cytokines including TNF-a, IL-1b, and IL-8. Many of P.acnes 2,333 genes are involved in degrading the human tissue as the bacterium lived off the products of this degradation.
=> acute meningitis
=> subacute endocarditis
=> orthopaedic prostheses infections
=> it is part of the normal skin flora but is significantly increased in the pilosebaceous units of patients with acne vulgaris, depending on hormonal mechanisms. The reason acne is common in adolescence (affects up to 80% of young adults) might be because this is a time when the skin produces more oils, which the bacterium feeds off.
=> sarcoidosis^ref
Therapy :
• acne lesions have long been noted to improve after exposure to sunlight. This improvement may be secondary to activation of endogenous porphyrins produced by Propionibacterium acnes
• tetracyclines/oxytetracycline and erythromycin > second-generation tetracyclines, such as lymecycline, doxycycline, and minocycline, show improved absorption (minocycline has the advantage of being rarely associated with Propionibacterium acnes antibacterial resistance, but can occasionally lead to potentially serious adverse effects) > trimethoprim
• Propionibacterium granulosum

=> sarcoidosis^ref
• Propionibacterium propionicum (a.k.a. Arachnia propionica, Actinomyces propionicus)
• Pseudonocardineae
• Pseudonocardiaceae : live in granaries, thermophilic
• Pseudonocardia
• Pseudonocardia autotrophica (a.k.a. Amycolata autotrophica, Streptomyces autotrophicus, Nocardia autotrophica)
• Saccharomonospora
• Saccharomonospora viridis (a.k.a. Thermoactinomyces viridis)
• Saccharopolyspora
• Saccharopolyspora rectivirgula (a.k.a. Micropolyspora faeni)
=> hypersensitivity pneumonia
• Streptomycineae
• Streptomycetaceae (aerobes)
• Streptomyces
• Streptomyces albus

=> hypersensitivity pneumonia
• Streptomyces griseus
• Streptomyces paraguayensis
• Streptomyces somaliensis
=> actinomycotic mycetoma / maduromycosis at the ends of limbs
• Streptosporangineae
• Nocardiopsaceae
• Nocardiopsis
• Nocardiopsis alba
• Nocardiopsis composta
• Nocardiopsis dassonvillei
• Nocardiopsis dassonvillei subsp. albirubida
=> actinomycotic mycetoma / maduromycosis
• Nocardiopsis exhalans
• Nocardiopsis halophila
• Nocardiopsis halotolerans
• Nocardiopsis kunsanensis
• Nocardiopsis listeri
• Nocardiopsis lucentensis
• Nocardiopsis metallicus
• Nocardiopsis prasina
• Nocardiopsis synnemataformans
• Nocardiopsis trehalosi
• Nocardiopsis tropica
• Nocardiopsis umidischolae
=> interstitial pneumonia by percutaneous route
• Thermomonosporaceae
• Actinomadura
• Actinomadura madurae
• Actinomadura pelletieri
=> actinomycotic mycetoma / maduromycosis
Treatment : long-term combination therapy, e.g., streptomycin + dapsone or cotrimoxazole. Surgical debridement + long-term ketoconazole or itraconazole is also used in treatment.
• Bifidobacteriales
• Bifidobacteriaceae
• Bifidobacterium (anaerobes)
• Bifidobacterium breve (a.k.a. Bifidobacterium parvulorum)
• Bifidobacterium dentium
• Bifidobacterium longum
• Bifidobacterium longum bv. Infantis (a.k.a. Bifidobacterium infantis, Bifidobacterium liberorum, Bifidobacterium lactentis)
• Gardnerella
• Gardnerella vaginalis (a.k.a. Haemophilus vaginalis)

=> bacterial vaginosis : increase in secretions, no leukorrhoea, no itching

• Coriobacteridae
• Coriobacteriales
• Coriobacteriaceae
• Eggerthella (obliged anaerobes)
• Eggerthella lenta (a.k.a. Eubacterium lentum)
Prevalence : 10%. It converts digoxinto an inactive metabolyte
• Tropheryma
• Tropheryma whipplei

Genomics : its 925,938 bp long genome contains 784 genes, but lacks the genes for many core functions such as a major energy-generating system (the TCA cycle) and synthesis of key amino acids (arginine, tryptophan, histidine), suggesting a host-restricted lifestyle.
=> Whipple's disease / intestinal lipodystrophy from oro-faecal route : arthritis (first mainfestations in > 90%; spondylitis in patients with HLA-B27 haplotype) => diarrhea, steatorrhoea, weight loss, fever (54%), edema, serositis, alveolar pneumonia, systemic arterial hypotension, diffuse skin hyperpigmentation (54%), lymphadenitis (54%), endocarditis (25% => murmurs), subcutaneous nodules, digital hippocratism, uveitis, neuro-Whipple (no real meningitis, only a subacute or chronic encephalitis : 80%), myoclonus of masticatory and extraocular skeletal muscles (ophthalmoplegia), ataxia, paresis, hyperreflexia.
Although Whipple's disease was first described in 1907^ref,1 the first successful culture of T. whipplei was performed nearly a century later, in 2000. This accomplishment led to a new level of understanding of the disease. During the 20th century, knowledge of this chronic disease slowly accumulated^{ref1, ref2, ref3, ref4, ref5}.2,3,4,5,6 At the dawn of the 21st century, 2 major events — molecular amplification of the 16S ribosomal RNA (rRNA) of T. whipplei by PCR assay and cell culture of the organism — greatly improved our understanding of Whipple's disease^{ref1, ref2, ref3}.7,8,9 Initially, the organism was named Tropheryma whippelii, from the Greek trophi (food) and eryma (barrier), because of the malabsorption frequently observed in the disease.8 The successful isolation and serial culture of the bacterium^ref9 were followed by the sequencing of its genome^{ref1, ref2}11,12 and made it possible to define the organism's antibiotic susceptibility^{ref1, ref2}.13,14 The name was subsequently changed slightly to Tropheryma whipplei^ref.10 Milestones in the History of Whipple's Disease and Tropheryma whipplei.

date	investigators	advance
1907	Whipple et al.ref	first description of the disease
1947	Olivier-Pascual et alref	first diagnosis before the death of a patient
1949	Black-Schafferref	development of PAS staining for diagnosis
1952	Paulleyref	first reported efficacy of antibiotic treatment
1961	Chears and Asworthref Yardley and Hendrixref	detection of bacteria in macrophages by electron microscopy
1991	Wilson et alref	partial sequencing of 16S rRNA of an unknown bacterium
1992	Relman et alref	confirmatio and extension of the 16S rRNA sequence; first naming of the bacterium : T.whippelii
2000	Raoult et alref	first cultivation of the Whipple bacillus
2001	La Scola et alref	first phenotypic characterization of the Whipple bacillus; renaming of the bacterium : T.whipplei
2003	Bentley et alref Raoult et alref	full sequencing of 2 genomes from 2 different strains of T.whipplei

Whipple's disease is rare, though there is no valid estimate of its actual prevalence. Only about 1000 cases have been reported to date^ref.15 In postmortem studies, the frequency of the disease is < 0.1%^ref.16 Although it occurs in people of all ages throughout the world, the typical patient is a middle-aged white man^ref.17 Whipple's disease is characterized by two stages — a prodromal stage and a much later steady-state stage. The prodromal stage is marked by protean symptoms, along with chronic nonspecific findings, mainly arthralgia and arthritis. The steady-state stage is typified by weight loss, diarrhea, or both, and occasionally there are other manifestations, since many organs can be involved^ref.17 The average time between the prodromal and the steady-state stages is 6 years. If a patient has received immunosuppressive therapy, such as treatment with corticosteroids or tumor necrosis factor antagonists, a more rapid clinical progression may occur^{ref1, ref2}.18,19 For example, diarrhea has been reported to develop shortly after the initiation of immunosuppressive therapy for chronic arthritis in patients with Whipple's disease^ref.19 Roughly 15% of patients with Whipple's disease do not have the classic signs and symptoms of the disease^{ref1, ref2}.20,21 Accordingly, the diagnosis should be considered in many different clinical circumstances. Indeed, Whipple's disease is in the differential diagnosis for a wide spectrum of diseases that includes inflammatory rheumatic diseases, malabsorption with small-intestine involvement (celiac disease, sarcoidosis, and lymphoma), Addison's disease, connective tissue diseases, and a variety of neurologic diseases. Characteristic signs and symptoms of Whipple's disease are listed, along with their frequencies^{ref1, ref2, ref3, ref4, ref5, ref6, ref7}.15,16,21,22,23,24,25 Some cases have been diagnosed in the absence of classic signs when typical histologic lesions were found on periodic acid–Schiff (PAS) staining of specimens from small-bowel biopsies. Demographic and clinical features of classic Whipple's disease :
• male sex : 770/886 (87%)
• arthralgia or arthritis : 244/335 (73%)
• diarrhea : 272/335 (81%)
• weight loss : 223/240 (83%)
• fever :128/335 (38%)
• adenopathy : 174/335 (52%)
• melanoderma : 99/240 (41%)
• neurologic signs (including supranuclear ophthalmoplegia) : 33/99 (33%)
• ocular signs : 6/99 (6%)
• pleural effusion : 26/190 (14%)
Thus, there are several presentations linked to T. whipplei infection: histologic lesions in the gastrointestinal tract in association with diverse clinical manifestations (classic Whipple's disease), endocarditis with negative blood cultures, and isolated neurologic infection. Without treatment, Whipple's disease is ultimately fatal. Even with a specific antibiotic regimen, clinical relapse occurs in 2 to 33% of cases after an average of 5 years; relapse is usually characterized by neurologic involvement^ref.26
• classic Whipple's disease :
• the most common gastrointestinal symptom of classic Whipple's disease is weight loss, often associated with diarrhea^{ref1, ref2, ref3, ref4}.15,21,24,25 Occult bleeding from the intestinal mucosa is observed in 20 to 30% of patients. Abdominal pain may be present. Hepatosplenomegaly and, occasionally, hepatitis may occur.15 Ascites has been reported in about 5% of patients^ref.15
• joint involvement has been reported in 65 to 90% of patients with classic Whipple's disease^{ref1, ref2, ref3, ref4}.17,21,24,25 The presenting symptom in most patients with joint involvement is intermittent migratory arthralgia, arthritis, or both^{ref1, ref2, ref3, ref4}.17,21,23,25 Polyarthritis is most common, but oligoarthritis may occur. Although joint involvement alone is uncommon, Whipple's disease should be considered in the differential diagnosis in any middle-aged man with intermittent episodes of unexplained polyarthritis or oligoarthritis of the large joints, even in the absence of digestive symptoms^{ref1, ref2}.17,27 Less frequent in Whipple's disease is chronic seronegative polyarthritis, which can be destructive and is often mistaken for rheumatoid arthritis^ref.17 On rare occasions, spondyloarthropathy, hypertrophic osteoarthropathy, and infection of a knee prosthesis have been described in patients with classic Whipple's disease^ref.28 Skeletal muscle myalgia and cramps in skeletal muscle may be present^ref.15
• neurologic involvement has been reported in 6 to 63% of patients with classic Whipple's disease^{ref1, ref2, ref3}.15,18,29 However, in a small autopsy series, central nervous system lesions were described in 10 of 11 patients (91%)^ref.16 The neurologic manifestations of classic Whipple's disease are diverse and can resemble those of almost any neurologic condition^{ref1, ref2}.18,29 Cognitive changes are common, affecting 71% of patients with neurologic signs, and may even extend to dementia^ref.29 Psychiatric symptoms such as depression and personality changes are observed in roughly half the patients who have neurologic involvement. Similarly, half have supranuclear ophthalmoplegia at presentation^ref.29 Myoclonus is observed in one quarter of patients with neurologic involvement. Hypothalamic involvement, evidenced by polydipsia, hyperphagia, a change in libido, and changes in the sleep–wake cycle, is present in less than one third of patients with neurologic signs. Movement abnormalities of the eye muscles, termed oculomasticatory, or oculofacioskeletal, myorhythmia, are considered pathognomonic for Whipple's disease^ref.29 The prognosis for patients with central nervous system infection remains poor. > 25% of such patients die within 4 years, and the same proportion of patients have major sequelae^ref.39 Asymptomatic neurologic involvement in classic Whipple's disease has been demonstrated through detection of DNA from T. whipplei in cerebrospinal fluid by means of a PCR assay^ref.40 Ocular involvement, excluding ophthalmoplegia, occurs in up to 11% of patients with classic Whipple's disease^{ref1, ref2, ref3}.15,24,41 Anterior or posterior uveitis, usually chronic and bilateral at diagnosis, is the most frequent ocular manifestation.
• cardiac involvement has been reported in a wide range of patients with classic Whipple's disease (17 to 55%)^{ref1, ref2}.21,42 However, 2 older autopsy studies showed nearly invariable involvement of the pericardium, myocardium, or endocardium; PAS-positive macrophages were found in 79% of reported cases^{ref1, ref2}.16,43 Pericarditis occurs in more than half of people with Whipple's disease^ref.24 Myocarditis occurs far less often and is sometimes first evident with the onset of heart failure or with sudden death. Pulmonary involvement occurs in an estimated 30 to 40% of patients with classic Whipple's disease^ref,15 and pleural effusion, pulmonary infiltration, or granulomatous mediastinal adenopathy was often described in the earliest reported cases^ref.15
• noncaseating epithelioid- and giant-cell granulomas, most often lymph-node granulomas, have been found in 9% of people with classic Whipple's disease^ref.15 Involvement of the abdominal, especially the mesenteric, lymph nodes is not uncommon, but peripheral lymphadenopathy is rare. Cutaneous manifestations vary^{ref1, ref2}.15,44 Melanoderma is a classic finding, but like other researchers^ref,21 we have found that it is rarely observed these days, since Whipple's disease is recognized earlier in its course. Kidney involvement, which is only occasionally described, typically occurs late in the course of the disease^ref.15 Other manifestations, such as hypothyroidism, epididymitis, and orchitis, have occasionally been reported in cases of classic Whipple's disease^{ref1, ref2, ref3}.15,45,46
• blood culture–negative endocarditis : this was initially observed by chance in one patient in a study by Goldenberger et al. in which cardiac valves obtained from 18 patients with endocarditis were screened with a broad-range PCR strategy that targeted the 16S rRNA sequence of T. whipplei^ref.47 4 additional cases were reported two years later^ref.30 To date, 17 cases of blood culture–negative endocarditis associated with T. whipplei have been described^{ref1, ref2, ref3, ref4, ref5, ref6, ref7, ref8, ref9},30,31,32,33,34,35,36,37,38 most of which have involved native cardiac valves in men with an average age of approximately 60 years. Arthralgia or arthritis, often preceding the diagnosis of blood culture–negative endocarditis by some years, has been the predominant extracardiac symptom in these cases^ref.30 Clinical signs of infection appear to be rare^ref.30 Physicians often use the Duke criteria to diagnose endocarditis^ref,42 but in patients with blood culture–negative endocarditis, 2 of the criteria — fever and a history of valvulopathy — are absent, making it difficult to diagnose endocarditis associated with T. whipplei^ref.48 To date, this manifestation of Whipple's disease has generally been confirmed by a PCR assay of DNA taken from surgically obtained cardiac valves, although in one case, an assay of intestinal tissue specimens was positive^ref.30
• males sex (82%)
• previous valvular disease (41%)
• acute rheumatic fever (18%)
• bicuspid aortic valve (12%)
• aortic bioprosthesis (12%)
• antecedent (71%)
• arthralgia or arthritis (47%)
• seronegative polyarthritis (12%)
• psoriatic arthritis (6%)
• myalgia (6%)
• interval between onset of symptoms and definitive diagnosis - range (mean) : 2 mo-20 yr (5 yr)
• involved valves
• aortic (47%)
• mitral  (24%)
• tricuspid (6%)
• aortic and mitral (18%)
• aortic and tricuspid (6%)
• fever (12%)
• cardiac vegetations (76%)
• congestive heart failure (59%)
• arterial emboli (59%)
• isolated neurologic manifestations : neurologic manifestations occur in three situations: neurologic relapse of previously treated Whipple's disease, neurologic involvement in classic Whipple's disease, and isolated neurologic symptoms due to T. whipplei without histologic evidence of intestinal involvement. 32 patients with isolated neurologic infection (18 males and 14 females) with a mean age of 46 years (range, 4 to 72) have been described^{ref1, ref2, ref3, ref4, ref5, ref6, ref7, ref8, ref9, ref10, ref11, ref12, ref13, ref14, ref15}.15,18,29,40,44,49,50,51,52,53,54,55,56,57,58 19 of these 32 patients had systemic symptoms, such as fever (10 patients), weight loss (8), articular pain (7), and peripheral lymphadenopathy (2). PCR assays of intestinal tissue specimens were positive in 4 of the 32 patients. The predominant symptoms included cognitive impairment, ophthalmoplegia, ataxia, and upper motor neuron disorder. Of the 30 patients for whom follow-up data were available, 18 (60%) had improvement, and 10 died (33%); in 1 patient, the disease stabilized. Whether earlier detection and treatment would have improved the outcome is unknown, though arguably likely.
• cognitive change (71%)
• supranuclear ophthalmoplegia (51%)
• altered level of consciousness (50%)
• psychiatric signs (44%)
• upper motor neuron signs (37%)
• hypothalamic manifestations (31%)
• cranial nerve abnormalities (25%)
• myoclonus (25%)
• seizures (23%)
• oculomasticatory, oculofacial skeletal, myorhythmia (20%)
• ataxia (20%)
• sensory deficits (12%)
• other presentations : cases of Whipple's disease with isolated arthritis^{ref1, ref2, ref3,},59,60,61 spondylodiskitis^ref,62 and uveitis^ref63 in the absence of clinical or histologic evidence of digestive involvement have also been described. In these cases, the diagnosis was established with PCR assays of synovial fluid or tissue^{ref1, ref2},59,61 specimens from disk puncture biopsy^ref,62 or aqueous humor^ref63 or with electron microscopical examination and PAS staining of synovial tissue^ref.60
• asymptomatic carriers : there is controversy regarding the prevalence of T. whipplei in duodenal-biopsy specimens, saliva, stool, and blood from healthy persons^ref.64 Some PCR studies have detected the organism in people without evident Whipple's disease. For example, in one small study in which a PCR assay for T. whipplei was performed on blood samples from apparently healthy donors, 1 of 174 samples was positive^ref.65 In 2 other studies, T. whipplei DNA was detected in saliva from 19%^ref66 and 35%^ref67 of healthy subjects. PCR assays have also detected DNA from T. whipplei in patients with disorders other than Whipple's disease; positive findings have been reported in duodenal-biopsy samples (in 5% of patients), gastric secretions (12%), and stool (11%)^{ref1, ref2, ref3}.66,68,69 However, neither our laboratory^ref70 nor that of Dr. David Relman at Stanford University^ref71 has identified T. whipplei DNA in samples from duodenal biopsies in control subjects. Among patients without Whipple's disease, we have detected T. whipplei using a PCR assay on DNA isolated from saliva in 4 of 620 patients (0.6%) and from stool in 2 of 133 patients (1.5%) (unpublished data).
T. whipplei appears to be present in the general environment, though neither its source nor its transmission is well established. Studies using PCR have demonstrated T. whipplei DNA in sewage plant effluent^ref72 as well as in human stool^ref.73 Furthermore, an association between Whipple's disease and Giardia lamblia infection has been reported^ref.74 Since the protozoan G. lamblia is present in the environment, it is plausible that both microorganisms occupy the same ecologic niche^ref.74 Indeed, it has been suggested that T. whipplei might be acquired through fecal–oral transmission^ref.75 The complete genome of 2 strains of the bacteria has been sequenced^{ref1, ref2}.11,12 T. whipplei possesses a very small circular chromosome (< 1 megabase), as reported for other intracellular bacteria. Organisms with adaptive strategies involving host dependence are generally associated with genome reduction, and genome annotation in T. whipplei has revealed that the biosynthetic pathways for 16 amino acids are missing or impaired, suggesting a requirement for external nutrients. Recombination of regions encoding for surface proteins has been detected, possibly associated with the production of many diverse membrane proteins, which may enable the bacterium to evade host immunity^ref.11 T. whipplei has been isolated from mammalian cell cultures^ref.9 With this approach, 18 novel isolates (7 from cerebrospinal fluid, 4 from blood, 2 from cardiac valves, 2 from lymph nodes, 1 from duodenal tissue, 1 from synovial fluid, and 1 from skeletal muscle) have been established in serial cultures^{ref1, ref2, ref3}.11,76,77 According to genomic analyses, it is also possible to culture T. whipplei without mammalian cells, simply by adding the missing amino acids to the culture medium^ref.78 Using this strategy, we have recently isolated and established two strains of T. whipplei from cerebrospinal fluid, two from blood, one from synovial fluid, one from a lymph node, one from a cardiac valve, one from skeletal muscle, and one from stool^ref.79
Pathogenesis : one concept concerning the pathogenesis of Whipple's disease is that in any given population, many people are exposed to T. whipplei and that the disease may subsequently develop in some of these people, presumably those with as yet undefined predisposing immune factors^ref.80 Genetic risk factors may be suggested by the predominance of men and the higher frequency of the HLA-B27 antigen among those with the disease. However, no causal association with any specific genetic factor has been demonstrated, and some studies do not support the existence of genetic risk factors^ref.81 Massive infiltration of infected tissues by macrophages on microscopy typifies Whipple's disease^ref.82 After treatment, bacteria disappear, yet macrophages persist. T. whipplei multiplies in macrophages but not in monocytes from healthy subjects^ref.83 In contrast, in patients with Whipple's disease, T. whipplei multiplies in both monocytes and macrophages^ref.83 Replication of T. whipplei in macrophages is associated with apoptosis of the host cell,83 which may be crucial for bacterial dissemination and is also correlated with expression and release of IL-16^ref.84 Antibodies neutralizing IL-16 inhibit the growth of T. whipplei in macrophages^ref.83 Serum IL-16 levels and markers of apoptosis correlate with the activity of Whipple's disease, decreasing to normal levels on successful treatment^ref.83  Humoral responses do not appear to be implicated in Whipple's disease^ref.80 Several studies have demonstrated defective macrophage function in patients with the disease. Although macrophages from affected patients phagocytose bacteria normally, they appear to be unable to degrade bacterial antigens efficiently^ref.15 Experimental data suggest that this inability to degrade bacterial antigens is related to inadequate production of IL-12^ref,85 which may lead to diminished interferon- production by T cells and defective macrophage activation. A decrease in IL-12 production might then prevent the development of an effective T_h1 immune response and would favor a shift toward a T_h2 response. In support of this hypothesis, the gene expression profile of macrophages in intestinal lesions from one patient with classic Whipple's disease indicated that genes encoding CCL18 and IL-10 were uniquely up-regulated in intestinal lesions^ref.86 A similar pattern in up-regulated genes has been associated with macrophage 2, also known as alternatively activated macrophages, reflecting a predominance of T_h2 cells in the local immune response.
Laboratory examinations :
• blood studies : several nonspecific findings may together suggest the diagnosis of Whipple's disease. For example, before treatment there may be elevated levels of acute-phase reactants, anemia, leukocytosis, thrombocytosis, and laboratory evidence of malabsorption^{ref1, ref2}.21,25 Thrombocytopenia is present on occasion^ref.44 Eosinophilia has also been reported^ref.42
• endoscopy : pale yellow, shaggy mucosa alternating with eroded, erythematous, or mildly friable mucosa has been described on endoscopic examination of the postbulbar region of the duodenum and jejunum in patients with classic Whipple's disease^ref.64
• other diagnostic tools : electron microscopy may detect the distinctive trilaminar cell wall of T. whipplei; laboratories with experience in detecting T. whipplei are best at identifying this feature^ref.75 However, the classic tool for diagnosing Whipple's disease is PAS staining of small-bowel–biopsy specimens, which on light-microscopical examination shows magenta-stained inclusions within macrophages of the lamina propria. Several biopsy samples should be studied, because the lesions can be focal and sparse.
• depending on clinical manifestations, other tissues might be biopsied and stained with PAS^{ref1, ref2, ref3}.64,75,81 However, the PAS-positive inclusions within cells are nonspecific^{ref1, ref2}.64,75 For example, PAS-positive cells are also seen in patients with Mycobacterium avium complex^ref.75 Ziehl–Neelsen staining, which is positive for patients infected with M. avium complex and negative for those with Whipple's disease, may be used to differentiate between these two infections. Noncaseous granulomas composed of epithelioid cells, which are PAS-negative in 40% of cases, may be present in the lymphatic tissue, gastrointestinal tract, bone marrow, kidneys, synovial tissue, liver, or lungs in patients with Whipple's disease^{ref1, ref2, ref3}.64,75,81 Immunohistochemical staining for antibodies against T. whipplei has been used to detect the organism in various tissues, in bodily fluids such as the aqueous humor, and on blood monocytes, providing direct visualization of the bacilli (Figure 1B and 1C)^{ref1, ref2, ref3, ref4, ref5, ref6}9,41,82,87,88,89 Although not yet widely available, immunohistochemical staining provides greater sensitivity and specificity than does PAS staining and can be used retrospectively on fixed samples^{ref1, ref2}.88,89 Recently, T. whipplei was detected with the use of autoimmunochemical staining in which anti–T. whipplei antibodies from the patient's own serum is used (rather than antibodies developed in the laboratory). With this technique, the organism was detected in heart-valve samples from five patients with blood culture–negative endocarditis^ref.90 As noted above, PCR can be used to detect T. whipplei in samples from a variety of tissue types and body fluids^ref.91 As with all PCR assays, it is critical to avoid contamination of the DNA sample and to include positive and negative controls to validate the test. Initially, PCR assays targeting the 16S rRNA gene and 16S–23S intergenic regions of the T. whipplei gene were used^{ref1, ref2}.8,81 More recently, a quantitative real-time PCR assay targeting this intergenic region was developed^ref70 that offers the advantages of a reduced detection time and a lower risk of sample contamination. Now, on the basis of genome analysis, a new quantitative real-time PCR assay has been developed that targets repeated sequences of T. whipplei, with substantially greater sensitivity than the earlier PCR assays and the same specificity^ref.92 When amplified product is detected, the identification of T. whipplei should be confirmed by sequencing or by using fluorescence-labeled oligonucleotide hybridization probes in a real-time PCR assay. Discrepancies between laboratories suggest that results obtained with "homemade" (not standardized) PCR should be interpreted with caution. The many positive PCR results from people without Whipple's disease have been obtained primarily with the use of nested or seminested techniques, which carry a high risk of contamination^{ref1, ref2, ref3, ref4, ref5}.66,68,69,93,94 Nonetheless, it is important to pay attention to a positive PCR assay, as suggested by the death of a patient in whom one of three PCR tests was positive but whose duodenal biopsy specimens were negative on PAS staining^ref95; the diagnosis of Whipple's disease was thought to be ruled out, yet the autopsy revealed Whipple's disease. Cultivation of T. whipplei from various samples can be achieved, but this technique is not generally available^{ref1, ref2, ref3, ref4, ref5, ref6}.9,14,41,76,77,87 Our strategy for diagnosing Whipple's disease uses the results of PAS staining and PCR in parallel. However, another group has recently proposed histologic examination of a small-bowel–biopsy specimen as the first step, with PCR performed only if the histologic findings are negative^ref.96 The main limitation of this approach is that the specificity of both histologic assessment and PCR is less than optimal.


The sampling hierarchy depends on the clinical manifestations of the disease and the interpretation of the obtained results. If PAS staining of the small-bowel–biopsy specimen is positive and the PCR assay is negative, the diagnosis of Whipple's disease must be confirmed; this can be done by immunohistochemical testing with an antibody to T. whipplei. If this test is positive, Whipple's disease is confirmed; if the test is not feasible, other tissues must be analyzed. If the PCR assay is positive and PAS staining is negative, the result must be confirmed by using another PCR target on the same sample or by analyzing other tissues. When a definite diagnosis of Whipple's disease has been established, the cerebrospinal fluid should be tested with a PCR assay, even in the absence of neurologic signs. When the diagnosis is in doubt, samples from saliva, stool, and blood can be tested; a positive PCR assay with one of these samples in conjunction with a positive test on another tissue may be helpful in confirming Whipple's disease.
Therapy : Whipple's disease was invariably fatal before the advent of antibiotics. However, current recommendations are not based on therapeutic trials or the susceptibility of T. whipplei to various antimicrobial agents. Tetracycline has long been prescribed as a first-line treatment, but the frequency of recurrence after treatment with this agent has been high (28% on average)^{ref1, ref2, ref3}.21,25,26 Thus, the standard for antibiotic therapy currently favors antibiotics that are capable of crossing the blood–brain barrier, such as trimethoprim–sulfamethoxazole. The recommended treatment is oral administration of 160 mg of trimethoprim and 800 mg of sulfamethoxazole twice per day for 1 to 2 years, usually preceded by parenteral administration of streptomycin (1 g per day) together with penicillin G (1.2 million U per day) or ceftriaxone (2 g daily) for 2 weeks. However, lack of a clinical response has been reported with this strategy, and recurrence is also possible (Table 4)^{ref1, ref2, ref3, ref4, ref5, ref6, ref7}.21,25,26,39,97,98,99 Patients with a neurologic recurrence of Whipple's disease have a poor prognosis^ref.39 IFN-g has been proposed for treatment of recurrent central nervous system disease, and one report noted that a positive effect was still present at least 1 year after interferon gamma therapy had been stopped^ref.100 The susceptibility of T. whipplei to various antimicrobial agents has been tested with the use of both cell and axenic cultures^{ref1, ref2}.12,13 Many antibiotics, including doxycycline and sulfamethoxazole, are active in vitro, but trimethoprim is not, as predicted from genomic analysis^{ref1, ref2, ref3},13,14,101 since T. whipplei lacks the coding sequence for dihydrofolate reductase, which trimethoprim targets^ref.101 In cell culture, cephalosporins (including ceftriaxone) and fluoroquinolones are not active^ref.13 In axenic medium, ceftriaxone and levofloxacin are active^ref.14 Vacuole acidification has been shown to be critical to the survival of T. whipplei in phagosomes, since agents that increase the intravacuolar pH decrease bacterial viability^ref.102 A regimen based on this observation — doxycycline (200 mg per day) and an alkalinizing agent, hydroxychloroquine (200 mg 3 times per day) — has been effective in vitro. This combination has, thus far, been the only successful bactericidal regimen against T. whipplei in vitro^{ref1, ref2}.13,102 Whether this regimen will work in a general clinical setting is unknown, though it has been successful in four of our patients: two with classic Whipple's disease and two with blood culture–negative endocarditis. On the basis of previous work^ref,102 we suggest using a regimen of doxycycline and hydroxychloroquine to eradicate the intracellular organisms in patients with Whipple's disease who do not have neurologic involvement (as indicated by a negative PCR assay on cerebrospinal fluid and the absence of neurologic signs). In patients with neurologic involvement, we suggest adding a high dose of sulfamethoxazole or sulfadiazine to the regimen described above. There is no established marker that can be used to determine how long treatment should be continued. By analogy with other chronic infections^{ref1, ref2},103,104 it would seem reasonable to use this regimen for at least 12 to 18 months. Clinical trials are needed to confirm our approach and to establish whether these personal suggestions are effective.

antibiotic	no. of relapses/no. of patients treated (%)ref1, ref2, ref3, ref4, ref5, ref6
tetracycline	43/13 (32%)
cotrimoxazole	1/46 (2%)
penicillin and streptomycin	2/6 (33%)
other	12/64 (19%)
total	58/249 (23%)

The recent cultivation of T. whipplei, along with the complete sequencing of its genome, should provide new opportunities for investigating, understanding, and treating Whipple's disease. The reservoir of T. whipplei remains to be established, and transmission mechanisms remain to be elucidated. The significance of possible asymptomatic carriers must be clearly addressed. Isolates of T. whipplei should be routinely genotyped to identify associations among clinical forms, different strains, and geographic origin. Although PCR has expanded the recognized clinical spectrum of the disease, many facets remain elusive. In the future, the development of an assay for detection of specific antibodies in the serum may help with diagnosis of the disease. Improvement in diagnostic approaches is of paramount importance for reliable detection. Improved detection will in turn lead to decreases in the morbidity, and perhaps the mortality, associated with the disease, which is treatable when diagnosed early but may have fatal consequences when the diagnosis is delayed. Prospective trials are needed to evaluate therapy.
Chemotherapy : penicillin (or ceftriaxone) and streptomycin for 2 weeks, followed by cotrimoxazole for 1-2 years. Jarisch-Herxheimer reaction (JHR) can occur.

• Bacillus / Clostridium group (low G+C Gram-positive Bacteria)
• Bacilli (facultative anaerobes or strictly aerobes spore-forming Bacteria)
• Bacillales
• Bacillaceae
• Bacillus

Bactridium-type sporulation : it doesn't occur in infected organisms.
• Bacillus cereus group
• Bacillus anthracis
• Bacillus atrophaeus (formerly Bacillus subtilis var niger).
• Bacillus cereus
• Bacillus cereus biovar toyoi
b-hemolytic, flagella => motile
Epidemiology : most often occurs in small clusters, accounting for 2% of food-related disease outbreaks with confirmed etiology reported to CDC (58 outbreaks during 1973 to 1987) in USA.
Genomics : a plasmid that is 99.6% genetically similar to the pX01 plasmid coding for anthrax toxin in Bacillus anthracis has been found in a sample of Bacillus cereus taken from a person who survived a life-threatening alveolar pneumonia symptomatic of inhaled anthrax^ref. Although the researchers did not find a homologue to pX02—the anthracis plasmid–containing genes that create an impenetrable capsule surrounding and protecting the bacterium while it lies dormant in soil—they found a different plasmid coding for a similar capsule, which may serve the same function. Normally, when microbiologists look for anthrax, they say that it has to be non-hemolytic and non-motile, whereas this B. cereus isolate is motile and hemolytic. The bacillus family of bacteria is known to be capable of gene jumping. All B. anthracis-sensitive miice injected i.p. with the plasmid-containing B. cereus died within 14 days : anyway rabbits are a better animal model for anthrax than mice. Moreover, injecting mice in their peritoneal cavities may not produce the same results as making them inhale the isolate. So what they really needed to do is get rid of that plasmid from that B. cereus isolate to see if it was still pathogenic or disrupt the gene that encodes one of the principal toxins
Transmission : from ingestion of reheated rice or other vegetables, contaminated fish, creams, potato purée, spices, cereals, sauces, and salads
=>food poisoning^ref, lasting < 24-48 hours (rarely 4-5 days) after onset :
• p5^{ST toxin} => "short-incubation" or emetic form (resembles Staphylococcus aureus food poisoning) : nausea and vomiting and abdominal pain after an incubation period of 30' to 6 hours. Occasionally, abdominal cramps and/or diarrhea may also occur. The vomiting-type outbreaks have generally been associated with rice products; however, other starchy foods such as potato, pasta (pasta salada) and cheese products have also been implicated. Food mixtures such as sauces, puddings, soups, casseroles, pastries, and salads have frequently been incriminated in food poisoning outbreaks.
• p50^{LT toxin} => "long-incubation" or diarrheal form (resembles Clostridium perfringens food poisoning) : abdominal pain and diarrhea with an incubation period of 8 to 24 hours.
=> in immunocompromised patients, sepsis, meningitis, alveolar pneumonia, and skin wound infections^{ref1, ref2}. Certain populations are at increased risk for B. cereus infection, including cancer patients, neonates, intravenous drug users, and patients with a history of trauma, surgery, or catheterization^{ref1, ref2, ref3, ref4}. Primary cutaneous disease attributed to B. cereus in immunocompetent persons or in non-health-care settings rarely has been reported^ref. On 24 Aug 2004, a local health department in Georgia received a call from a university health center describing 90 cadets with nonpruritic, impetigo-like lesions on their scalps; B. cereus was the common organism among the 3 patients whose lesions were cultured. The cases occurred during the freshman military orientation week that preceded the start of the fall term. The Georgia Division of Public Health (GDPH) conducted an investigation to determine the source of the infections, identify associated risk factors, and implement control measures. This report summarizes the results of the outbreak investigation, which identified receiving a short haircut at the start of orientation week, sharing sunscreen during the week, and membership in Company B as strongly associated with having scalp lesions. Recommendations to the university included changing the type of haircut required, increasing time allowed for showering, and issuing individual sunscreen. The results of this investigation underscore the need for military programs to incorporate good hygiene and infection-control measures into school orientation events. GDPH reviewed the events of orientation week, investigated cases of scalp dermatitis, collected environmental samples, and conducted a cohort study of participants in the military program during 4 site visits to the university. University personnel provided a schedule of orientation activities and a tour of each event location. Medical records from patients were reviewed and clinical findings discussed with university health-care staff. Patients were interviewed, and available clinical isolates were sent to the Georgia Public Health Laboratory for confirmation. Samples, including talc, Barbicide(r) disinfectant, and swabs of electric clippers, were collected from 2 barbershops providing haircuts to cadets. Soil and water samples were collected from event sites, and swabs were taken of shared helmets and sunscreen. 5 patients donated their hats for the environmental and laboratory investigation. CDC analyzed the environmental samples and characterized bacterial isolates by biochemical analysis, 16S rRNA gene sequencing^ref, and multilocus sequence typing (MLST)^ref. After the initial investigation, GDPH conducted a cohort study of all cadets in the military program at the university. GDPH distributed questionnaires to all 660 cadets, including upperclassmen, 3 weeks after orientation week. The cadets were asked about demographic information, company and dormitory assignment, clinical symptoms, orientation vent participation, exposure to soil and water, and hygiene practices, including laundry, bathing, and shared products. A case was defined as an occurrence of scalp lesions in a cadet treated with oral cephalexin from the school health center during 10-30 Aug 2004. Measures of association were estimated using multivariate logistic regression to control for confounding. The 4-year military program at the university had 660 students (292 freshman and 368 upperclassmen) organized into 7 discrete companies. Cadets lived in 5 separate dormitories, 2 per room, organized by company, sex, and class year. Each floor shared a bathroom and a common living room. Orientation directly involved 292 freshmen; 115 upperclassmen supervised the events. Orientation started with a short haircut for all 255 freshman males at 1 of 2 civilian barbershops. Haircuts were performed by 1 of 8 barbers in random order using electric clippers without a scalp guard. The 3rd day of orientation week, the cadets completed an obstacle course involving immersion in mud and river water. On the final day, participants were required to rappel from rock walls and participate in survival training exercises. Helmets were worn and sunscreen was shared among cadets during these activities. 94 (14%) of 660 cadets had scalp lesions, and 1 cadet was infected twice during the period from the start of orientation to when the questionnaire was administered. 33 patients sought care at the student health center on the 4th day of orientation week, and 57 sought care on the 5th day. 5 more cases, including the recurrent case, occurred 1 week after the start of school. All patients participated in orientation week; all were male and ranged in age from 16 to 24 years. The majority of patients were freshmen (84/94; 89%) and received a haircut on the 1st day of orientation (89/94; 95%). Approximately 1/3 of the patients (33/94; 35%) were in Company B. The index patient noted onset of symptoms on the 3rd day of orientation. Yellow sticky discharge followed by honey-colored crusts on the crown of his head were noted. Lesions were nonpruritic. Other patients had similar lesions with the same distribution. Infections resolved within 48 hours with the use of antibacterial soap and oral cephalexin (5-day prescription). Health care providers obtained samples for culture from lesions of 3 cadets. B. cereus  was the only common organism isolated from all 3 patients and was identified by using biochemical tests and 16S rRNA gene sequencing. When analyzed by MLST, all 3 clinical B. cereus isolates were indistinguishable. B. cereus also was cultured from 2 separate barbershop clippers (2 isolates), soil from the school grounds and orientation events (5 isolates), and helmets (2 isolates) worn during rappelling exercises. 5 environmental isolates (3 soil samples and 2 clippers) matched the clinical isolates by 16S rRNA. MLST was performed on these isolates, resulting in 4 unique sequence types (3 from the soil samples and 1 from the 2 clippers), with no matches to the clinical B. cereus sequence type. The response rate for the cohort study was 73% (483/660); the response rate for freshmen was 84% (248/292). Of the respondents, 423 (88%) were male, and 248 (51%) were freshmen, which was representative of the entire cohort. The median age was 19 years, and 405 (84%) cadets were white. After adjusting for sex, freshman class status, and participation in orientation week, the multivariate logistic regression model indicated a statistically significant association between having scalp lesions and receiving a haircut (adjusted odds ratio [AOR] = 10.6), membership in Company B (AOR = 9.7), and sharing sunscreen (AOR = 2.7). Other risk factors examined included demographic information, exposure to soil and water, and hygiene practices (e.g., laundry, bathing, and use of shared products). B. cereus is a recognized bacterial pathogen in humans. Non-gastrointestinal infections are usually the result of a breakdown in natural protective barriers such as the skin or immune system^{ref1, ref2, ref3}. The findings in this report indicate that immunocompetent persons can be vulnerable to cutaneous B. cereus infections when skin is compromised. Isolation of 3 indistinguishable B. cereus isolates from 3 patients on 2 separate days suggested that this was a common-source outbreak and not a laboratory contaminant, even though the environmental source of B. cereus was not identified during the investigation. All but 5 cases were diagnosed on 2 concurrent days, making person-to-person transmission unlikely. Transmission most likely occurred from an exposure at the beginning of the orientation week. The short haircut likely caused microabrasions, compromising the protective effect of scalp epidermis. Exposure to mud, sun, and sunscreen further provided an environment suitable for bacterial growth. The findings in this report are subject to at least 3 limitations. First, only 3 clinical samples were available for culture. Because of the number of cases and the positive response to therapy, the health-center staff treated cases empirically before GDPH involvement. Second, other risk factors and potential confounders might not have been identified during the site visits. Finally, cadets were asked about their orientation exposures nearly 3 weeks after the events occurred; recall bias might have influenced the findings. As a result of this investigation, GDPH made recommendations to the university military program for future orientations to minimize the risk for another outbreak. These included 1) changing the type of haircut required for male cadets that would allow for more hair and less injury to the scalp, 2) allowing adequate time for personal hygiene, and 3)  distributing individual packets of sunscreen and discouraging sharing of sunscreen. These recommendations were implemented during the 2005 orientation activities; no skin infections were reported. University military programs should establish infection-control practices including good hygiene as part of their organized orientation events. Since many laboratories may not identify B. cereus from a skin culture and refer to it as Bacillus species -- which may well be thought of as a contaminant from a typical staphylococcal-streptococcal impetigo -- sporadic cases may indeed occur. Reference 7 above describes a 29-year-old with a chronic (2-month) leg ulceration that initially developed during a 3-month stay in French Polynesia and developed into a superficial ulceration with dark, adherent eschar and surrounding erythematous halo.  The culture was obtained from a biopsy instead of a swab and revealed a pure culture of B. cereus^ref
=> large toxin loads may cause quite severe, less frequent manifestations of toxin illness such as pulmonary hemorrhage and acute liver failure^{ref1, ref2}
Laboratory examinations : the presence of large numbers of B. cereus (> 6 logs of organisms/gram) in a food is indicative of active growth and proliferation of the organism and is consistent with a potential hazard to health
Prevention : check time/temperature parameters, cool rapidly, preserve at > 60°C, heat at 74°C
• Bacillus thuringiensis
Proteomics : Cry5B, a bacterial pore-forming toxin
• Bacillus thuringiensis serovar israelensis
It produces an intracellular parasporal (or pyramidal) crystal in association with spore formation. Crystal toxins damage intestines of :
• Lepidoptera : anyway Helicoverpa zea can develop resistance
• multiple Nematoda species, including a rat intestinal nematode (4 crystal proteins)
The bacteria and protein crystals are sold as "Bt" insecticide (used for the biological control of certain garden and crop pests), while the Bt toxin gene is added to many GM plants.
• Bacillus circulans
• Bacillus fusiformis

=> noma / cancrum oris / gangrenous stomatitis
• Bacillus pumilus
• Bacillus subtilis
=> hypersensitivity pneumonia
Some strains of B. subtilis and B. licheniformis have been isolated from lamb and chicken and incriminated in food poisoning episodes. These organisms demonstrate the production of a highly heat-stable toxin which may be similar to the vomiting type toxin produced by B. cereus.
• Listeriaceae
• Listeria (facultative anaerobes, psychrophilic, peritrichous, halophilic)
• Listeria grayi

• Listeria monocytogenes
Epidemiology : in USA the disease is found nationwide, and accounts for 2% to 3% of bacterial meningitis episodes. In 2004, the CDC reported 2500 cases across the country and 500 deaths.
• the estimated incidence was 1,965 in 1989 (481 fatal) and 1,092 in 1993 (248 fatal).
• an outbreak in Massachusetts in 1983 involved 49 cases (4 fatal, 7 perinatal) - milk was implicated but not proven.
• an outbreak in California in 1985 involving 142 cases (48 fatal, 93 perinatal) was traced to contaminated soft cheese.
• an outbreak in Philadelphia during 1986 to 1987 involved 36 cases (16 fatal, 4 perinatal) - source unknown.
• contaminated hommus (chickpea paste) was implicated in an outbreak during 1997.
• the rate of perinatal disease decreased from 17.4/100,000 births in 1989, to 8.6/100,000 in 1993
• food-borne listeriosis outbreaks in the USA :
• dairy products:
• 1983 : an outbreak in Massachusetts (49 cases, 40 confirmed, 4 fatal, 7 perinatal) - milk was implicated but not proven.
• 1985 : an outbreak in California (142 cases, 48 fatal, 93 perinatal) was traced to soft cheese.
• 1994  : an outbreak in Illinois (45 cases, 11 confirmed) was ascribed to chocolate milk.
• 2000 to 2001 : an outbreak in North Carolina (12 cases) was ascribed to homemade Mexican-style cheese.
• meat and poultry:
• 1998 to 1999 : an 11-state outbreak (62 cases, 10 fatal) was caused by contaminated hot dogs and other meat products. A recall of 15 million pounds of meat was projected as a result.
• 2000 : a multistate outbreak of infection from deli turkey meat (8 perinatal and 21 non-perinatal cases; 4 fatal) involved New York, Georgia, Connecticut, Ohio, Michigan, California, Pennsylvania, Tennessee, Utah, and Wisconsin. The outbreak resulted in recall of 16.7 million pounds of ready-to-eat poultry products from one company.
• 2001 : 189 000 pounds of luncheon meat sold in 10 states were recalled because of contamination by Listeria.
• 2001 : 16 people attending a catered party in Los Angeles, California were infected by contaminated delicatessen meat.
• 2002 : a multistate outbreak in Pennsylvania, Pennsylvania, New York, Delaware, Connecticut, Maryland, Michigan and Ohio involved 46 cases (7 fatal, 3 stillbirths and miscarriages) and was ascribed to turkey meat.
• 2002 : one company recalled 27.4 million pounds of cooked sandwich meat, and another recalled 4.2 million pounds of ready-to-eat turkey and chicken because of possible Listeria contamination.
• seafood:
• 1989 : an outbreak in Connecticut involving 10 cases (1 fatal) was ascribed to shrimp.
• other and unknown:
• 1986 to 1987 : an outbreak (36 cases, 16 fatal, 4 perinatal) was reported in Philadelphia.
• 1997 : an outbreak was ascribed to contaminated hommus (chickpea paste)
Hispanic women may have a higher incidence of listeriosis than pregnant non-Hispanic women. This is most likely because they might make and eat homemade soft cheese and other traditional foods made from unpasteurized milk. "Queso fresco"-- a traditional homemade cheese, prepared from unpasteurized milk and widely consumed by Hispanics -- has led to miscarriages, death of newborns, and premature delivery caused by L. monocytogenes^ref
Proteomics :
• 15 O and 5 H Ags => 6 subtypes (92% belongs to 1a, 1b and 4b), 5 phagotypes. b-hemolytic.
• p60 extracellular protein is a major virulence factor
• p60-like proteins and lipoproteins
• virulence factors are encoded by chromosomal genes organised in operons
• LPXTG proteins
• internalin gene family
• internalin A is a virulence factor which binds to E cadherin.
• actA protein is essential for the accumulation of actin, and as Listeria properls through the host cell cytoplasm via its actin tail, it is required for survival and spread in the host.
• listeriolysin O (LLO) is a dermonecrotic pore-forming exotoxin that binds cholesterol and allows the bacteria to escape from the endosomal compartment  and to enter the cytosol of the host cell where intracellular growth occurs.
• phospholipases
• Listeria monocytogenes phosphatidylinositol-specific phospholipase C (PI-PLC) plays a critical role in escape of this human pathogen from host cell vacuoles. Unlike classical bacterial PI-PLCs, the L. monocytogenes enzyme has very weak activity on glycosylphosphatidylinositol (GPI)-anchored proteins. Previous crystal structure analysis has revealed that a small b-strand (Vb) is present in Bacillus cereusPI-PLC and is absent in the enzyme from L. monocytogenes. This Vb b-strand in B. cereus PI-PLC forms contacts with the glycan linker of GPI anchors, which presumably increases its activity on GPI-anchored proteins. Of all known bacterial PI-PLCs, those from listeriae are the only ones that lack the b-strand. Expression by L. monocytogenes of B. cereus PI-PLC, which has strong activity on GPI-anchored proteins, inhibited bacterial escape from a vacuole and cell-to-cell spread, resulting in greatly reduced virulence in mice. Deletion of the Vb b-strand from B. cereus PI-PLC abolished its ability to cleave GPI-anchored proteins, decreased its inhibitory effects, and increased its virulence in mice. These results strongly suggest that L. monocytogenes PI-PLC has evolved as an important determinant of L. monocytogenes pathogenesis by absence of the Vb b-strand, thus leading to greatly reduced activity on GPI-anchored proteins^ref.
• lipoate protein ligase (LplA1) uses host-derived lipoic acid to make a lipoyl modification on the E2 subunit of pyruvate dehydrogenase (PDH) required for intracellular growth and virulence. Some other bacterial pathogens, like Chlamydia trachomatis, Staphylococcus aureus, and Streptococcus pyogenes, also have two lplA-like genes but no lipB homolog, which suggests that utilization of host-derived lipoic acid may play a critical and underappreciated role in the replication of many bacterial pathogens
Transmission : ingestion of raw milk, supposedly pasteurized fluid milk, cheeses (particularly soft-ripened varieties whose rind is covered with mould), ice cream, raw vegetables, fermented raw-meat sausages, cold cuts, raw and cooked poultry, raw meats (all types, including Oryctolagus cuniculus), and raw and smoked fish. Its ability to grow at temperatures as low as 3°C permits multiplication in refrigerated foods. Expecially frequent in immunosuppressed individuals, alcoholists, pregnants and newborns. The greatest threat of listeriosis is from ready-to-eat products that do not require further cooking at home. L. monocytogenes in raw food that will be cooked before consumption is less of a concern to the food industry, since the bacteria are killed during cooking. Listeriosis can be acquired from seafood, although most think of the risk from processed deli meats 1st. Yearly, recalls of seafood, especially smoked salmon, are posted on FDA's website. Although not generally linked to large outbreaks, those at high risk, such as pregnant women and those individuals with compromised cell-mediated immunity, should avoid the food described below. L. monocytogenes has been isolated from raw fish, cooked crabs, raw and cooked shrimp, raw lobster, surimi (minced, processed fish used in the preparation of imitation seafood, especially imitation shellfish) and smoked fish (Ward D, Bernard D, Collette R, et al. (Eds.): Hazards Found in Seafoods, Appendix III. In HACCP: Hazard Analysis and Critical Control Point Training Curriculum, 2nd ed., p. 173-188. UNC-SG-96-02. North Carolina Sea Grant, Raleigh, NC, 1997).
Pathogenesis : it is a facultative intracellular pathogen which invades macrophages and most tissue cells of infected hosts where it can proliferate. Following internalisation into host cells, the bacteria escape from the phagosomal compartment and enter the cytoplasm. They then spread from cell to cell by a process involving actin polymerisation. In infected hosts, the bacteria cross the intestinal wall at Peyer's patches to invade the mesenteric lymph nodes and the blood. The main target organ is the liver, where the bacteria multiply inside hepatocytes. Early recruitment of PMN cells lead to hepatocyte lysis, and thereby bacterial release. This causes prolonged septicaemia, particularly in immunocompromised hosts, thus exposing the placenta and brain to infection.
=> listeriosis (monocytosis > 75%) : 100 to 1,000 cells can cause the illness.
organ listeriosis
cutaneous listeriosis
oculoglandular listeriosis
URT listeriosis
urogenital tract listeriosis
febrile gastroenteritis (diarrhea with mucous stools)
lymphogenic listeriosis (i.e. cervicoglandular listeriosis)
hematogenic listeriosis
in pregnants : lower levels of protective cytokines and were unable to eliminate the pathogen => facilitated bacterial multiplication in the liver, placenta and ultimately in the fetal tissues => severe necrotizing hemorrhagic hepatitis and Listeria chorioamnionitis  => Listeria-induced placental and fetal necrosis with unrestricted bacterial multiplication, increasing the incidence of postimplantation loss and poor pregnancy outcome (intrauterine and neonatal death, abortion, stillbirth or severe neonatal infections similar to neonatal Group B Streptococcus sepsis, with early and late onset forms of disease)

Laboratory examinations : amniocentesis
Therapy : if Listeria chorioamnionitis is diagnosed preterm, in contrast to other types of chorioamnionitis, in utero therapy with high-dose penicillin or cotrimoxazole is possible, and preterm delivery may be avoided
the prognosis of listeriosis depends on the severity of meningoencephalitis (Listeria neuromeningitis), due to the elective location of foci of subacute infection and inflammation in the brain stem by intraaxonal (unilateral) bacterial spread from peripheral sites to the ipsilateral CNS : listeria rhombencephalitis (50%). The disease has a characteristic biphasic course: a nonspecific prodrome of headache, nausea and vomiting, and fever lasting for a several days is followed by progressive and persistent asymmetrical cranial-nerve palsies (sometimes complex auditory hallucinations; rarely central apnea with simultaneous consciousness impairment due to pons and medulla lesions of the reticular formation)
generalized miliary listeriosis
septicemiawith pharyngitis, mononucleosis and subacute endocarditis
=> a 13 amino acid peptide (HKEMPFPKYPVEP) derived from digestion of bovine ß-casein by the combined actions of the L. monocytogenes thermolysin-like metalloprotease Mpl and a collagen-associated trypsin-like serine protease stimulates the motility and invasion of human colon cancer cells via binding to delta opioid receptor (dOR)^ref
Laboraotry examinations : an antibody-based fibre-optic biosensor created by food scientists at Purdue University can detect Listeria monocytogenes in < 24 hours at concentrations as low as 1,000 cells per millilitre of fluid
Therapy : combination of ampicillin and gentamicin or, for patients who are intolerant of b-lactam agents, cotrimoxazole
Prevention :
• avoid cross-contamination; cook at right temperatures, disinfects devices; do not drink unpasteurized milk. Risk groups should rigorously respect usage and preservation indications on labels
• small amounts of oregano (Origanum vulgare) extracts added to meat : the flavor cannot be totally eliminated because some intensity of flavor is linked to the compounds that are inhibitory
• dipping hot dogs into a calcium sulfate solution did not have any major effect on the flavor or the chemical composition of the hot dogs
• using lactic acid and other so-called "good bacteria" to kill listeria inside the floor drains of meat plants.
• fish smoking with the traditional oak chips supplemented with teak causes little difference between the 2 tastes but the one treated with the teak lasts longer (it doesn't spoil for about a week or so longer than the others) and reduces the number of listeria in the smoked tissues. Hazards from L. monocytogenes can be prevented by thoroughly cooking seafood and by preventing cross-contamination once the seafood is cooked. The CDC's recommendations regarding the risk of acquiring listeriosis from seafood^ref include not eating refrigerated smoked seafood unless it is contained in a cooked dish, such as a casserole. Refrigerated smoked seafood, such as salmon, trout, whitefish, cod, tuna or mackerel, is most often labeled as "nova-style," "lox," "kippered," "smoked," or "jerky." The fish is found in the refrigerator section or sold at deli counters of grocery stores and delicatessens. Canned or shelf-stable smoked seafood may be eaten
• don't eat :
• hot dogs and luncheon meats unless they're reheated until steaming hot.
• soft cheeses like Feta, Brie, and Camembert, "blue-veined cheeses," or "queso blanco," "queso fresco," or Panela unless they're made with pasteurized milk; Make sure the label says, "made with pasteurized milk"
• refrigerated pates or meat spreads
• refrigerated smoked seafood - unless it's in a cooked dish, such as a casserole (refrigerated smoked seafood, such as salmon, trout, whitefish, cod, tuna, or mackerel is most often labeled as "nova-style," "lox," "kippered," "smoked," or "jerky." These types of fish are found in the refrigerator section or sold at deli counters of grocery stores and delicatessens.)
• raw (unpasteurized) milk or foods that contain unpasteurized milk
Prognosis : despite bactericidal antibiotic therapy, the overall mortality is still 25-30%
• Staphylococcaceae
• Gemella : a genus of aerobic or facultatively anaerobic cocci, occurring singly or in pairs with adjacent sides flattened; they are found as parasites of mammals.
• Gemella haemolysans (a.k.a. Neisseria haemolysans) : a species found in bronchial secretions and slime from the respiratory tract.
• Gemella morbillorum (a.k.a. Peptostreptococcus morbillorum, Diplococcus morbillorum, Streptococcus morbillorum) an anaerobic-to-aerotolerant Gram-positive coccus, is a normal flora of the oral cavity, respiratory tract, urogenital organ and gastrointestinal tract, and infections caused by this organism are unusual. It has been associated mainly with endocarditis and bacteremia, and rarely with arthritis, spondylodiscitis, meningitis, brain abscess and septic shock. Liver abscess is very rare, and only a few cases have been reported^ref.
• Staphylococcus (facultative anaerobes, fermentation, very resistant, lysozyme resistant, lysostaphyn sensitive; catalase⁺ (differential feature from Streptococci)) => > 80% of all suppurative infections with yellow and dense pus.
• Staphylococcus aureus
• Staphylococcus auricularis

=> 2% all acute otitis externa (AOE)
• Staphylococcus capitis

Proteomics : coagulase^-
=> peritonitis due to continuous ambulatory peritoneal dialysis
• Staphylococcus capitis subsp. urealyticus

=> 1.4% all acute otitis externa (AOE)
• Staphylococcus caprae

=> 2.6% all acute otitis externa (AOE)
• Staphylococcus epidermidis (a.k.a. Staphylococcus albus)

Proteomics : coagulase^-, Chapman medium^-. Symbiontic microflora on skin surface.
=> bacteraemia
=> endophthalmitis
=> septic arthritis in individuals with prosthesis
=> endocarditis
=> 9.1% all acute otitis externa (AOE)
  : vancomycin-resistant Staphylococcus epidermidis (VRSE) !
• Staphylococcus haemolyticus

Proteomics : coagulase^-.  Biofilm production is very low regardless of the experimental conditions used.
=> 1.3% all acute otitis externa (AOE), skin and soft-tissue infections, infant staphylococcal septicemia
=> peritonitis due to continuous ambulatory peritoneal dialysis
Therapy : methicillin-resistant
• Staphylococcus hominis
Proteomics : coagulase^-.
=> infant staphylococcal septicemia, CAPD-related peritonitis
• Staphylococcus intermedius

Proteomics : nitrate reductase converts dietary nitrates in saliva into nitrites.
• Staphylococcus lentus (a.k.a. Staphylococcus sciuri subsp. lentus)

Proteomics : coagulase^-.
=> symptomatic urinary tract infections (UTI) and asymptomatic bacteriuria
• Staphylococcus lugdunensis

Proteomics : coagulase^-.
During the past decade, it has emerged as an important pathogen implicated in both community-acquired and nosocomial infections^{ref1, ref2}. Clinical manifestations of infections with these organisms include ction due to S. lugdunensis SCVs and other colony variants of this species has been reported^ref
=> peritonitis due to continuous ambulatory peritoneal dialysis, abscesses^ref, meningitis^ref, ventriculoperitoneal shunt infection^ref, spondylodiscitis^ref, prosthetic joint infection^ref, catheter-related bacteremia^ref, and endocarditis^ref. Infections with S. lugdunensis tend to have a more fulminant course, with an outcome resembling that of S. aureus infections rather than that caused by coagulase-negative staphylococci^ref. In addition, these organisms are frequently misidentified as S. aureus because of their morphologic appearance with yellow pigmentation and complete hemolysis when cultured on blood agar. A case of a device-related bloodstream infe
• Staphylococcus saccharolyticus
• Staphylococcus saprophyticus (aerobes)

Proteomics : coagulase^-. Chapman medium^-.
=> peritonitisdue to continuous ambulatory peritoneal dialysis
=> symptomatic urinary tract infections (UTI)
• Staphylococcus schleiferi
• Staphylococcus schleiferi subsp. coagulans
• Staphylococcus schleiferi subsp. schleiferi
Proteomics : coagulase^-.
=> pathogenic ?
• Staphylococcus sciuri
• Staphylococcus sciuri subsp. carnaticus
• Staphylococcus sciuri subsp. sciuri
Proteomics : coagulase^-. Nitrate reductase converts dietary nitrates in saliva into nitrites.
Epidemiology : principally found in animals (bovine mastitis and part of skin, nasal and oral flora in healthy dogs and horses), but also of nosocomial origin.
=> skin and soft-tissue infections (including surgical wound infection)
=> symptomatic urinary tract infections (UTI) and asymptomatic bacteriuria
=> infant staphylococcal septicemia, intravenous catheter-related septic shock
=> peritonitis due to continuous ambulatory peritoneal dialysis
Therapy : susceptible to cotrimoxazole, erythromycin, chloramphenicol, neomycin, ciprofloxacin and vancomycin (but vancomycin-intermediate strains have been reported) and resistant to gentamicin, clindamycin, rifampin, methicillin, ampicillin and ceftriaxone.
• Staphylococcus simulans

Proteomics : coagulase^-.
=> peritonitis due to continuous ambulatory peritoneal dialysis
• Staphylococcus vitulinus

Proteomics : coagulase^-.
=> symptomatic urinary tract infections (UTI) and asymptomatic bacteriuria
• Staphylococcus warneri (a.k.a. Staphylococcus warnerii)

Proteomics : coagulase^-.
=> a normal inhabitant of the skin but occasionally causes septicemia, endocarditis^ref, and multifocal discitis^ref
Therapy : glycopeptide-intermediate Staphylococcus species (GISS)
• Thermoactinomycetaceae
• Thermoactinomyces : thermophilic, lives in granaries.
• Thermoactinomyces candidus (a.k.a. Thermoactinomyces vulgaris)
• Thermoactinomyces sacchari
=> hypersensitivity pneumonia
• Lactobacillales
• Enterococcaceae
• Enterococcus (in Lancefield group D Streptococci; fecal streptococci). There are 5 recognized groups of enterococci (groups I to V), which include a total of 21 species^{ref1, ref2, ref3, ref4, ref5} (Facklam, R. R., D. F. Sahm, and L. M. Teixeira. 1999. Enterococcus, p. 297-305. In P. R. Murray, E. J. Baron, M. A. Pfaller, F. C. Tenover, and R. H. Yolken (ed.), Manual of clinical microbiology, 7th ed. ASM Press, Washington, D.C). The majority of these can be identified to the species level by conventional identification techniques. Classic species identification of enterococci involves assays for a combination of biochemical and morphological characteristics of the unknown organism. Biochemical characteristics refer to the ability of enterococci to utilize approximately > 10 different substrates, resulting in a characteristic pattern for a particular species^ref. This identification scheme also involves assays for 2 morphological characteristics, motility and yellow pigmentation. There are only two motile enterococci, Enterococcus gallinarum and E. casseliflavus. They can be differentiated from each other on the basis of their pigmentation; E. casseliflavus is yellow and E. gallinarum is not. There are only 2 yellow-pigmented enterococci of clinical significance to humans, E. mundtii and E. casseliflavus, and they can be distinguished from each other by their motilities. E. flavescens was proposed as a new species of motile yellow-pigmented enterococci; however, further work has suggested that this species is a variant of E. casseliflavus and does not warrant designation as a separate species^{ref1, ref2, ref3}. A third yellow-pigmented enterococcal species is E. sulfureus^ref. The environmental niche for this organism appears to be plants, whereas E. mundtii and E. casseliflavus are animal derived^{ref1, ref2}. E. casseliflavus (E. flavescens), E. gilvus, E. mundtii, E. pallens, E. sulfureus are the yellow-pigmented enterococci. Commensal symbiosis in gut.
• Enterococcus avium (a.k.a. Streptococcus avium)

a- or g-hemolytic.
=> endocarditis^ref, brain abscess^ref
• Enterococcus casseliflavus, first considered as a subspecies of E. faecium, is a motile enterococcus that produces a yellow pigment in agar and often has a VanC phenotype determining an intrinsic low level resistance to vancomycin. It has been implicated in a wide variety of infections in humans, especially immunocompromised hosts
=> bacteremia^{ref1, ref2, ref3}
=> endocarditis^ref
=> meningitis^ref
• Enterococcus cecorum
=> septicemia in a malnourished adult patient^ref
=> recurrent bacteremic peritonitis^ref
=> CAPD peritonitis^ref
=> pleural empyema^ref
• Enterococcus dispar^ref
• Enterococcus durans
• Enterococcus faecalis (a.k.a. Streptococcus faecalis)

b- or g-hemolytic. Only strains containing a pathogenicity island are pathogenic. Nitrate reductase converts dietary nitrates in saliva into nitrites.
=> 1.9% all acute otitis externa (AOE)
• Enterococcus faecium (a.k.a. Streptococcus faecium)

a-, b- or g-hemolytic.
• Enterococcus flavescens
• Enterococcus gallinarum
• Enterococcus mundtii was discovered in 1986 as nonmotile, yellow-pigmented enterococci isolated from cow teats, the hands of milkers, soil, and plants^ref. The species has rarely been isolated from environmental^ref or human sources^ref since then. Misidentification by commercial biochemical assays, which also happened in our case, may account for the scarcity of reports on the organism^ref. With regard to the pathogenecity of E. mundtii in humans, no clear evidence of virulence has been reported in any body sites, including the eye. Kaufhold and Ferrieri^ref isolated 2 strains of E. mundtii from a chronic thigh abscess and sinus mucosa, but they could not determine whether the bacteria were commensals or pathogens.
• Enterococcus raffinosus : a recently described species that is occasionally isolated from human clinical specimens^ref. The natural habitat of E. raffinosus is unknown, but the organism has been described to occur among the oropharyngeal flora of domestic cats, second only to E. faecalis^ref. E. raffinosus has been implicated as a cause of endocarditis and has been recovered from a urine specimen and wound swabs, but clinical and microbiological details confirming the ability of this bacterium to cause serious invasive disease have not been published^{ref1, ref2, ref3}. 2 studies have provided epidemiological evidence that colonization with E. raffinosus can be associated with nosocomial acquisition^ref

=> vertebral osteomyelitis^ref. Infective discitis due to enterococci has been reported on 6 previous occasions since 1969, each one associated with advanced age^ref
=> infected haematoma in an immunosuppressed elderly^ref
=> clinical manifestations :
• urinary tract infections (UTI)
• skin wound infections => septicemia => subacute endocarditis, pyogenic liver abscess
• alveolar pneumonia
• acute meningitis : enterococcal meningitis is an uncommon disease accounting for only 0.3% to 4% of cases of bacterial meningitis which is nevertheless associated with a high mortality rate. It has been described most frequently in patients with neurosurgical conditions (i.e. head trauma, shunt devices, or CSFd leakage), although it can also occur as a "spontaneous" infection complicating remote enterococcal infections such as endocarditis or pyelonephritis^ref. Enterococcus faecalis and Enterococcus faecium are the 2 species most frequently isolated during the course of meningitis (76–90% and 9–22% respectively)
• postoperative endophthalmitis with a poor visual prognosis^{ref1, ref2}. They are, however, rarely identified in endogenous endophthalmitis^{ref1, ref2, ref3}.
Chemotherapy : ampicilin-resistant Enterococcus faecium (AREF) => vancomycin-sensitive Enterococcus (VSE) => plasmid-mediated vancomycin-resistant Enterococci (Van A strain VRE, expecially vancomycin-resistant Enterococcus faecium (VREF)) thanks to 57.9 kb multiresistance, conjugative plasmid with vancomycin resistance encoded in the integrated mobile genetic element Tn1546 (first detected in 1988) => mortality = 37% vs. 16% in VSE^ref. Following their initial recognition in a south London hospital in 1987, vancomycin-resistant enterococci (VRE) had been isolated in at least 71 UK hospitals by 1995^ref. They are an even greater problem in the USA, and have been isolated in many other countries. Although 85–90% of clinical isolates of enterococci are Enterococcus faecalis, most VRE are Enterococcus faecium^ref. After allowing for the effect of blood, which raised the MICs of quinupristin/dalfopristin four-fold, 98.3% of E. faecalis isolates and all the Enterococcus avium, Enterococcus casseliflavus and Enterococcus gallinarum appeared resistant to quinupristin/dalfopristin, whereas 98.8% of the E. faecium isolates and the single Enterococcus raffinosus isolate were susceptible^ref.
• Lactobacillaceae
• Lactobacillus (anaerobes or facultative anaerobes)
• Lactobacillus acidophilus (a.k.a. Döderlain or Holland bacillus, Bacillus vaginalis)

=> caries, commensal in vagina
• Lactobacillus casei

=> caries
• Lactobacillus salivarius

=> caries
• Leuconostocaceae
• Weissella
• Weissella confusa
=> bacteremia^ref
• Streptococcaceae
• Lactococcus (lactic streptococci)
• Lactococcus lactis
• Lactococcus lactis subsp. cremoris (in Lancefield group D Streptococci)
• Lactococcus lactis subsp. lactis (in Lancefield group N Streptococci)
• Lactococcus lactis subsp. lactis bv. diacetylactis (in Lancefield group D Streptococci)
a- or g-hemolytic. Milk infections.
=> bacteraemia => pleural empyema
• Streptococcus (facultative anaerobes-microaerophiles, non-immunogenic capsules made up of hyaluronic acid, catalase^- (differential feature from Staphylococci), fluid and evil-smelling pus). Nitrate reductase converts dietary nitrates in saliva into nitrites.
Aggressins :
• cell wall C-polysaccharide (PnC) / C substance / group carbohydrate Ag is bound to both teichoic and lipoteichoic acid in the cell wall via a phosphorylcholine / phosphocholine (ChoP / PC) moiety : such compound molecules represent bacterial Forssman-Skoog Ag. ChoP can be bound by CRP. Lancefield classification of b-hemolytic Streptococci (1933) : a serologic classification of the hemolytic streptococci, based on extraction and examination by a precipitin technique of group-specific carbohydrate antigens contained in the cell wall. 18 serotypes / groups (A-H and K-V) can be distinguished (please note that for A-C, E-H, K, L, O and R serotypes the Ag determinant is contained in C-polysaccharide, while for D and N it is a teichoic acid and it is unknown for the remaining serotypes !).
• Ag T (25 serotypes)
• Ag M / M protein : it is a LTA-associated protein arising from inner membrane that ...
• acts as a SAg
• binds to CD46 / MCP on keratinocytes
• inhibits fibrinogen and factor H
• the NH₂-terminal, highly variable region of several members binds to C4BP => blocks the binding of complement to the underlying PGN => prevents PMN phagocytosis
• M-associated protein (MAP, only in Ag M⁺ strains).
• Ag B masks Ag M
• Ag R (R3 or R28),
• Ag opacity factor (OF)
• substance P is a mix of all the above mentioned molecules extracted by treatment with weak alkales.
• fibronectin-binding proteins (FnBP)
• Ag F / protein F is a nonfimbrial adhesin
• lipoteichoic acid (LTA) expression on the GBS surface plays a role in bacterial interaction with BBB endothelium and the pathogenesis of neonatal meningitis independent of TLR2-mediated signaling. Invasion associated gene (iagA), which encodes a glycosyltransferase homolog required for synthesis of glycolipid diglucosyldiacylglycerol, a cell membrane anchor for LTA, is required for human brain microvascular endothelial cells invasion in vitro^ref
Sherman classification (1937) is made on the basis of tissue localization and pathogenesis : Streptococci are divided in pyogenic, pneumococci, oral, faecal, lactic, anaerobes and various.
Chemotherapy : penicillins, sulfonamides or cotrimoxazole.
• Streptococcus acidominimus (in Lancefield group E; various)

g-hemolytic
=> 2.5% of all bacteraemias^ref in children on chemotherapy for cancer^ref
=> massive ascites^ref
=> alveolar pneumonia, pericarditis^ref and meningitis^ref
=> otitis media and Gradenigo syndrome^ref
=> endocarditis^{ref1, ref2}
=> bacterial vaginosis and upper genital tract infection^ref
• Streptococcus agalactiae (in Lancefield group B => group B Streptococcus (GBS); apart from B type polysaccharide C, they may contain other polysaccharidic or proteic antigens that allow to further distinguish 5 subserotypes, among which subserotype III is the most virulent; pyogenic)
Genomics : pan-genome consisting of a core genome shared by all isolates, accounting for 80% of any single genome, plus a dispensable genome consisting of partially shared and strain-specific genes^ref
a-, b- or g-hemolytic. It causes bovine mastitis.
=> in adults : pyelonephritis, endocarditis, alveolar pneumonia, endometritis, otitis media, meningitis, septic arthritis
=> in premature newborns (contaminated during birth) : 31% of all meningitis
acute pulmonary syndrome with meningitis within 48 hrs (lethality 50%)
purulent meningitis within 2 months (lethality : 20÷30%)
• Streptococcus anginosus (in Lancefield group F; "viridans"; pyogenic)
b-hemolytic.
=> pharyngitis, endocarditis, liver abscess, puerperal sepsis, skin wound infections, purulent pleurisy^ref.
• Streptococcus bovis (in Lancefield group D; faecal)
a- or g-hemolytic.
=> bacteraemia and endocarditis (expecially in individuals with colon neoplasms)
• Streptococcus canis (in Lancefield group G; pyogenic)

b-hemolytic.
=> pharyngitis
=> infections of soft tissues
=> osteitis
=> endocarditis
=> CNS infections
=> erysipela after 6-7 days incubation
• Streptococcus constellatus (in no Lancefield group; "viridans"; anaerobes)

b- or g-hemolytic.
=> acute and subacute endocarditis, purulent pleurisy^ref
• Streptococcus criceti (in no Lancefield group; "viridans" ; oral)
g-hemolytic.
=> caries
=> acute and subacute endocarditis
• Streptococcus cristatus ("viridans")
• Streptococcus downei (a.k.a. Streptococcus downensis) has been isolated from human dental plaques^ref
• Streptococcus dysgalactiae group (in Lancefield group C; pyogenic)
• Streptococcus dysgalactiae
• Streptococcus dysgalactiae subsp. equisimilis
• Streptococcus equi
• Streptococcus equi subsp. equi
• Streptococcus equi subsp. zooepidemicus
b-hemolytic.
=> erysipela after 6-7 days incubation
=> pharyngitis
=> infections of soft tissues
=> osteitis
=> endocarditis
=> CNS
• Streptococcus equinus (in Lancefield group D; faecal)

a- or g-hemolytic.
=> ?
• Streptococcus gordonii ("viridans")
Genomics : fully sequenced by TIGR
=> plaque development
• Streptococcus iniae
=> golf ball disease in Amazon River dolphin (Inia geoffrensis)
Epidemiology : Canada and China
Transmission : eating fresh fish (Tilapia spp. grown by aquaculture)
=> bacteremic cellulitisand osteomyelitis
• Streptococcus intermedius (in no Lancefield group; "viridans"; anaerobes)

g-hemolytic
Proteomics : intermedilysin (ILY), via its domain 4 structure, binds to the GPI–linked membrane protein human CD59 (an inhibitor of the MAC of human complement) via residues that are the binding site for the C8a and C9 complement proteins^ref.
=> acute and subacute endocarditis
• Streptococcus milleri (in Lancefield groups A, C, F and G or in no group; oral)
g-hemolytic.
=> pharyngitis (?)
=> caries
=> acute meningitis
=> liver abscess, lung abscess and cerebral abscess => peritonitis
=> erysipela after 6-7 days incubation
Streptococcus mitis (a.k.a. Streptococcu mitior; in Lancefield group K, M and O or in no group; "viridans" ; oral)
a-hemolytic.
=> caries, gingivitis.
=> acute meningitis
=> acute and subacute endocarditis
• Streptococcus mutans (in Lancefield E group or in no group; "viridans" ; oral)
• Streptococcus mutans serotype C
a- or g-hemolytic.
Genomics : fully sequenced by University of Oklahoma
=> it continues the caries process initiated by S.sanguinis.
=> subacute endocarditis (type II hypersensitivity)
=> acute meningitis
• Streptococcus parasanguinis ("viridans")
• Streptococcus pneumoniae (a.k.a. Diplococcus pneumoniae or Pneumococcus. Lanceolate or pear-shaped ends. a(with O₂)- or b(without O₂)-hemolytic; in no Lancefield group; microaerophiles => need buffering terminal acid byproducts of homolactic fermentations (inuline included); need for catalase; generally (but not always) sensitive to optocin / ethylhydrocuprein chlorhydrate and tensoactives (biliary salts 10% and saponins activate autolysins))
Epidemiology : clonal outbreaks of invasive pneumococcal infection with additional individuals carrying the same serotype can occur. In the pre-antibiotic period, epidemic pneumococcal disease was observed in a variety of settings including military training centers, psychiatric hospitals, and correctional institutions (Hodges RG, MacLeod CM, Bernhard WG: Epidemic pneumococcal pneumonia. Am J Hyg 1946; 44:183-236; Heffron R: Pneumonia with special reference to pneumococcus lobar pneumonia. Cambridge, Massachusetts: Harvard University Press, 1939, 1979). Pneumococcal outbreaks are rarely reported now, although 2 epidemics have occurred in shelters for homeless men^ref (Nguyen J, Grosset J, Dautzenberg B, et al: Type 1 pneumococcal diseases: two successive outbreaks in men's shelters in Paris, France
(Abstract). In: Program and abstracts of the 29th Interscience Conference on Antimicrobial Agents and Chemotherapy. Houston: American Society for Microbiology, 1989:145). Additionally, an outbreak of invasive infection due to S. pneumoniae, including cases of primary septicemia and meningitis as well as pneumonia, was described in 12 inmates of an overcrowded jail in Texas in 1989^ref. All patients were male; their mean age was 30 (range: 19-53) years. 5 additional inmates with pneumonia had S. pneumoniae isolated from sputum specimens. All isolates from the 17 patients were serotype 12. 14 patients had underlying conditions including alcoholism and intravenous-drug abuse, cirrhosis, and asplenia. Only one inmate had been previously immunized with pneumococcal vaccine. More recently, in 1998, an outbreak of multidrug-resistant pneumonia and bacteremia was described among unvaccinated nursing home residents^ref. Pneumonia developed in 11 of 84 residents (13%), 3 of whom died. Multidrug-resistant S. pneumoniae, serotype 23F, was isolated from blood and sputum from 7 of the 11 residents with pneumonia (64%) and from nasopharyngeal specimens from 17 of the 74 residents tested (23%) and 2 of the 69 employees tested (3%). All the serotype 23F isolates were identical according to pulsed-field gel electrophoresis. Recent use of antibiotics was associated with both colonization (RR = 2.3; IC₉₅ = 1.3 to 4.2) and disease (RR = 3.6; IC₉₅ = 1.2 to 10.8). Only 3 residents (4%) had undergone pneumococcal vaccination. After residents received pneumococcal vaccine and prophylactic antibiotics, there were no additional cases of pneumonia, and the rates of carriage decreased substantially. Additionally, a 1996 outbreak in a NY nursing home was discussed in ProMED
Proteomics :
• 1 capsular Ag (soluble-specific substance (SSS) => > 90 serotypes (I-IC) : serotype III is a type II T-independent Ag, serotype XIV is cross-reactive with human blood group Ag A.
• 3 somatic Ags  => 46 groups (1÷25, 27÷29 and 31÷48).
• M protein (type-specific antigen)
• carbohydrate or substance C (group-specific antigen)
• F protein
Toxins :
• autolysins : they allow cell lysis and liberation of ..
• pneumolysin O (PLO : O₂-sensitive, ~ SLO, see below) from the cytoplasm : it is a pore-forming toxin that binds to cholesterol inhibiting neutrophils chemotaxis and cilia in respiratory epithelium
• purporogenic factor from the peptidoglycan
• neuraminidase
• IgA₁ protease (monomers and dimers)
=> clinical manifestations (only in immunodeficiencies) :
• in babies : self-limiting bronchopneumonia by types 1, 3, 6, 7, 12, 14, 16, 18, 19 and 23.
• in adults (1:500÷1000) : Frankel-Weichselbaum pneumococcal acute lobar pneumonia. Sequelae :
• metapneumonic pleuritis, pleural effusion, pleural empyema
• contiguity pericarditis
• in 25÷30% sepsis / pneumococcemia => invasive pneumococcal disease (IPD) : endocarditis, septic arthritis, acute liver failure, ileus, conjunctivitis, acute otitis media (66% of those before age 4, 50% of those before age 6; expecially from types 6, 14, 19 and 23; if untreated may lead to perforation with 40% lethality), myringitis, parotitis, mastoiditis, sinusitis => meningitis (the most common bacterial meningitis in adults), Waterhouse-Friderichsen syndrome (WFS).
Laboratory examinations :
• PCR and sequencing of the housekeeping genes, gdh (zwf) and gki, based on the primers and alleles from multilocus sequence typing can be used to delineate and support the identity of clinical isolates of Streptococcus pneumoniae and differentiate from the closely related Streptococcus mitis and Streptococcus oralis^ref.
• direct diagnosis.
Prevention : subunit vaccine. A 9-valent pneumococcal conjugate vaccine, PncCV, prevents 31% (95% confidence interval = 15–43%) of pneumonias associated with any of 7 respiratory viruses in children in hospital^ref. Worldwide, most antibiotic-resistant infections are caused by 5 of the 7 serotypes in the 7-valent pneumococcal conjugate vaccine (PCV-7) (6B, 9V, 14, 19F, and 23F)^ref. A second major direct effect of PCV-7, which was not specifically anticipated, has been a reduction in nasopharyngeal carriage of vaccine strains^ref. Strains targeted by the vaccine were those that had been most commonly isolated in young children; they were also strains that had been most consistently exposed to the pressure of antibiotic overuse and, therefore, the most likely to be resistant to antibiotics. In 1998, 24% of invasive pneumococcal isolates in the USA were nonsusceptible to penicillin, and these five serotypes comprised 78% of such strains^ref. Modeling predicted that in the absence of a pneumococcal conjugate vaccine, the proportion of pneumococcal strains that were nonsusceptible to both penicillin and erythromycin could reach 41% by 2004^ref. Because of the association between serotype and resistance, the conjugate vaccine would be expected to reduce the incidence of disease caused by resistant strains, even though the vaccine is designed to induce antibodies against certain capsular types. Whether vaccine use would induce the emergence of serotypes that were typically not resistant as clinically significant causes of resistant infections was unknown. In addition, the possibility that use of a vaccine that targets only 7 of 90 pneumococcal serotypes would lead to an increase in disease by nonvaccine types (so-called replacement disease) was a concern. Rates of invasive disease caused by penicillin-nonsusceptible strains and strains not susceptible to multiple antibiotics peaked in 1999 and decreased by 2004, from 6.3 to 2.7 cases per 100,000 (a decline of 57%; 95% confidence interval, 55 to 58%) and from 4.1 to 1.7 cases per 100,000 (a decline of 59%; 95% confidence interval, 58 to 60%), respectively. Among children under 2 years of age, disease caused by penicillin-nonsusceptible strains decreased from 70.3 to 13.1 cases per 100,000 (a decline of 81%; 95% confidence interval, 80 to 82%). Among persons 65 years of age or older, disease caused by penicillin-nonsusceptible strains decreased from 16.4 to 8.4 cases per 100,000 (a decline of 49%). Rates of resistant disease caused by vaccine serotypes fell 87%. An increase was seen in disease caused by serotype 19A, a serotype not included in the vaccine (from 2.0 to 8.3 per 100,000 among children under < years of age). In addition to reductions in the rates among young children, reductions > 50% in the rates of invasive disease caused by resistant strains were documented among older children and adults, who would not have received the conjugate vaccine ("herd effect"). With all age groups considered together, the estimated number of cases caused by strains with reduced susceptibility to penicillin or multiple antibiotics fell by half after the introduction of the conjugate vaccine. Studies of adults have shown that exposure to children can increase the risk of colonization^ref and invasive disease^ref. Conjugate pneumococcal vaccines have been shown to reduce the risk of carriage and transmission of vaccine-type strains among vaccinees and their household members^ref. The change that we observed in the rate of resistant disease among adults was due to a reduction in disease caused by vaccine serotypes — a finding suggesting that the vaccine interrupts the transmission of resistant pneumococci from children to adults. No reduction in the incidence of resistant disease caused by serotypes included in the 23-valent polysaccharide vaccine but not in the 7-valent conjugate vaccine was found (data not shown); therefore, it appears that the decline in invasive antibiotic-resistant disease among adults was not linked to an increase in the use of the polysaccharide vaccine. Polysaccharide-vaccine coverage among adults 65 years of age or older increased from 54% in 1999 to 64% in 2003^{ref1, ref2}. An increase in resistant disease caused by nonvaccine types (so-called replacement disease) was found, but the magnitude of this effect was relatively small. Most resistant infections from serotypes not in the vaccine were caused by serotypes 6A and 19A. A drop in the rate of disease caused by serotype 6A and a concurrent increase in the rate of disease due to serotype 19A suggest, as previously reported, that the 6B vaccine component provides cross-protection^{ref1, ref2, ref3} against serotype 6A disease but that the 19F component does not protect against 19A disease^{ref1, ref2}. The increase in resistant disease caused by serotype 19A is a concern. Serotype 19A is often resistant and is a common cause of respiratory tract infections^{ref1, ref2}. It is difficult to predict whether the increase in resistant serotype 19A or other serotypes not covered by the vaccine will continue. Nevertheless, this replacement disease has the potential to reduce the overall benefit of the vaccine against resistant infections^ref. According to estimates of U.S. vaccine coverage, only 73% of children 19 to 35 months old in 2004 had received at least 3 of the recommended four doses of conjugate pneumococcal vaccine^ref.
Therapy : doxycycline ; by the summer of 2004, as many as 40.6% of the strains could be resistant to both penicillin (penicillin-resistant Streptococcus pneumoniae (PRSP)) and erythromycin (erythromycin-resistant Streptococcus pneumoniae (ERSP)) from just 8.6% in 1996; cefotaxime for meningitis
• Streptococcus pyogenes (in Lancefield group A => group A Streptococci (GAS) ; pyogenic)
Commensal in oral or nasal cavities of 5-30% individuals.
Endotoxins (apart from Ag M (> 80 serotypes), Ag R (1 serotype), Ag T, LTA and hyaluronic acid capsule) :
• C5a peptidase inhibits C5a
• p15^{streptolysin S (SLS) / hemolysin} => b-hemolytic : ribonucleoprotein, non immunogenic. It is found in 95% of S.pyogenes but also in Lancefield C, E, G, H and L groups. The 9-gene GAS locus (sagA-sagI) resembling a bacteriocin biosynthetic operon is necessary and sufficient for SLS production. sagA, sagB, sagC, sagD, sagE, sagF and sagG are each individually required for SLS production, and sagE may further serve an immunity function. Limited site-directed mutagenesis of specific amino acids in the SagA prepropeptide supports the designation of SLS as a bacteriocin-like toxin. No significant pleotrophic effects of sagA deletion were observed on M protein, capsule or cysteine protease production. In a murine model of NF, the SLS-negative M1T1 GAS mutant was markedly diminished in its ability to produce necrotic skin ulcers and spread to the systemic circulation. The SLS toxin impaired phagocytic clearance and promoted epithelial cell cytotoxicity, the latter phenotype being enhanced by the effects of M protein and streptolysin O. All genetic components of the sag operon are required for expression of functional SLS, an important virulence factor in the pathogenesis of invasive M1T1 GAS infection^ref.
Exotoxins :
• p60^{streptolysin O (SLO) / hemolysin} => b-hemolytic (=> group A b-hemolytic streptococci (GABHS)) : (O₂-sensitive; ~ PLO, see above) an immunogenic cholesterol-dependent cytolysin (CDC). It is produced by species in Lancefield groups A, C and G. Toxic even for myocardiocytes and WBCs. It allows Streptococcus pyogenes NAD-glycohydrolase (SPN) to enter host keratinocytes.
• p29^{erythrogenic toxin or streptococcal pyrogenic exotoxin (SPE)} : serotypes
• SPE-A (coded by a lysogenous phage)
• SPE-B (chromosome coded)
• SPE-C (coded by a lysogenous phage)
• SPE-F
• SPE-X / SMEZ
• SPE-K
It is produced by 90% of S.pyogenes strains but also in Lancefield C and G groups following phagic conversion. SPE-A, SPE-C and SPE-X / SMEZ are SAgs. SPE-A is also complexed with hyaluronic acid and induces a type IV hypersensitivity reaction at the second challenge, causing skin lesions typical of scarlet fever. Titre of neutralizing Abs after exposure to a first challenge (i.e. susceptibility to scarlet fever) can be evaluated by Dick test : after intracutaneous injection of SPE-A, type IV hypersensitivity (local erythema) occurs only in individuals with low titres of neutralizing Ig, susceptible to scarlet fever at the next challenge. Diagnosis of scarlet fever is instead acquired by Schultz-Charlton reaction : after intracutaneous injection of anti-SPE-A antitoxin or scarlet fever convalescent serum is injected into an area of the skin showing a bright red rash, a blanching of the skin at the site of the injection occurs. Serum from scarlet fever patients does not produce this reaction.
• streptokinase converts plasminogen to plasmin [also used in therapy to clear blocked arteries in patients who have heart attacks]
• hyaluronidase / spreading factor destroys capsule of Lancefield C and G serotypes.
• Leu-aminopeptidase destroys Ag M allowing binary fission
• fibronectin-binding protein (FnBP)
• DPNase / NAD glycohydrolase
• DNAases / streptodornases A-D
• IgA₁ protease
• phospholipase A₂
• ScpC serine peptidase degrades IL-8, impairing neutrophil chemotaxis^ref : infected subcutaneous tissues from an necrotizing fasciitis patient and mice challenged with the same GAS strain possessed high bacterial loads but a striking paucity of infiltrating neutrophils. SilCR pheromone downregulates scpC transcription via the two-component system-SilA/B. In addition in vitro, ScpC degrades the CXC chemokines: IL-8 (human), KC, and MIP-2 (both murine). Furthermore, using a murine model of human necrotizing fasciitis, ScpC, but not the C5a peptidase ScpA, is an essential virulence factor. An ScpC-deficient mutant is innocuous for untreated mice but lethal for PMN-depleted mice. ScpC degrades KC and MIP-2 locally in the infected skin tissues, inhibiting PMN recruitment. In conclusion, ScpC represents a novel GAS virulence factor functioning to directly inactivate a key element of the host innate immune response^ref
=> clinical manifestations
• skin
• type 4 and 22 : 2-5 days incubation => (streptococcal) scarlet fever / scarlatina : pharyngitis and tonsillitis, with an erythematous rash produced by an erythrogenic toxin elaborated by the streptococci, progressing from the trunk and neck to the arms, legs, forehead, and face, with flushed face and circumoral pallor, white strawberry mucosa ===detersion==> red (hyperhemic) strawberry tongue (enanthema), Rumpel-Leede phenomenon (the appearance of minute subcutaneous hemorrhages below the area at which a tourniquet is applied not too tightly for 10' upon the upper arm) and lines of skin hyperpigmentation (Pastia's sign) in the body creases; the rash disappears and is followed by desquamation of the skin. Similar clinical manifestations, but usually with involvement of the pharynx and tonsils, may follow infection of wounds, burns, or the skin with group A b-hemolytic streptococci, or with any strain of streptococci that elaborates an erythrogenic toxin. Complications : otitis media, tonsillar abscess, suppurative lymphadenitis, mastoiditis, sinusitis, cerebral abscess, tubulointerstitial nephritis. Now usually milder than in the past when septic complications were common
• Fox' streptococcal impetigo (contagiosa) / pyoderma
• erysipela after 6-7 days incubation
• cellulitis
• myositis and necrotizing fasciitis (hence named "skin-eating streptococci" or "flesh eating Bacteria") from M1 types (alone or in association with Staphylococcus aureus). Several reports suggest that the incidence of invasive GAS infections, including streptococcal toxic shock syndrome and necrotizing fasciitis, is increasing. During 1992 and 1993 a prospective, population-based surveillance of invasive group A streptococcal disease was conducted in Ontario, Canada, where there is an annual incidence of 1.5 cases per 100 000 population. The rates were highest in young children and the elderly. 56% of the patients had underlying chronic illness. Risk factors for disease included infection with the HIV, cancer, diabetes, alcohol abuse, and chickenpox. The most common clinical presentations were soft-tissue infection (48%), bacteremia with no septic focus (14%), and pneumonia (11%). Necrotizing fasciitis occurred in 6% of patients, and toxic shock in 13%. The mortality rate was 15% overall, but it was 29% among those over 64 years of age (P<0.001) and 81% among those with toxic shock (P<0.001). 14% of the cases were nosocomial, and 4% occurred in nursing home residents, often in association with disease outbreaks. Invasive disease occurred in 2 household contacts of patients with infection, for an estimated risk of 3.2 per 1000 household contacts (95% confidence interval, 0.39 to 12 per 1000). The elderly and those with underlying medical conditions are at greatest risk for invasive GAS disease, toxic shock, and necrotizing fasciitis. Invasive steptococcal infection is associated with a substantial risk of transmission in households and health care institutions. Most cases occur outside of the hospital setting. 2 patients were described with nosocomial streptococcal toxic shock syndrome (StrepTSS). In patient 1, the syndrome was associated with the development of necrotizing fasciitis following inguinal hernia repair. Patient 2 suffered from StrepTSS shortly after receiving a tetanus vaccine in her left deltoid. Epidemiologic investigations of these cases, which were noted within 48 hours of each other, showed that the same surgeon performed the vaccination on patient 2 after assisting a colleague during the hernia repair procedure on patient 1. He was found to be a nasal carrier of GAS. All GAS isolates from the patients and the surgeon were indistinguishable by PFGE. PCR analysis demonstrated the presence of streptococcal pyogenic exotoxins A and F. All strains !were of the T-1 serotype and possessed the gene for M-protein 1. This report demonstrates that a virulent strain of GAS may be spread by asymptomatically colonized medical personnel via the air route^ref. An outbreak of infection due to Streptococcus pyogenes occurred in a geriatric rehabilitation unit between Feb and Sep 1981, affecting 10 patients and 2 staff. The severity of the illness ranged from asymptomatic throat carriage, through skin and soft-tissue sepsis, to fulminant septicemia and necrotizing fasciitis: 2 patients died of their infection. Streptococcus pyogenes infection may present in a variety of ways, and may be dangerous. Recently developed serological tests have been found useful in the surveillance of an outbreak. Although Streptococcus pyogenes is sensitive to penicillin and other antibiotics, good ward hygiene is still essential for controlling such an outbreak in an institution^ref
• Fournier's gangrene on male genitals
Strep-EURO : there had been little surveillance on GAS infections in countries like Italy, Cyprus and Romania. Incidence is more or less the same everywhere: between 3.8 and 4 cases per 100,000 population. Some suspect that the 25 countries of the newly expanded European Union harbour up to 20,000 cases each year. Evidence from countries where surveillance has always been most efficient, such as Britain, Scandinavia and the Czech Republic, suggests that the incidence rates are increasing : in Britain alone, the number of reported cases has doubled in the past 5 years. Diversity of the M protein implies that the bacteria are evolving rapidly, making developing a vaccine difficult.
• pharyngotonsillitis / streptococcal angina / strept throat (15% all pharyngitis) after 2-4 days incubation : spots are smaller than in diphteria. Leukocytosis with relative neutrophilia. Self-limiting within 5-7 days.
• otitis
• sinusitis
• mastoiditis
• alveolar pneumonia
• bronchopneumonia
• pleurisy
• epiglottitis
• puerperal fever
• urinary tract infections (UTI)
• septic arthritis
• acute or subacute endocarditis
• toxic shock-like syndrome (TSLS) / streptococcal toxic shock syndrome (TSS) from serotype M1, M2, M3, M12 or M28 : 80% of strains produce SPE-A. Maculopapular exanthema and DIC ; rarely necrotizing fasciitis, myositis and gangrene.
• post-streptococcal nonsuppurative sequels related to HLA-DR2 and HLA-DR4 : such people must be maintained under antibacterial prophylaxis because further challenges would make the disease worse.
• acute poststreptococcal glomerulonephritis (PSGN) (APSGN) by nephritogenous strains
• up to 10%, 1-2 weeks after pharyngotonsillitis from serotype M12 or M25
• 2-3 weeks after a skin infection such as impetigo (most common) from serotype M1, M2, M3, M4, M25, M49, M55, M57, M59, M60 or M61)
At least 2 antigens isolated from nephritogenic streptococci, zymogen
(a precursor of exotoxin B) and glyceraldehyde phosphate dehydrogenase (GAPDH), have been identified and are believed to be capable of initiating the immunologic response. These fractions have a particular affinity for the glomerulus and have been demonstrated to induce an antibody response (type II hypersensitivity). If also type III hypersensitivity occurs, it may cause chronic glomerulonephritis.
• acute rheumatic fever almost always related to streptococcal pharyngotonsillitis
• post-streptococcal reactive arthritis (PSRA)
• neurological sequelae :
• Sydenham's chorea
• paediatric autoimmune neuropsychiatric disorders associated with streptococcal infection (PANDAS)
• autoimmune Gilles de la Tourette's syndrome
Acquired immunity to Streptococcus pneumoniae has long been assumed to depend on the presence of anticapsular antibodies. However, colonization with live pneumococci of serotypes 6B, 7F, or 14 protected mice against recolonization by any of the serotypes and protection from acquisition of a heterologous or homologous strain did not depend on anticapsular antibody. Further, intranasal immunization by live pneumococcal colonization or by a killed, nonencapsulated whole-cell vaccine protected antibody-deficient mice against colonization, suggesting independence of antibodies to any pneumococcal antigens. Protection by intranasal immunization with whole-cell vaccine was completely abrogated in T cell-deficient mice, and in mice that were congenitally deficient in CD4⁺ T cells or depleted of these cells at the time of challenge. In contrast, mice congenitally deficient in, or depleted of, CD8⁺ T cells were fully protected. Protection in this model was observed beyond 2 months after immunization, arguing against innate or nonspecific immune mechanisms. Thus, immunity to pneumococcal colonization can be induced in the absence of antibody, independent of the capsular type, and this protection requires the presence of CD4⁺ T cells at the time of challenge^ref.
Web resources :
• UK Health Protection Agency: Group A Streptococcal Infections
• Streptococcus fact sheet at NIAID
• Streptococcus ratti (in no Lancefield group; "viridans" ; oral)
g-hemolytic.
=> in plaque
=> acute and subacute endocarditis
• Streptococcus salivarius (in Lancefield group K or in no group; "viridans" ; oral)
a- or g-hemolytic
=> subacute endocarditis, acute meningitis, sinusitis, caries
• Streptococcus sanguinis (in Lancefield H group or in no group; "viridans" ; oral)
a- or b-hemolytic. Toxins : IgA₁ protease.
=> the first agent of caries, gingivitis
=> Behçet-Adamantiades disease
=> acute meningitis
=> subacute endocarditis
• Streptococcus sobrinus (in no Lancefield group; "viridans" ; oral)
g-hemolytic
=> acute and subacute endocarditis
=> plaque
• Streptococcus suis (in Lancefield groups D, R, S and T; pyogenic)
a- or b-hemolytic
Epidemiology : endemic in swine in most pig-rearing countries in the world. Human infections are rare, with < 150 sporadic cases reported in the world literature according to the UK Health Protection Agency, mainly in countries and regions breeding pigs and eating pork in Northern Europe and Southern Asia. The 1st-ever recorded case was in Denmark in 1968. Though endemic in swine, human infections are rare. And where they have occurred, mortality rates have been < 10%. In past literature, there have been 1 or 2 cases when people died within 36 hours, but those were exceptions rather than the rule.
• Germany : a carrier prevalence study was reported to assess the amount of culture-positive throats among workers in swine slaughterhouses and processing plants. 7 of 132 workers (5.3%) were found to have positive throats cultures with no colonization in control individuals^ref.
• Thailand usually had < 20 known cases a year.
• In 1998, 25 cases of Streptococcus suis type 2 infection were reported in Jiangsu, China -- characterized by toxic shock-like illness or meningitis^ref. Zhonghua Yu Fang Yi Xue Za Zhi 2000; 34:150-2). Identical strains were identified in local swine^ref. S. suis (type not specified) may be the 2nd most common cause of adult streptococcal meningitis in Thailand. Single hospitals reviewed 8 (1993 to 1999)^ref, 10 and 12 cases (1997 to 2002). Associated skin and soft tissue infections were common^ref. 25 cases were treated in 2 hospitals in Hong Kong during 1984 to 1993^ref. 30 cases of S. suis meningitis were reported in the Netherlands during 1968 to 1984^ref. Additional cases have been reported in Greece^ref, Spain^ref, Japan (S. suis type 2)^ref, Croatia (S. suis type 1) (Kopi J, Paradzik MT, Pandak N: [Streptococcus suis infection, a zoonosis we should have in mind--2 case reports]. Lijec Vjesn 2003; 125:134-7),  Taiwan^ref, Singapore^ref, the United Kingdom^ref, Austria^ref, Belgium^ref, Canada^ref, Italy^ref, New Zealand^ref, Sweden^ref, and Latin America^ref. Cases in Germany^ref, Netherlands^ref and France^ref have been acquired from wild boar. Occupational seropositivity has been documented in New Zealand^ref and the Netherlands^ref. S. suis infection is found in all pig-raising countries, worldwide. Pigs develop meningitis, arthritis, pneumonia, septicemia, endocarditis, encephalitis, polyserositis, and abscesses. The disease is not considered to be highly infectious, and most outbreaks are limited to the affected farms. Pig infection is not notifiable on the national or international level. Affected farms may suffer economic loss. Vaccination and antibiotic therapy in pigs have been used with varying success. The rarity of human disease to date suggests that the outbreak in China is due to a new strain of the bacterium. Clinical features of S. suis type 2 infection in these case reports have included high fever, malaise, nausea and vomiting -- followed by meningitis, subcutaneous hemorrhage, multi-organ failure (hepatic, renal, pulmonary, cardiac) and coma in severe cases.  Deafness is common.  Individual reports of peritonitis, endocarditis, rhabdomyolysis, spondylodiscitis, sacroilitis, monoarthritis, endophthalmitis and cranial nerve palsy are documented. Virtually all patients have been farmers and butchers, of whom 80% were men. Most had been involved in butchering sick pigs or selling the pork. > 40% of the patients were in the age group 50 to 60 years, and none were children.
• China : the last outbreak of Streptococcus suis in China was in 1998 (Jiangsu province), and involved 22 people causing 14 deaths. But in 2005, ...
•  in China's western Sichuan province between 24 Jun and 30 Jul 2005 204 farmers (44 laboratory-confirmed, 131 diagnosed at a clinic, and 39 suspected) (80% males, > 40% aged between 50 and 60 years) from 108 villages of 40 different townships in 11 cities/prefectures (first in Ziyang (414 pigs affected and 2899 destroyed since 25 Jun) and its neighboring city of Neijiang (193 pigs affected and 3159 destroyed since 15 Jul), then Jianyang (9 pigs affected and 583 destroyed since 17 Jul), Zigong, Suining, Deyang (5 pigs affected since 29 Jul : 66 destroyed), Luzhou (2 pigs affected since 12 Jul : 7 destroyed), Mianyang (1 pig destroyed on 24 Jul), Nanchong (2 pigs affected and destroyed since 29 Jul), Yibin, Leshan, and the provincial capital Chengdu (15 pigs affected since 2 Aug : 19 destroyed)), were admitted to hospital with high fever, fatigue, nausea, and vomiting and became comatose later with bruises under the skin. The area has a population of 7 million, in a 100-km (62-mile) belt stretching from the cities of Ziyang to Neijiang. From 24 Jun through 21 Jul 2005, the authorities reported 20 cases of illness of unknown cause admitted to 3 hospitals in that city. WHO was officially informed of the outbreak on 22 Jul 2005, at which time, 20 cases and 9 deaths had been reported. By 22 Aug 2005, 40 patients had died, 58 had been discharged from hospital, 117 are in hospita, with 12 still in a critical condition. They all butchered sick pigs or sheep before coming down with the strange disease, but the detected cases are not interrelated and no infection has been found in any close contact of the patients. There have been 36 counties (districts), 132 towns (streets), and 202 villages (community offices) infected in areas. > 450 pigs infected with Streptococcus suis were burned in the area. 50 checkpoints are in place to prevent swine from being moved around. No new cases have been reported since 5 Aug 2005. The data provided by China depict an outbreak that peaked from the 2nd through the 4th week of Jul 2005, and dwindled rapidly thereafter

Transfer to humans is rare -- which makes the Sichuan mortality rate alarming. In addition, this province is China's largest pig center, producing > 50 million swine annually. S.suis type 2 (B) was identified in 5 patients on 26 Jul. One differential diagnosis was CCHF, first reported in China in 1964, and is known locally as Xinjiang hemorrhagic fever. Cases are reported from the south west region. 260 cases (54 fatal) were reported in Xinjiang (southern desert region) during 1964 to 1995. 10 to 20% of sheep, goats, and cattle in Sichuan are seropositive. This latter information raises the index of suspicion that CCHF is a likely candidate. While CCHF is usually thought of as a tickborne disease, it can also be transmitted through contact with infected bodily fluids from people (in nosocomial outbreaks) and animals. Another of the hemorrhagic fevers seen in the region is hemorrhagic renal syndrome associated with hantavirus infection. The description above makes that diagnosis less likely, although one must recognize that newswire descriptions may not necessarily be representative of the actual clinical picture. Some of the features of these illnesses are not characteristic of avian influenza; in particular, the unrelatedness of the victims, the development of hemorrhagic symptoms and shock, and the association with slaughter of pigs and sheep. The one caution towards that being the diagnosis is the lack of mention of that in the press articles, as one would expect that specimens have been sent for testing of previously known hemorrhagic fever organisms. Virtually all infection diseases begin with "flu-like" symptoms and this cannot be taken as indicative of avian influenza virus infection. Furthermore the role of pigs as a mixing vessel allowing interactions between human and avian influenza viruses is an attractive hypothesis, but one that has still to be substantiated. As of April, 23% of 450 Chinese pigs tested were carrying a less virulent avian flu strain : H₉N₂. If it is the case that the porcine streptococcus is the cause of these illnesses, perhaps the organism has acquired one or more virulence factors (from, for instance, the Group A streptococcus or Staphylococcus aureus) to increase its transmissibility and virulence in humans. It would be interesting to assess any medical co-morbidities in the infected cohort. The authorities have dismissed speculation that the deaths were caused by bird flu, a virus that has killed over 50 people in Asia since late 2003. Nevertheless, medical experts outside mainland China said the unusually high mortality rate of 20% and reports that many of the 27 victims died within a day of showing symptoms were inconsistent with what is known so far about human Streptococcus suis infection.
The deaths in China are very unusual. Many patients in Sichuan were bleeding under the skin, a symptom that has been cited in only 2 or 3 cases in medical literature on the bacteria. According to experts with the team sent by the Ministry of Agriculture to the area of the outbreak, the vaccines for Streptococcus suis type II, a bacterium carried by pigs, will soon be batch-produced in south China's Guangdong Province and are expected to reach Sichuan Province in about 1 week after being inspected by the Ministry of Agriculture. Yongshun biomedical company in Guangdong will be the first to mass-produce the vaccines. The Chinese government responded on Sun 31 Aug 2005 by airlifting the 1st batch of a vaccine for the infection -- enough to treat 360 000 pigs -- from the southern city of Guangzhou to the affected towns. The vaccine's manufacturers will be producing enough vaccine to treat 10 million pigs in the coming days, but vaccines take 3 weeks to produce immunity in the pigs^ref. It is plausible that the organism (and possibly toxin) load to which the patients were exposed was higher if the swine had been dug up after being buried, with the possibility of further S. suis replication and toxin production while buried. This could explain the different disease observations, which have caused observers to be somewhat unsure if the S. suis is indeed the etiology. From the perspective of a researcher in human streptococcal infection, this emergence of Streptococcus suis infection in humans resembles the outbreaks of group B streptococcal infection that emerged in human neonates during the 1970s and then in debilitated adults in the 1980s. Both instances remain unexplained. Indeed, S. suisresembles group B streptococcus (S. agalactiae) in many respects. Both are encapsulated hemolytic streptococci that have propensity to cause bacteremia and meningitis in newborns after exposure to the organism in vaginal secretions. Most newborns remain asymptomatically colonized but in a minority progress serious infection including sepsis, meningitis, pneumonia and localized infections. Both organisms remain susceptible to beta-lactam antibiotics and, in humans, control of the infection has been largely achieved by use of antibiotic prophylaxis of maternal carriers of group B strep. during childbirth. Diagnosis of S. suis infection in both pigs and humans is based upon culture of the organism from normally sterile sites and should not be difficult. Clinical details from the current outbreak (both from the pigs and the humans) are thus far lacking and it is therefore difficult to assess whether some co-infection (or other co-morbidity) may be accounting for this unprecedented cluster of human disease.
Inspectors swooped down on the unregistered abattoir in the city of Gongzhuling in Jilin province in the 1st week August 2005, and found it had been supplying meat to a sausage factory in the provincial capital, Changchun, which had also been shut down. Inspectors found 6 to 8 tons of pork in the underground slaughterhouse, and our tests showed at least one ton came from pigs who had died of illness^ref. Several aspects of the current outbreak still remain unanswered. What are the morbidity and mortality rates in pigs? Is there any differential age susceptibility? What are the pathological and histopathological changes? Are there any performed/envisaged virological investigations besides excluding influenza and Nipah? Have there been any experimental infection trials in animals? All these unanswered questions cloud the perception of transparency in disease reporting.  At this point, might it not be useful to have an international presence on outbreak swine farms so that some of these questions can be answered sooner rather than later? Applying "stamping out" is an unusually severe measure when related to a bacterium which -- at least, according to existing knowledge -- is rather endemic in many countries in piggeries. It would be helpful to note how screening is to be applied, and what criteria will be used for farms to be "stamped out."
A circular has been issued by the Sichuan Provincial Propaganda Department...which forbids local press from sending reporters to the infected areas or hospitals. No amendments of Xinhua reports are allowed, including the headline: Xinhua's is currently the only version of events available to both Chinese and overseas reporters alike. Please note that S. suis does not spread from person-to-person. The symptoms of the disease have led some experts to speculate that Ebola virus could be the cause : the Chinese Communist Party (CCP) has prohibited news coverage, and has forbidden the use of the words ‘Ebola virus’ in reports, instead requiring the use of alternate wording. Doctor Wang (?) said that the virus sample specimen was examined as soon as it was received and a type of Ebola virus was extracted from the specimen. When asked why “low dissemination” was added to the name of the Ebola virus in China, Doctor Wang explained that it was done to reduce public concern, and also because a variation of the Ebola virus had actually occurred in China. They started the examination quickly after receiving the sample, they extracted SZ77++A3231 virus from the sample, which is a kind of Ebola virus. The previous classification of Ebola in the country used the EBO – location (where it was discovered) – model; later on, for unknown reasons, the news of classification leaked out. Therefore the classification method changed, they abandoned EBO, increasing the infection extent, infection speed, etc. The disease that occurred at the beginning of June is SZ77++A3231 virus, sometimes we do not specify the source region but directly use ++A3231, so that people will not think of the Ebola virus.” The CCP formed 3 departments specifically to conduct these examinations, so obviously Sichuan is not the only area to have experienced the illness caused by the Ebola virus. Many Mainland Chinese recognize that the current mystery disease in Sichuan is the EB-SZ77 type Ebola virus. The earliest occurrence of this Ebola virus disease can be traced back to Shenzhen city in Guangdong Province. On March 25, 2005, The Epoch Times published an article on the first appearance of the Ebola virus in Shenzhen during February. The virus had already caused several deaths and cases of ‘missing people’ [Editor’s note: rather than accurately reporting the cause of death, the authorities simply claim that victims are ‘missing’]. This article mentioned that medical personnel who had been working in hospitals for years said that they had never seen an illness like it. The bodies of those who died of the illness appeared to be dissolved, much like the Ebola virus in Africa. The main spread of the virus was through blood, causing doctors to die after contact with infected blood. On March 26, Shenzhen Customs and related hospitals and government departments held a confidential meeting to pass an order from higher authorities to strengthen the hygiene-related work. An insider also disclosed that at dawn on March 26, another suspected Ebola virus death case occurred in Nanao Town, Shenzhen. There are indications that the Ebola virus was already spreading in Mainland China. The CCP blocked this information, telling the outside world that the deaths were caused by the advanced stages of AIDS. On March 29, China’s Ministry of Health announced that, “Presently, this virus has not been found in the mainland.” The source of the information regarding the death case in Nanao Town couldn’t be contacted further, and the company and hospitals denied the existence of the Nanao Town case or any existence of a patient record. All websites in mainland China have now started using official language to report this case. Although the Ministry of Health said that Ebola virus has not been found on the mainland, according to inside information on July 14, frequent confidential meetings were held by the Guangdong Province government, Guangzhou military region, Shenzhen municipal government and Shenzhen Customs during late June and early July, discussing the slow spread of the Ebola virus in Guangdong Province. People were strictly prohibited from spreading information about the Ebola virus and bird flu that appeared in Guangdong and media reports were also forbidden. Why don’t CCP officials allow the WHO to investigate and provide help? Veterinary pathology scholar Liu Zhenyi said that the CCP has always flaunted its “greatness, honor, and correctness”, and is most concerned about saving face. This appears to be a higher priority than people’s lives. Guan Yi, scholar and bird flu expert at Hong Kong University disclosed in Nature magazine that bird flu had infected southern China. Chinese officials subsequently shut down his laboratory, slandered him and said that his laboratory was “illegal.” Doctor Wang, quoted earlier, who examined this strange Sichuan disease, also believes that the CCP would not allow the involvement of the WHO because it would be extremely disadvantageous for the international image of the CCP. It wouldn’t be just a medical question, but could lead to exposure on issues such as the local medical environment, survival conditions, environmental pollution and political corruption^ref.
A total of 647 pigs have died as a result of Streptococcus suis infection in Sichuan province. The deaths occurred in 149 villages of 88 municipalities in 21 counties of the following 8 regions: Chengdu, Deyang, Luzhou, Mianyang, Nanchong, Neijiang, Zigong, Ziyang. The epizootic began in late June 2005, reached a peak around 20 Jul, and then declined sharply. No new cases have occurred since 6 August 2005. This epizootic was caused by Streptococcus suis type 2. The LD₅₀ (dose lethal to 50% of the animals) of the bacterial strain isolated in Sichuan was determined using the new laboratory animal model, zebra fish (pure breeding line), and the virulence genes of the bacterium were also tested. The results of the tests showed that the virulence of the isolate is not significantly different from that of isolates obtained from other places in the past, and no evidence of genetic variation has been found. The main characteristics of the epizootic were as follows:
• 1.1. Spatial distribution : the outbreak areas were mainly centralised in the historical endemic areas of S. suis infection in Ziyang, Neijiang, and other places. The outbreaks occurred sporadically, and did not occur densely over a large region. Infected points were far apart and had no direct epidemiological relationship. There is therefore little likelihood of transmission having occurred between them.
• 1.2. Temporal distribution : the disease was first recognised on 24 Jun 2005, and mainly occurred in July. During this period the weather was hot, humid and rainy. The season when the epizootic occurred was the same as in the past. This shows that the occurrence of S. suis infection in pigs is specific to a particular season.
• 1.3. Herd distribution : all outbreaks occurred in remote rural areas with poor economic conditions, and only in small backyard farms, where animal health conditions are poor, and pigpens are dimly lit, damp and inadequately ventilated. No outbreaks were reported in intensive farms and large-scale premises with better sanitary conditions. The morbidity observed in pigs within each affected group was low.
• 2. Control measures : the recent S. suis epizootic was effectively controlled by applying all of the following measures:
• - preventive treatment of pigs in the same herd as infected and dead animals using highly sensitive antimicrobials, and improvement of resistance to the disease by adding preventive medicine to animal feed;
• - regular disinfection of swine holdings in infected places and zones, livestock markets and designated slaughterhouses, aimed at improving sanitary conditions;
• - destruction of cadavers of dead pigs by deep burial;
• - stepping up of inspection and quarantine, and movement control of animals and animal products;
• - development and production of vaccine, and emergency vaccination of pigs in high-risk areas aimed at improving their level of immunity.
• 3. Vaccination : pigs have been vaccinated with Streptococcus suis type 2 vaccine.
In the regions of Ziyang, Neijiang and Zigong, where highest morbidity was found, vaccination was performed in all counties; in the other 5 regions, vaccination was performed only in the infected counties and in the zones at risk adjacent to infected zones. No vaccination was performed in pigs for slaughter within 20 days, one month old piglets, pregnant sows, or weak pigs. To date, about 14 million pigs have been vaccinated, and the vaccination cover is up to 90%. Testing of vaccinated pigs with indirect ELISA showed that 70% of pigs had a significant serum antibody titre 14 days after vaccination. The application of vaccine in the field has demonstrated that Streptococcus suis type 2 inactivated vaccine is effective, safe and has few side effects. While this report indicates all swine cases were confined to 647 cases in Sichuan province, there appear to have been human cases in Hong Kong. In fact, the disease is recognized, rarely in ig-producing areas worldwide^ref
• in Jiangsu province (in eastern China and not at all geographically close to Sichuan) : the 1st man (a butcher) to fall ill was admitted to the hospital of Suzhou with a high fever on 28 Jul 2005 and died on 2 Aug 2005. The 2nd case (a meat seller) was hospitalized on 2 Aug 2005 and died a few days later. In the summer of 1998 (Jul and Aug), an epidemic of deadly S. suis infection struck people in Jiangsu, resulting in 14 deaths and > 80 000 dead pigs. The epidemiological investigation and clinical description (including diagnosis, microbiological confirmation and treatment) of the epidemic were well-reported in Chinese medical journals. The epidemiologic link of the victims to dead or diseased pigs is similar to that in the recent outbreak in Sichuan, and cases were sporadic in occurrence and scattered in geographic distribution. No point-source outbreak or human-to-human transmission was documented. In one of the reports, 25 persons were affected and 14 died (overall mortality rate 56%). 13 out of 16 persons who developed streptococcal toxic shock syndrome (STSS) died (crude mortality rate 81%). Of the 9 persons who developed streptococcal meningitis, only 1 died (crude mortality rate 11%). The clinical picture is similar to that reported recently in Sichuan, except that the Sichuan cases are now classified into 4 categories, (1) ordinary type (milder febrile illness with no shock or meningitis), (2) STSS (with high mortality), (3) meningitis (with high incidence of sensorineural deafness), and (4) mixed type (with both STSS and meningitis, and with high mortality). The culprit was confirmed to be S. suis serotype 2, the same as that which caused the recent Sichuan outbreak. The epidemiologic links are the same as those

identified in Sichuan. Thus, the disease occurring in epidemic proportion is not new in China, but may be new in the English or world medical literature. One thing that is not clear up to this moment is the extent of swine deaths in Sichuan. In an official news report dated 5 Aug 2005, only 644 pigs were reported to have been killed by the deadly bacterium in Sichuan as of 4 Aug 2005. Readers may be interested to look up some of the Chinese publications (with English abstracts) on the Jiangsu outbreak:
• Zhang X, Ding J, Qin H: Clinical analysis of 22 cases of the disease contracted both by man and pigs with swine streptococcus infections. Journal of Tropical Medicine 2002; 2:361-3, 372.
• Ying H, Zhu F, Shi Z, et al: Isolation and identification of streptococcus suis. Jiangsu Preventive Medicine 2001; 12:9-10.
• Tang J, Zhu J, Guo H, et al: Epidemiological and pathogenic study on the outbreak of toxic shock syndrome and meningocephalitis caused by swine streptococcus. Acta Academiae Medicinae Militaris Tertiae 2001; 23:1292-5.
• Yang H, Zhu F, Shi Z, et al: Analysis on pathogenic feature of syndrome infected by S. suis from human and swine. Chinese Journal of Zoonoses 2001; 17:92-3, 120.
• You Y, Shen J: The epidemiological study on human streptococcal infections syndrome caused by infected pigs. Chinese Primary Health Care 2001; 15:20-1.
• Zhu J, Tang J, Zhang Y, et al: Biological characters and identification of the pathogen contributing to the outbreaking epidemic toxic shock like syndrome. Chin J Infect Dis 2001; 19:84-6.
• Zhu F, Yang H, Hu X, et al: Homogeneity study on the Streptococcus suis isolated from human and swine. Chin J Epidemiol 2000;21(6):427-9.
• Zhu J, Tang J, Guo H, et al. Epidemiologic and pathogenic study on an outbreak of acute streptococcal disease in pigs. J Prev Med Chin PLA 2000; 18:257-60.
• Hu X, Zhu F, Wang H, et al Studies on human streptococcal infectious syndrome caused by infected pigs. Chin J Prev Med 2000; 34:150-2.
• Wang H, Hu X, Zhu F, et al: A epidemiological study on the human streptococcal infective syndrome among men and pigs. Modern Preventive Medicine 2000; 27:312-4.
• in Guangdong province, which borders Hong Kong and is hundreds of miles southeast of Sichuan, 4 cases and 1 death occurred, including :
• a 43-year-old slaughterhouse worker in Chaozhou was affected on Jul 31 through a wound on his hand as he slaughtered a sick pig: he recovered and was discharged. Investigators suggest the infected pigs came from 300 small farms with poor sanitary conditions.
• a man who has slaughtered pigs from Yangjiang town died
• Chao'an County
• Nanxiong city
• Shenzhen city
No pigs were reported sickened by S. suis, the bacteria blamed for the human cases
• in Hong Kong : in Kay's paper published in 1995^ref, the authors mention a "small outbreak" of 38 cases between 1981 and 1983.  These cases, indeed most cases including the cases occurring now, tend to present in the summer months. The 1981-83 cases appear to have occurred following the importation of "10 000 live pigs per day from neighboring China in hot and crowded conditions."  Small clusters, therefore, appear to have occurred before but not to this degree and generally linked to meningitis due to this organism (Chau PY, Huang CY, Kay R: Streptococcus suis meningitis: an important underdiagnosed disease in Hong Kong. Med J Aust 1983; 1:414-17). From 1983 to 1994, there were 25 cases of human Streptococcus suis infections in Hong Kong. In 1983, it was shown that the virus was the leading cause of meningitis in Hong Kong^ref : in 2005 there were 12 cases including 2 deaths (4 since the outbreak in China was 1st reported in June 2005; related to the Sichuan outbreak ? a 26-year-old interior decorator who has not traveled to the mainland recently and has had no contact with pigs was admitted to hospital 5 Jul 2005 and discharged a week later; a 78-year-old woman resident of Mong Kok who had not left Hong Kong came down with the infection on 3 Aug 2005 and was admitted to Kwong Wah Hospital in Mong Kok with a fever and pain in her right hip on 8 Aug 2005; a 44-year-old butcher working at Wellcome Supermarket admitted to the hospital on Tue 16 Aug 2005 with fever and pain in his finger and left thigh and is now in stable condition; a 79-year-old woman resident at Kowloon City developed fever, right knee pain, redness and swelling on 16 Aug 2005, was admitted to Queen Elizabeth Hospital and confirmed on Mon, 22 Aug 2005; A 62-year-old woman; a 43-year-old, who had no recent travel history, was admitted to the hospital and immediately died on 13 Oct 2005). Pork contaminated with this organism was found worldwide and as much as 50% of pork imported from Holland, New Zealand and Australia bore the bacterium. So far in 2005, Hong Kong has imported > 18,000 tons of frozen pork from Sichuan, of which 5000 tons came from the 2 most affected cities -- Ziyang and Neijiang. On Mon 1 Aug 2005, the Hong Kong authorities said that, to better monitor the situation, they would classify Streptococcus suis as a statutorily notifiable disease, which would require all local doctors to report cases (in humans) to the government. They also stepped up inspections and quarantine procedures on live pigs and frozen pork imported from mainland provinces and said they would crack down on illegal pork imports^ref. Pork from Sichuan and Henan provinces, and also Shenzhen, which supplies > 60% of the frozen and chilled pork to Hong Kong, will re-enter Hong Kong on Aug 24 for the 1st time since imports were banned late in Jul 2005. Genetic characterization of the first 9 of the 11 cases known in Hong Kong have shown different bacterial strains, suggesting the previous cases were sporadic and that there was no link between them. It would not be surprising if multiple strains of S. suis are behind the outbreak in Sichuan. If the digging up of dead, infected pigs (with high titers of different strains of type 2 S. suis in them) for meat is behind the outbreak rather than evolution of a more virulent, toxin-producing strain, multiple Sichuan strains should be found in pigs and man. Streptococcus suis was isolated from 6.1% of raw pork meat from 3 of the 6 wet markets in 6 districts in Hong Kong. S. suis was particularly isolated in sites from the tongue, tonsil, bone, and tail, but not from lean meat/minced pork or internal organs. Isolates were confirmed by PCR using S. suis-specific primers, did not belong to serotype 2 using serotype 2-specific antiserum, and were clustered closely with other known serotypes by phylogenetic analysis. 10 strains from patients admitted to Hong Kong hospitals with sepsis or meningitis in the past 10 years all belonged to type 2, with closely related PFGE types that were distinct from the S. suis strains isolated from pork in this study^ref. 13 cases (2 fatal) were reported in 2005, 8 cases in 2006 and 3 cases in 2007 (54-year-old man^ref)
Serious infections with Streptococcus suis have been recorded in the past in China : of the 22 cases, 5 cases which were ordinary type were cured; 10 cases were meningitis 2 type, 8 of which were cured and 2 of which improved; an 7 cases were toxicosis shock syndrome (TTS) 2 type , none of which was  able to avoid death. The total mortality was 31.8%. At the time the disease was widely epidemic and worsened (Zhang X , Ding J, & Qin H: Clinical analysis of 22 cases of the disease contracted both by man and pigs with swine streptococcus Infections. (Chinese) Journal of Tropical Medicine, 2, 2002; 2:361-63). The abstract implies that an outbreak of human (and swine) infections occurred but the exact details of the length of time that the cases were found is not given.
• USA : a 59-years old man reported in 2006 (occupational exposure)^ref
Kay and colleagues^ref present a cogent discussion on the classification of S. suis. Based on analysis of porcine streptococcal strains in the 1950s and 1960s that were ungroupable using the Lancefield typing sera, serogroups R, S and T were designated for these porcine strains.  The S capsular strain became referred to as S. suis type 1 and the R capsular strain as type 2. Although almost 30 capsular types have been now characterized, type 2 S. suis remains the most relevant serotype in porcine and human infection.
Transmission : reservoir : Sus scrofa (occupational disease expecially in breeders and slaughterers). The organism is carried on the pig's tonsils and is spread pig-to-pig through nose rubbing or coughing. But it's only found in small concentration on the pigs' tonsils, so it's difficult for a human to catch it that way. When the infection spreads to the brain, causing meningitis, it's in far greater concentration, and so it can be transmitted to humans who eat raw infected pork or handle the dead animal with open cuts. Although the governmental official states that risk of infection is only present with open wounds, Kay's study^ref reported that only 20% of patients were noted to have sustained minor cuts or burns before symptoms occurred. Finding that many patients had no history of any injury, the authors speculate that respiratory or oral routes may be important.
=> a wide range of infections in pigs, including meningitis, arthritis, pneumonia, septicemia, endocarditis, encephalitis, polyserositis, and abscesses. The bacterium is endemic in all pig-raising countries world-wide, especially affecting large, intensively managed pig farms. The disease is not regarded to be highly infectious, most outbreaks are limited to the affected farms, and is not notifiable, nationally or internationally. Nevertheless, in the affected farms, significant economic losses may be observed, and, since antibiotic therapy gives unsatisfactory results, vaccines have been developed and widely used. The results of vaccination have been inconsistent.
Human infection may occur, but it has generally been known as occupational, affecting farmers and personnel engaged with pig breeding and their handling, including slaughter, not a food-borne disease. The current spread of Streptococcus suis in China seems odd. Something must be perturbing the usual epidemiology of this occupational infection. There may be several guesses (and I emphasize guesses at this point) based on the rereading of the reports:
• 1) The disease is being spread by the foodborne route, and, therefore, is being transported to markets at substantial distances. This would probably be associated with some clinical outbreak in swine in Sichuan, while sick pigs -- instead of being presented for slaughter -- are sold on the open market at heavily discounted prices. As knowledge of the outbreak in people dries up the local market, unscrupulous dealers would send the meat further afield, thus explaining the new cities involved. The farmer eating his own sick pig falls in this category as well. The articles above, and many others, refer incorrectly to this disease as swine flu. Swine influenza is a well known disease but it caused by the influenza virus, not Streptococcus suis.
• 2) There might be a co-infection with a virus that weakens certain human immune systems in the outbreak area and, therefore, allows opportunistic Streptococcus suis infection. What virus can only be speculated.
• 3) There might be a synergism between 2 pathogens, say a virus and Streptococcus suis . If the latter was occult and widespread in a latent form, it is just adding a match to tinder.
• 4) The old epidemiological adage: seek and ye shall find. This is more applicable to the newer cases and rather doubtful if representing the explanation for the outbreak in Sichuan.
Unfortunately, there is little information on the swine populations in Sichuan, because one key factor in putting together the cause of the outbreak would be to know the status of local swine farms where the cases are occurring. There is little information, other than bans on pork, coming from the animal side, but unless there is evidence of an outbreak in pigs indicating a new, more virulent strain, occupational exposure to normal Streptococcus suis could hardly explain the magnitude of the cases in humans generated this far.
Additionally, the organism could have acquired a toxin or some other factor, increasing its virulence. To date, it has not clearly been spread from human to human, and the speculation of an analogy to pneumonic plague and its transmissibility is just that. Short latent period and multi-organ failure are ultimate causes for the higher-than-expected mortality rate of the pig-borne disease : most patients suffered failures in the kidneys, livers, lungs and heart shortly after they were contracted, and some of them died before timely treatment. The latent period of the disease is so short that some patients died
within 10 hours after infection : in one case, a man died 2 hours after slaughtering a sick pig. In comparison, it normally takes a week or 2 for an ordinary bacterial infection to break out. On the other hand, the disease was caused by Streptococcus suis type 2, the deadliest of all the 35 forms of pig-borne S. suis bacteria. These are different capsular types of S. suis. Type 2 has always represented the most virulent type in both swine and humans. 2 bacterial pathogens come immediately to mind that may have a short time, in hours not days, from inoculation and onset of infection. Both Group A streptococcal and Pasteurella multocida (the latter usually associated with feline bites) wound infections can occur within hours of exposure, but the rapidity of onset does not necessarily correlate with severity or fulminating infection. Such rapidly fulminating infections can be seen in pneumococcal (S. pneumoniae) postsplenectomy infection and in meningococcemia. Marcelo Gottschalk, one of the world's leading experts on the disease, works at the world's only reference laboratory for S.
suis at the University of Montreal in Canada. Some farmers in Hong Kong and the mainland "vaccinate" by feeding the tissue of sick pigs to healthy pigs, according to the chairman of the Hong Kong Pig Farm Association, Wong Kwong-wing. On Wed, 17 Aug 2005, he said these practices could lead to mutations of bacteria. Gottschalk warned that homemade vaccination is "extremely dangerous" because, instead of preventing the disease, healthy pigs may get infected by the live bacteria which could lead to a serious outbreak. While Wong said the overuse of antibiotics on pig farms is common and could be a factor in the outbreak, Gottschalk said this isn't likely. Overusing antibiotics could increase the resistance of bacteria, he said, but he doesn't think this carries a greater threat since antibiotics still kill bacteria like Streptococcus suis easily.
=> severe flu-like symptoms (such as fever and nausea ) => septicemia and streptococcal toxic shock-like syndrome (STSS / STSLS)^ref => fulminant sepsis, meningitis followed by partial or permanent hearing loss), endocarditis, and a hemorrhagic diathesis can be associated with many bacteremic syndromes
Laboratory examinations : multiple PCR gives results in 4 hours
Therapy : although a substantial case fatality rate has been recognized so far, if the mechanism of pathogenesis here is elaboration of toxins, it is likely that antimicrobials would not be as useful in established cases. In a 2002 report^ref, 110 strains of S. suis from swine in France and 25 strains of the organism from humans (in different countries of origin) were assessed for antimicrobial sensitivity.  Macrolide and tetracycline resistance was found in some strains, especially serotype 2, but the beta-lactam class antimicrobial agents were active. Of note, among porcine isolates, there was no correlation between antimicrobial resistance and virulence.
Prevention : I am not aware of any trials using a S. suis type 2 vaccine in humans. Several approaches have been used in swine, however, including sonicated organisms^ref, a non-encapsulated mutant^ref, and suilysin, the thiol-activated haemolysin^ref.
• Streptococcus thermophilus (in no Lancefield group; "viridans" ; various)

g-hemolytic. It is widely used for the manufacture of yogurt and cheese.
Genomics : sequences of 2 yogurt strains have a striking level of gene decay (10% pseudogenes, expecially involved in carbon utilization, in line with the paucity of carbon sources in milk). Notably, most streptococcal virulence-related genes that are not involved in basic cellular processes are either inactivated or absent in the dairy streptococcus^ref
=> acute and subacute endocarditis
• Streptococcus uberis (in Lancefield groups C, D, E and P; various)

g-hemolytic.
=> erysipela after 6-7 days incubation
• Streptococcus vestibularis ("viridans")

=> acute and subacute endocarditis
• Streptococcus viridans

a-hemolytic.
=> acute and subacute endocarditis
• Clostridia (anaerobic spore-forming Bacteria)
• Clostridiales
• Acidaminococcaceae
• Acidaminococcus
• Acidaminococcus fermentans
• Veillonella are anaerobic, gram-negative cocci, part of the normal flora of the mouth, gastrointestinal tract, and vaginal tract
• Veillonella atypica
• Veillonella dispar : endocarditis^{ref1, ref2}
• Veillonella montpellierensis has recently been isolated from the gastric fluid of a newborn and from the amniotic fluid of 2 women^ref, and from a patient with endocarditistis^ref
• Veillonella parvula (a.k.a. Veillonella alcalescens (Mays TD, Holdeman LV, Moore WEC, Rogosa M, Johnson JL. Taxonomy of the genus Veillonella Prévot. Int J Syst Evol Microbiol. 1982;32:28–36)) was isolated from patients with endocarditis^{ref1, ref2, ref3} (Loewe L, Rosenblatt P, Alture-Werber E. A refractory case of subacute bacterial endocarditis due to Veillonella gazogenes clinically arrested by a combination of penicillin, sodium paraaminohippurate, and heparin. Am Heart J. 1946;32:327–38.) and from a lung abscess in a patient with echocardiographic vegetations, but blood cultures were negative^ref
Nitrate reductase converts dietary nitrates in saliva into nitrites.
They have been cultured from human specimens. They are infrequently isolated in human infections. Rarely, Veillonella species have been the only etiologic agents identified in serious infections such as meningitis, osteomyelitis, prosthetic joint infection, pleuropulmonary infection, endocarditis, and bacteremia. Veillonella spp. had also been isolated from intravenous drug users with polymicrobial endocarditis^ref
Therapy : penicillin has been the antimicrobial agent of choice^ref. However, recent studies found a notably high resistance to penicillin G (MIC >= 2 mg/mL)^ref. These penicillin G–resistant isolates showed generally reduced susceptibility to ampicillin or amoxicillin but remained susceptible to amoxicillin and clavulanate^ref
• Selenomonas
• Selenomonas sputigena

=> gingivitis
• Clostridiaceae
• Clostridium : they produce terminal endospores that can be killed by ...
• > 15' at 123 °C (dry heat)
• 1 hour at 150 °C (wet heat)
• 2 hours at 100°C
They can't germinate at pH < 4.6, T < 2 °C or A_w < 0.97.
Proteomics : clostridial neurotoxins (CNT) impair neuronal exocytosis through specific proteolysis of essential proteins called SNAREs. SNARE assembly into a low-energy ternary complex is believed to catalyse membrane fusion, precipitating neurotransmitter release; this process is attenuated in response to SNARE proteolysis. Site-specific SNARE hydrolysis is catalysed by the CNT light chains, a unique group of zinc-dependent endopeptidases. The means by which a CNT properly identifies and cleaves its target SNARE has been a subject of much speculation; it is thought to use one or more regions of enzyme–substrate interaction remote from the active site (exosites), but actually there are an array of exosites that determine substrate specificity. Substrate orientation is similar to that of the general zinc-dependent metalloprotease thermolysin. There are significant structural changes near the toxin's catalytic pocket upon substrate binding, probably serving to render the protease competent for catalysis^ref.
• Clostridium baratii
=> botulism
• Clostridium bifermentans

=> skin wound and surgical infections that lead to clostridial myonecrosis / gas gangrene
• Clostridium botulinum
• Clostridium botulinum serotype A (affects human (51% of all botulism cases) via toxinfections from anaerobically conserved vegetables and meats)
• Clostridium botulinumserotype B (affects human (21% of all botulism cases) and Equus caballus via toxinfections from anaerobically conserved vegetables and meats)
• Clostridium botulinumserotype C (affects Equus caballus and Bos taurus)
• Clostridium botulinum serotype D (affects Equus caballus and Bos taurus)
• Clostridium botulinum serotype E (affects rarely human (12% of all botulism cases) and Aves spp.)
Epidemiology :
• Norway : 35 cases of foodborne botulism have been reported since 1975. There were 2 outbreaks of botulism in 2003, with a total of 6 people affected.
• Finland, where C. botulinum type E is naturally highly prevalent in aquatic environments and fish^{ref1, ref2} : outbreaks  occurred in 1999^ref and 2006^ref.
• Germany : an outbreak affected 2 people in 1997^ref
Type E botulism is much more likely to have an initial lethargic mental status and more autonomic dysfunction (Hughes JM, Hatheway CL, Ostroff SM. Botulism. In: Scheld WM, Whitley RJ, Durack DT, editors. Infections of the central nervous system. 2nd edition. Philadelphia: Lippincott-Raven, 1997, pp. 615-28)
Transmission : toxinfections from anaerobically conserved marine mammals^ref, e.g.
• raw beached
• "muktuk", the skin and pink blubber layer from whales in Alaska
• 'oerakfisk' : semi-fermented fish often prepared at home in Norway and eaten traditionally around Christmas. Salt and sugar are added to a gutted fish, which is put into a pressurized container and stored for several weeks at 5-8°C before being eaten without cooking. Should the temperature during fermentation be > 8°C and/or the salt added be < 5% of the weight of the fish, C. botulinum may germinate and produce toxin. Air-drying of the salted fish without further preparation enables bacteria to survive. If C. botulinum survive, reproduction of the bacteria and formation of botulinum toxin E is prevented only at comparatively low temperatures (< 3°C)
• the hot-smoking processes are usually too low to eliminate botulinum spores^ref. Growth and toxin production from spores in vacuum-packed smoked fish products with anaerobic atmosphere and limited preservative factors is likely during extended storage at temperatures > 3°C. Therefore the most important factors controlling C. botulinum growth and toxin production are efficient heat treatments, restricted shelf life and continuous storage below 3°C
• Clostridium botulinum serotype F (rarely affects human)
• Clostridium botulinum serotype G (rarely affects human)
It is widely distributed in soil, sediments of lakes and ponds, and decaying vegetation. Hence, the intestinal tracts of Aves spp., herbivore mammals and home-caught and -prepared fish may occasionally contain the organism as a transient.
Peritrichous, a-hemolytic, 7 serotypes (A-G) according to toxin epitopes.
Epidemiology : botulism, or sausage poisoning as it was originally termed, was first seriously studied following an outbreak in Wildbad, Germany in 1793. The outbreak involved 13 people, 6 of whom died, and was associated with consumption of a locally produced blood sausage. Following this outbreak, the number of reported cases of sausage poisoning rapidly increased prompting a study of the disease by local health officer, Justinius Kerner (1829). He described 230 cases, most of which were attributed to the consumption of sausage. The illness became known as "botulism" after "botulus" the Latin word for sausage. Many years later, Van Ermengem (1897) investigated an outbreak of botulism involving 34 individuals who had consumed raw, salted ham served at a gathering of amateur musicians in Ellezelles, Belgium. In the investigation of this outbreak, Van Ermengem established that botulism was an intoxication, not an infection, and that the toxin was produced by a spore-forming obligate anaerobic bacterium, Clostridium botulinum. A later outbreak in Darmstadt, Germany associated with canned white beans established that there was a 2nd type of botulism. The new strain was type A and the Van Ermengem strain was probably type B (Landmann 1904). In 1922, type C botulism was identified as causing disease in chickens (Bengston 1922) and cattle (Seddon 1922). Robinson (1929) identified type D in cattle and type E was identified by Gunnison (1936-1937) as causing botulism in people after consuming fish. Type F was first described by Moller and Scheibel (1960) from a Danish outbreak of botulism involving homemade liver paste. Finally, type G botulism was identified in soil from cornfields in Argentina by Gimenez and Ciccarelli (1978). The principal types of botulism involved in human disease are types A, B, and E^ref
• Thailand : normally experiences only one or 2 patients per year from the illness annually
• In 1998, a smaller outbreak of botulism associated with home-canned bamboo shoots was reported in the same Thai province^ref
• since 14 Mar 2006, 163 of the 354 people (of whom 200 (56%) ate food served at the event) attending an annual local village Buddhist festival in Nawaimai village, Pakaluang subdistrict, Baan Luang district, Nan^ref Province, developed symptoms suggestive of botulism (dysphagia, dysarthria, ptosis, abdominal discomfort, muscle weakness). All of the affected people had eaten pickled bamboo shoots prepared in a traditional manner, with symptoms developing and progressing over 24-48 hours following consumption. Of the 163 persons with illness, 141 (86.5%) were admitted to area hospitals, and 40 have since required intubation and respirator support. To date, no deaths have been reported^{ref1, ref2}. The last case was identified on 21 Mar 2006. 20 vials of heptavalent antitoxin (A-G) were provided by the UK Department of Health with assistance from the WHO, 50 vials of bivalent antitoxin (A, B) were donated by CDC, and 23 vials of trivalent antitoxin (A, B, E) were donated by the National Institute of Infectious Diseases in Japan. Thailand purchased an additional 10 vials of bivalent antitoxin (A, B) from a Canadian company. Antitoxin was administered to patients with the most severe symptoms; 70 vials were administered on 19 and 20 Mar 2006, and the last of the 93 vials used was administered on 23 Mar 2006. Although published data suggest that antitoxin is most effective if administered within the 1st 24 hours of illness onset^ref, botulism antitoxin was administered to patients later in the course of illness to halt the progression of paralysis and potentially shorten the duration of illness. A study to assess the short- and long-term outcomes of a subset of patients is under way. Bamboo shoot products on shelves and in the markets were collected and destroyed by the provincial public health office^ref. People should boil home-canned bamboo shoots for 10 minutes before eating, and to discard cans with defects (e.g., dents, swelling, discoloration, rust, or foul smell). A Thai Air Force C-130 cargo aircraft transported 17 patients -- including 12 women, 4 men and 1 girl -- to 7 hospitals in Bangkok on Thu 23 Mar 2006 : most were in critical condition^{ref1, ref2}.
• USA : In the past 30 years, 2 notable USA food-borne outbreaks related to distributed food have occurred.  One was in the New York area, involving commercially produced vichyssoise soup June/July 1971 (type A) (CDC: Botulism associated with commercial vichyssoise (Morbid Mortal Week Rep 1971;20: 242) and another involving home-canned green peppers in Michigan in March/April 1977