Pathogens and selected non-pathogens, and their genomes

The following are summary tables of information about each pathogen whose genome has been sequenced, or is currently being sequenced, along with equivalent info for selected non-pathogens (dashes mark organisms not yet in the Pathogenomics Database).



Pathogens

 
Organism Strain Pathogen? "Primary" Disease Intracellular parasite? Host range (approximate) Domain Complete Genome? Size (Mb) % GC Genome Publication
Actinobacillus actinomycetemcomitans HK1651 yes Periodontal disease facultative intracellular humans Bacteria no 2.2 40  
Bacillus anthracis Ames yes Anthrax extracellular humans and other animals, spores survive in soil Bacteria no 4.5 34  
Bartonella henselae Houston 1 yes Cat scratch disease, Bacillary angiomatosis in HIV patients facultative intracellular humans, cats, may be flea vector Bacteria almost 2.0 41  
-Bordetella bronchiseptica RB50 yes Respiratory disease in a range of animals facultative intracellular wide range of mammalian species Bacteria no 4.9 66  
-Bordetella parapertussis 12822 yes Whooping cough extracellular humans and ovine species (sheep) Bacteria no 3.9 66  
-Bordetella pertussis Tohama I yes Whooping cough (strict human pathogen) extracellular humans Bacteria almost 3.9 66  
Borrelia burgdorferi B31 yes Lyme disease facultative intracellular field mice and other rodents, humans, tick vector Bacteria yes - published 1.44 29 Fraser et al., Nature, 390: 580-586 (1997)
Campylobacter jejuni NCTC 11168 yes Gastroenteritis  extracellular humans, fowl, cattle, sheep, dogs, cats Bacteria yes 1.7 31  
Candida albicans 1161 yes - opportunistic Yeast infection (opportunistic) extracellular humans and other mammals Eukarya no 15.0 37  
Candida albicans SC5314 yes - opportunistic Yeast infection (opportunistic) extracellular humans and other mammals Eukarya no 16.0 37  
Chlamydia trachomatis  D/UW-3/Cx yes Chlamydia (strict human pathogen) obligate intracellular humans Bacteria yes - published 1.05 42 Stephens et al., Science 282: 754-759 (1998)
Chlamydia trachomatis  MoPn yes Chlamydia (strict human pathogen) obligate intracellular humans Bacteria yes 1.1 42   
Chlamydophila pneumoniae CWL029 yes Chlamydial pneumonia (strict human pathogen) obligate intracellular humans Bacteria yes - published 1.23 41 Kalman et al., Nat Genet 21: 385-389 (1999)
Chlamydophila pneumoniae   yes Chlamydial pneumonia (strict human pathogen) obligate intracellular humans Bacteria yes 1.2 41 Kalman et al., Nat Genet 21: 385-389 (1999)
Clostridium difficle 630 yes Antibiotic-associated diarrhea (opportunistic) extracellular humans Bacteria almost 4.4 26  
Corynebacterium diphtheriae NCTC13129 yes Diphtheria extracellular humans Bacteria no 3.1 52  
-Encephalitozoon cuniculi   yes - opportunistic cornea/conjunctiva infect. or disseminated - HIV patients (opportunistic) obligate intracellular humans and other animals Eukarya no 2.9 52  
-Enterococcus faecalis V583 yes - opportunistic Range of infections - often hospital acquired (opportunistic) extracellular humans and other animals Bacteria almost 3.0 37  
Escherichia coli a number of strains including  yes Diarrheal, urinary tract infections - certain strains cause severe disease
 		 invasive strains: facultative intracellular
 		 humans and warm-blooded animals 
 		 Bacteria no   51  
Francisella tularensis schu 4 yes Tularaemia facultative intracellular small wild mammals, especially rabbits, humans, deer fly vector Bacteria no 2.0 39  
- Giardia lamblia WB yes Giardia extracellular beavers, muskrats, humans and other animals (can survive in water) Eukarya no 12.0 49  
Haemophilus influenzae KW20 yes Upper respir. infect. and Meningitis (strict human pathogen) extracellular humans Bacteria yes - published 1.83 39 Fleischmann et. al., Science 269:496-512 (1995)
Helicobacter pylori 26695 yes Peptic ulcers and gastritis (strict human pathogen) extracellular humans Bacteria yes - published 1.66 40 Tomb et. al., Nature388:539-547 (1997)
Helicobacter pylori J99 yes Peptic ulcers and gastritis (strict human pathogen) extracellular humans Bacteria yes - published 1.64 40 Alm et.al., Nature, 397:176-180 (1999)
Klebsiella pneumoniae M6H 78578 yes Pneumonia extracellular humans Bacteria yes - only 3x coverage   56  
-Legionella pneumophila Philadelphia-1 yes Legionnaires' disease  facultative intracellular humans (can survive in water) Bacteria no 4.0 41  
Leishmania major  Friedlin yes Leishmaniasis, aka kala azar  obligate intracellular humans, dogs, Phlebotomus perniciosus vector Eukarya no - but 1 chrom. Complete 35.0 64  
-Leptospira interrogans Lai yes Leptospirosis extracellular humans and animals (can survive in water) Bacteria no 4.8 39  
-Listeria monocytogenes EGD-e yes Listeriosis  facultative intracellular humans (and can thrive when inoculated into food during preparation) Bacteria no 3.2 38  
Mycobacterium avium 104 yes - opportunistic chronic lung disease in HIV patients (opportunistic) facultative intracellular fowl and a range of animals including humans Bacteria almost 4.7 66  
Mycobacterium bovis AF2122/97 spoligotype 9 yes - opportunistic Usually bone or lymphatic system infection (opportunistic). Not vaccine strain facultative intracellular cattle, badgers, humans and some other animals Bacteria no 4.4 66  
Mycobacterium leprae   yes Leprosy (strict human pathogen) facultative intracellular humans Bacteria no 2.8 58  
Mycobacterium tuberculosis H37Rv yes Tuberculosis  facultative intracellular humans Bacteria yes - published 4.40 65 Cole et al., Nature393:537 (1998)
Mycobacterium tuberculosis CSU#93 yes Tuberculosis  facultative intracellular humans Bacteria almost 4.4 65  
Mycoplasma genitalium G-37 yes - opportunistic Urethritis (usually HIV patients- opportunistic pathogen) extracellular humans Bacteria yes - published 0.58 32 Fraser et. al., Science 270:397-403 (1995)
Mycoplasma mycoides subsp. mycoides SC  PG1 yes - but not humans contagious bovine pleuropneumonia (CBPP) extracellular cattle, primarily in Africa, and other animals Bacteria no 1.3 25  
Mycoplasma pneumoniae M129 yes Mycoplasmal pneumonia (aka "walking pneumonia") extracellular humans Bacteria yes - published 0.81 40 Himmelreich et. al., Nuc. Acid Res. 24:4420-4449 (1996)
-Mycoplasma pulmonis   yes Murine respiratory mycoplasmosis extracellular rodents Bacteria no 1.0 27  
Neisseria gonorrhoeae FA1090 yes Gonorrhea (strict human pathogen) facultative intracellular humans Bacteria almost 2.2 52  
Neisseria meningitidis MC58 yes Meningitis (strict human pathogen) facultative intracellular humans Bacteria no 2.3 52  
Neisseria meningitidis  serogroup A strain Z2491 yes Meningitis (strict human pathogen) facultative intracellular humans Bacteria yes 2.2 52  
-Pasteurella haemolytica 2.4 yes - but not humans Cattle shipping fever extracellular cattle, swine Bacteria no   38  
Pasteurella  multicoda Pm70 yes - but primarily other animals fowl cholera, cattle septicemia, pig rhinitis, human bite (dog/cat) infections extracellular fowl, cattle, pigs, dogs, cats, humans  Bacteria no 2.4 39  
Plasmodium falciparum 3D7 yes Malaria facultative intracellular humans, mosquito vector  Eukarya no - but 2 chrom. complete 30.0 82  
-Pneumocystis carinii f. sp. carinii yes - opportunistic Repiratory infection - rats extracellular rats and likely other mammals Eukarya no 7.7 36  
-Pneumocystis carinii f. sp. hominis yes - opportunistic Repiratory infection - primarily HIV patients (opportunistic) extracellular humans and likely other mammals Eukarya no 7.5 36  
-Porphyromonas gingivalis W83 yes Periodontal disease facultative intracellular humans Bacteria no 2.2 48  
Pseudomonas aerguinosa PAO1 yes - opportunistic Variety of mucosal infections (opportunistic) extracellular Humans and other animals (also on plants, and in soil, water) Bacteria no 5.9 67  
-Ralstonia solanacearum    yes - but not humans Plant bacterial wilt extracellular plants and soil Bacteria no   69  
Rickettsia conorii   yes Fievre boutonneuse (Mediterranean fever) obligate intracellular Arthropods. Brown dog tick vector Bacteria no 1.2 38  
Rickettsia prowazekii Madrid E yes Epidemic typhus obligate intracellular humans and other animals, lice vector Bacteria yes - published 1.10 31 Andersson et al., Nature 396: 133-140 (1998)
-Salmonella paratyphi A ATCC 9150 yes Paratyphoid/enteric fever facultative intracellular humans (can survive in water) Bacteria yes - only 2x coverage 4.6 52  
Salmonella typhi CT18 yes Typhoid fever facultative intracellular humans (can survive in water) Bacteria almost 4.5 52  
Salmonella typhimurium SGSC1412  yes Salmonellosis facultative intracellular humans and warm-blooded animals Bacteria no 4.8 53  
-Shigella flexneri 2a 301 yes Shigellosis (bacillary dysentry) facultative intracellular humans (can survive in water) Bacteria no 4.7 44  
Staphylococcus aureus COL yes Variety (abcesses, food poisoning, toxic shock syndrome) extracellular humans (and can thrive when inoculated into food during preparation) Bacteria no 2.8 37  
Staphylococcus aureus 8325 yes Variety (abcesses, food poisoning, toxic shock syndrome) extracellular humans (and can thrive when inoculated into food during preparation) Bacteria no 2.8 37  
-Streptococcus mutans UAB159 yes Dental caries extracellular humans Bacteria no 2.2 39  
-Streptococcus pneumoniae type 4 yes Pneumococcal (typical) pneumoniae, meningitis (strict human pathogen) extracellular humans Bacteria no 2.2 39  
-Streptococcus pyogenes M1GAS yes Strep throat, scarlet fever etc... (strict human pathogen) extracellular, some strains intrcellular humans Bacteria almost 2.0 39  
-Treponema denticola   yes Periodontal disease extracellular humans Bacteria no 3.0 41  
Treponema pallidum Nichols yes Syphillis (strict human pathogen) extracellular humans Bacteria yes - published 1.14 53 Fraser et al., Science 281: 375-388 (1998)
Trypanosoma brucei rhodesiense TREU 927/4 yes Sleeping sickness extracellular humans and other animals, tsetse fly vector Eukarya no 35.0 50  
-Ureaplasma urealyticum serovar 3 yes Urethritis extracellular humans Bacteria yes - published on web 0.8 35  
-Ustilago maydis   yes - but not humans Corn blight  extracellular plants Eukarya no 20.0 56  
Vibrio cholerae  sero: O1, El Tor, str: N16961 yes Cholera extracellular humans (can survive in water) Bacteria yes 2.5 44  
-Xanthomonas citri   yes - but not humans Cankers - Citrus plants  extracellular Rutaceae species (Citrus and close relatives) Bacteria no 5.0 66  
-Xylella fastidiosa 8.1.b clone 9.a.5.c yes - but not humans Pierce’s Disease - grapevines  extracellular? plants Bacteria no 2.0 55  
Yersinia pestis CO-92 Biovar Orientalis yes Plague extracellular? rats and other rodents, humans, flea vector Bacteria almost 4.4 47  



Non-pathogens

 
Organism Strain Pathogen? "Primary" Disease Intracellular parasite? Host range (approximate) Domain Complete Genome? Size (Mb) % GC Genome Publication
Aeropyrum pernix  K1 no n/a     Archaea yes - published 1.67  58 Kawarabayasi et al., DNA Research 6: 83-101 (1999)
Aquifex aeolicus VF5 no n/a     Bacteria yes - published 1.50  44 Deckert et al., Nature392:353 (1998)
Archaeoglobus fulgidus DSM4304 no n/a     Archaea yes - published 2.18  49 Klenk et al.,Nature 390:364-370 (1997)
Bacillus subtilis 168 no - very rare opportunistic n/a     Bacteria yes - published 4.20  44 Kunst et.al., Nature390: 249-256 (1997)
Deinococcus radiodurans R1 no n/a     Bacteria yes - published 3.28 67 White et al., Science 286: 1571-1577 (1999)
Escherichia coli K-12 no - but other strains are Strains(not K12): Diarrheal and urinary tract infections K-12: extracellular humans and warm-blooded animals  Bacteria yes - published 4.60 51 Blattner et. al., Science 277:1453-1474 (1997)
Lactococcus lactis IL1403 no n/a     Bacteria yes - published - but only 2x coverage 2.35 35 Bolotin et al., Antonie Van Leeuwenhoek 76: 27-76 (1999)
Methanobacterium thermoautotrophicum delta H no n/a     Archaea yes - published 1.75 50 Smith et.al., J. Bacteriology, 179:7135-7155 (1997)
Methanococcus jannaschii DSM 2661 no n/a     Archaea yes - published 1.66  32 Bult et. al., Science 273:1058-1073 (1996)
Mycobacterium bovis BCG-Pasteur 1173P2 no - vaccine strain n/a vaccine strain facultative intracellular n/a Bacteria no 4.4 65  
Pseudomonas putida KT2440 no - beneficial to plants n/a  extracellular plants (and soil and water) Bacteria almost 6.1 63  
Pyrococcus horikoshii  OT3 no n/a     Archaea yes - published 1.80  43 Kawarabayasi et al., DNA Research 5: 55-76 (1998)
Saccharomyces cerevisiae S288C no - strains rarely opportunistic n/a     Eukarya yes - published 13  40 Goffeau et. al., Nature 387 (Suppl.) 5-105 (1997)
Synechocystis sp.  PCC 6803 no n/a     Bacteria yes - published 3.57  49 Kaneko et. al., DNA Res. 3: 109-136 (1996)
Thermotoga maritima MSB8 no n/a     Bacteria yes - published 1.80  46 Nelson et al., Nature 399: 323-329 (1999)