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All species MLST databases and published schemes

MLST databases are hosted at the University of Oxford, UK; Imperial College, London, UK; the University of Warwick, UK, and the Pasteur Institute, Paris, France.

Order by: Organism | Profiles | Isolates

Databases ordered by numbers of organism

Chart shows databases with at least 1000 profiles or isolates.

* Data updated automatically: 2016-04-30.

Organism Website and link to database Sequence types Isolates Applications to date Selected references
Achromobacter spp. http://pubmlst.org/achromobacter 321 * 733 * Isolate characterisation Spilker et al. (2012) J Clin Microbiol 50:3010-5.
Acinetobacter baumannii#1 http://pubmlst.org/abaumannii/ 1282 * 3168 * Isolate characterisation and population structure analysis Bartual et al. (2005) J Clin Microbiol 43:4382-90.
Acinetobacter baumannii#2 http://pubmlst.org/abaumannii/ 836 * 3168 * -
Aeromonas spp. http://pubmlst.org/aeromonas/ 398 * 455 * Strain characterization
Anaplasma phagocytophilum http://pubmlst.org/aphagocytophilum/ 118 * 338 * Strain characterization and population structure analysis
Arcobacter spp. http://pubmlst.org/arcobacter/ 536 * 712 * Isolate characterisation and population structure
Aspergillus fumigatus http://pubmlst.org/afumigatus/ 48 * 22 * Isolate characterisation
Bacillus cereus http://pubmlst.org/bcereus/ 1270 * 2001 * Population and evolutionary analyses. Priest et al. (2004) J Bacteriol 186:7959-70.
Bacillus licheniformis http://pubmlst.org/blicheniformis/ 27 * 62 * Isolate characterisation and population structure analysis Madslien et al. (2012) BMC Microbiol 12:230.
Bacillus subtilis http://pubmlst.org/bsubtilis/ 155 * 316 * Isolate characterisation and population structure analysis
Bartonella henselae http://pubmlst.org/bhenselae 32 * 434 * Isolate characterisation and population structure analysis
Batrachochytrium dendrobatidis n/a 10 35 Population and evolutionary analyses.
Bordetella spp. http://pubmlst.org/bordetella/ 82 * 443 * -
Borrelia spp. http://pubmlst.org/borrelia/ 675 * 1886 * Isolate characterisation and epidemiological analyses
Brachyspira hampsonii http://pubmlst.org/brachyspira/ 20 * 513 * Strain characterization and population structure analysis
Brachyspira hyodysenteriae http://pubmlst.org/brachyspira/ 184 * 513 * Molecular epidemiology and population structure analyses.
Brachyspira intermedia http://pubmlst.org/brachyspira/ 83 * 513 * Molecular epidemiology and population structure analyses.
Brachyspira pilosicoli http://pubmlst.org/brachyspira/ 124 * 513 * Strain characterization and population structure analysis
Brachyspira spp. http://pubmlst.org/brachyspira/ 36 * 513 * Isolate characterisation and population structure analysis
Burkholderia cepacia complex http://pubmlst.org/bcc/ 1063 * 1987 * Isolate characterisation and population structure analyses Baldwin et al. (2005) J Clin Microbiol 43:4665-73.
Burkholderia pseudomallei http://pubmlst.org/bpseudomallei 1465 * 4491 * Isolate characterisation and species identification. Godoy et al. (2003) J Clin Microbiol 41:2068-79.
Campylobacter concisus/curvus http://pubmlst.org/campylobacter/
(Isolate database contains other non-jejuni/coli Campylobacter species and the number of isolates reported reflect all of these together)
130 * 278 * Isolate characterisation and population structure analysis
Campylobacter fetus http://pubmlst.org/campylobacter/
(Isolate database contains other non-jejuni/coli Campylobacter species and the number of isolates reported reflect all of these together)
67 * 278 * Isolate characterisation and population structure analyses van Bergen et al. (2005) J Clin Microbiol 43:5888-98.
Campylobacter helveticus http://pubmlst.org/campylobacter/
(Isolate database contains other non-jejuni/coli Campylobacter species and the number of isolates reported reflect all of these together)
9 * 278 * -
Campylobacter hyointestinalis http://pubmlst.org/campylobacter/
(Isolate database contains other non-jejuni/coli Campylobacter species and the number of isolates reported reflect all of these together)
131 * 278 * Isolate characterisation and population structure analysis
Campylobacter insulaenigrae http://pubmlst.org/campylobacter/
(Isolate database contains other non-jejuni/coli Campylobacter species and the number of isolates reported reflect all of these together)
43 * 278 * Isolate characterisation and population structure analysis
Campylobacter jejuni http://pubmlst.org/campylobacter/ 8180 * 40603 * Epidemiological surveillance of food-borne infections, population structure analyses. Dingle et al. (2001) J Clin Microbiol 39:14-23.
Campylobacter lanienae http://pubmlst.org/campylobacter/
(Isolate database contains other non-jejuni/coli Campylobacter species and the number of isolates reported reflect all of these together)
147 * 278 * Isolate characterisation and population structure analysis
Campylobacter lari http://pubmlst.org/campylobacter/
(Isolate database contains other non-jejuni/coli Campylobacter species and the number of isolates reported reflect all of these together)
32 * 278 * -
Campylobacter sputorum http://pubmlst.org/campylobacter/
(Isolate database contains other non-jejuni/coli Campylobacter species and the number of isolates reported reflect all of these together)
16 * 278 * Isolate characterisation and population structure analysis
Campylobacter upsaliensis http://pubmlst.org/campylobacter/
(Isolate database contains other non-jejuni/coli Campylobacter species and the number of isolates reported reflect all of these together)
203 * 278 * -
Candida albicans http://pubmlst.org/calbicans 3058 * 4121 * Isolate characterisation and identification of nosocomial outbreaks Bougnoux et al. (2003) J Clin Microbiol 41:5265-6.
Candida glabrata http://pubmlst.org/cglabrata/ 68 * 212 * Isolate characterisation and population structure analyses Dodgson et al. (2003) J Clin Microbiol 41:5709-17.
Candida krusei http://pubmlst.org/ckrusei/ 188 * 245 * Isolate characterisation and population structure analyses Jacobsen et al. (2007) J Clin Microbiol 45:317-23.
Candida tropicalis http://pubmlst.org/ctropicalis/ 571 * 659 * Isolate characterisation and epidemiological analyses Tavanti et al. (2005) J Clin Microbiol 43:5593-600.
Carnobacterium maltaromaticum http://pubmlst.org/cmaltaromaticum 39 * 50 * Strain characterization and population structure analysis
Chlamydiales spp. http://pubmlst.org/chlamydiales/ 147 * 3976 * Isolate characterisation and population structure analysis Pannekoek et al. (2008) BMC Microbiol 8:42.
Citrobacter freundii http://pubmlst.org/cfreundii 103 * 65 * Isolate characterisation and population structure analysis Bai et al. (2012) PLoS One 7:e33054.
Clonorchis sinensis http://pubmlst.org/csinensis/ 254 * 256 * Strain characterization and population structure analysis
Clostridium botulinum http://pubmlst.org/cbotulinum/ 98 * 276 * Isolate characterisation and evolutionary analyses
Clostridium difficile http://pubmlst.org/cdifficile 349 * 1551 * Isolate characterisation and population structure analysis Griffiths et al. (2010) J Clin Microbiol 48:770-8.
Clostridium septicum http://pubmlst.org/csepticum/ 8 * - Isolate characterisation and evolutionary analyses
Corynebacterium diphtheriae http://pubmlst.org/cdiphtheriae/ 385 * 532 * -
Cronobacter spp. http://pubmlst.org/cronobacter/ 462 * 1584 * -
Enterobacter cloacae http://pubmlst.org/ecloacae/ 808 * - Strain characterization and population structure analysis
Enterococcus faecalis http://pubmlst.org/efaecalis/ 706 * 1413 * Isolate characterisation and population structure analysis
Enterococcus faecium http://pubmlst.org/efaecium/ 1153 * 2893 * Strain characterization and population structure analysis
Escherichia coli#1 http://mlst.warwick.ac.uk/mlst/dbs/Ecoli 5787 * 6492 * Examination of the evolution of virulence. Wirth et al. (2006) Mol Microbiol 60:1136-51.
Escherichia coli#2 http://bigsdb.web.pasteur.fr/ecoli/ 733 * 1032 * -
Flavobacterium psychrophilum http://pubmlst.org/fpsychrophilum/ 166 * 995 * Strain characterization and population structure analysis
Haemophilus influenzae http://pubmlst.org/hinfluenzae/ 1482 * 2466 * Isolate characterisation and population structure analysis Meats et al. (2003) J Clin Microbiol 41:1623-36.
Haemophilus parasuis http://pubmlst.org/hparasuis/ 215 * 240 * Population and evolutionary analyses.
Helicobacter cinaedi http://pubmlst.org/hcinaedi 18 * 68 * Molecular epidemiology and population structure analysis
Helicobacter pylori http://pubmlst.org/helicobacter/ 2971 * 2001 * Tracking the patterns of human migration. Wirth et al. (2004) Proc Natl Acad Sci U S A 101:4746-51.
Helicobacter suis http://pubmlst.org/hsuis/ 25 * 29 * Strain characterization and population structure analysis
Kingella kingae http://bigsdb.web.pasteur.fr/kingella/ 64 * 107 * -
Klebsiella oxytoca http://pubmlst.org/koxytoca/ 170 * 120 * Isolate characterisation and population structure analysis
Klebsiella pneumoniae http://bigsdb.web.pasteur.fr/klebsiella/ 2280 * 3246 * Isolate characterisation and epidemiological analyses
Kudoa septempunctata http://pubmlst.org/kseptempunctata/ 3 * 104 * Isolate characterisation
Lactobacillus salivarius http://pubmlst.org/lsalivarius/ 25 * 33 * Population and evolutionary analyses. Raftis et al. (2011) Appl Environ Microbiol 77:954-65.
Leptospira spp. http://pubmlst.org/leptospira/ 202 * 579 * Isolate characterisation and epidemiological analyses
Leptospira spp.#2 http://pubmlst.org/leptospira/ 102 * 579 * Strain characterization and population structure analysis Varni et al. (2014) Infect Genet Evol 22:216-22.
Leptospira spp.#3 http://pubmlst.org/leptospira 137 * 579 * Strain characterization and population structure analysis Ahmed et al. (2006) Ann Clin Microbiol Antimicrob 5:28.
Listeria monocytogenes http://bigsdb.web.pasteur.fr/listeria/ 988 * 3129 * -
Mannheimia haemolytica http://pubmlst.org/mhaemolytica/ 36 * 115 * Isolate characterisation
Melissococcus plutonius http://pubmlst.org/mplutonius/ 33 * 373 * Isolate characterisation and population structure analysis
Moraxella catarrhalis http://mlst.warwick.ac.uk/mlst/dbs/Mcatarrhalis 308 * 346 * -
Mycobacterium abscessus http://pubmlst.org/mabscessus/ 26 * - Isolate characterisation and population structure analyses
Mycobacterium massiliense http://pubmlst.org/mabscessus/ 12 * - Isolate characterisation and population structure analyses
Mycoplasma agalactiae http://pubmlst.org/magalactiae/ 18 * 104 * Isolate characterisation and population structure analysis McAuliffe et al. (2011) J Med Microbiol 60:803-11.
Mycoplasma bovis http://pubmlst.org/mbovis 32 * 136 * Isolate characterisation and population structure analysis Register et al. (2015) Vet Microbiol 175:92-8.
Mycoplasma hyorhinis http://pubmlst.org/mhyorhinis/ 55 * 59 * Isolate characterisation and population structure analysis
Neisseria spp. http://pubmlst.org/neisseria/ 12005 * 38357 * Epidemiological surveillance, post-vaccine studies, population and evolutionary analyses. Maiden et al. (1998) Proc Natl Acad Sci U S A 95:3140-5.
Orientia tsutsugamushi http://pubmlst.org/otsutsugamushi/ 92 * 163 * Population and evolutionary analyses
Ornithobacterium rhinotracheale http://pubmlst.org/orhinotracheale/ 14 * 87 * Isolate characterisation and population structure analysis Thieme et al. (2016) PLoS One 11:e0148158.
Paenibacillus larvae http://pubmlst.org/plarvae 23 * 301 * Isolate characterisation and population structure analysis
Pasteurella multocida#1 http://pubmlst.org/pmultocida/ 305 * 562 * Isolate characterisation and population structure analysis
Pasteurella multocida#2 http://pubmlst.org/pmultocida/ 63 * 125 * Evolutionary analyses between isolates from different host species
Pediococcus pentosaceus http://pubmlst.org/ppentosaceus/ 17 * 31 * Strain characterization and population structure analysis
Pencillium marneffei http://mlstdb.hku.hk:14206/MLST_index.html 35 44 -
Porphyromonas gingivalis http://pubmlst.org/pgingivalis/ 138 * 144 * Isolate characterisation and population structure analyses Enersen et al. (2006) J Clin Microbiol 44:35-41.
Propionibacterium acnes http://pubmlst.org/pacnes/ 123 * 5 * Isolate characterisation and population structure analyses
Pseudomonas aeruginosa http://pubmlst.org/paeruginosa/ 2265 * 5515 * Population and evolutionary analyses.
Pseudomonas fluorescens http://pubmlst.org/pfluorescens/ 102 * 114 * Strain characterization and population structure analysis
Riemerella anatipestifer http://pubmlst.org/ranatipestifer/ 17 * 54 * Isolate characterisation and populations structure analysis
Salmonella enterica http://mlst.warwick.ac.uk/mlst/dbs/Senterica 3015 * 6286 * -
Salmonella typhi n/a 4 26 Estimation of age and time of emergence of S. typhi.
Sinorhizobium spp. http://pubmlst.org/sinorhizobium/ 136 * 550 * -
Staphylococcus aureus http://pubmlst.org/saureus 3528 * 31226 * Identification of predominant epidemic MRSA isolates, species evolution, population analyses
Staphylococcus epidermidis http://pubmlst.org/sepidermidis/ 607 * 1056 * Isolate characterisation and population structure analysis Thomas et al. (2007) J Clin Microbiol 45:616-9.
Staphylococcus haemolyticus http://pubmlst.org/shaemolyticus/ 41 * 80 * Strain characterisation and population structure analysis
Staphylococcus lugdunensis http://bigsdb.web.pasteur.fr/staphlugdunensis/ 45 * 126 * -
Staphylococcus pseudintermedius http://pubmlst.org/spseudintermedius/ 643 * 721 * Strain characterization and population structure analysis Solyman et al. (2013) J Clin Microbiol 51:306-10.
Stapylococcus hominis http://pubmlst.org/shominis 40 * 108 * Isolate characterisation and population structure analysis
Stenotrophomonas maltophilia http://pubmlst.org/smaltophilia/ 173 * 259 * -
Streptococcus agalactiae http://pubmlst.org/sagalactiae/ 860 * 1580 * Identification of clones associated with neonatal infections. Jones et al. (2003) J Clin Microbiol 41:2530-6.
Streptococcus canis http://pubmlst.org/scanis/ 25 * 90 * Strain characterization and population structure analysis Pinho et al. (2013) J Clin Microbiol 51:1099-109.
Streptococcus dysgalactiae equisimilis http://pubmlst.org/sdysgalactiae/ 290 * 1005 * Isolate characterisation and population structure analysis McMillan et al. (2010) PLoS One 5:e11741.
Streptococcus gallolyticus http://pubmlst.org/sgallolyticus/ 108 * 362 * Strain characterization and population structure analysis
Streptococcus oralis http://pubmlst.org/soralis/ 78 * 651 * Isolate characterisation and population structure analyses Do et al. (2009) Microbiology 155:2593-602.
Streptococcus pneumoniae http://pubmlst.org/spneumoniae/ 11847 * 31722 * Identification of antibiotic resistant clones, epidemiological surveillance, population analyses. Enright et al. (1998) Microbiology 144 ( Pt 11):3049-60.
Streptococcus pyogenes http://pubmlst.org/spyogenes 869 * 2661 * Identification of relationships between emm-type and clonal complex Enright et al. (2001) Infect Immun 69:2416-27.
Streptococcus suis http://pubmlst.org/ssuis 751 * 1583 * Population characterisation and population structure analysis
Streptococcus thermophilus http://bigsdb.web.pasteur.fr/streptococcus/ 125 * 174 * -
Streptococcus thermophilus#2 http://pubmlst.org/sthermophilus 119 * 257 * Isolate characterisation and population structure analysis
Streptococcus uberis http://pubmlst.org/suberis/ 670 * 988 * - Coffey et al. (2006) Appl Environ Microbiol 72:1420-8.
Streptococcus zooepidemicus http://pubmlst.org/szooepidemicus/ 359 * 1323 * Isolate characterisation and population structure analysis
Streptomyces spp http://pubmlst.org/streptomyces/ 234 * 270 * Species identification
Taylorella spp. http://pubmlst.org/taylorella/ 54 * 291 * Strain characterization and population structure analysis Duquesne et al. (2013) Vet Microbiol 167:609-18.
Tenacibaculum spp. http://pubmlst.org/tenacibaculum/ 82 * 114 * Isolate characterisation and populations structure analysis
Trichomonas vaginalis http://pubmlst.org/tvaginalis/ 60 * 68 * -
Vibrio cholerae http://pubmlst.org/vcholerae/ 268 * 204 * Strain characterization and population structure analysis
Vibrio parahaemolyticus http://pubmlst.org/vparahaemolyticus/ 1531 * 2216 * -
Vibrio spp. http://pubmlst.org/vibrio 149 * 182 * Species identification
Vibrio tapetis http://pubmlst.org/vtapetis/ 10 * 30 * Isolate characterisation and populaton structure
Vibrio vulnificus http://pubmlst.org/vvulnificus/ 344 * 452 * Isolate characterisation and epidemiological analyses. Bisharat et al. (2005) Emerg Infect Dis 11:30-5.
Wolbachia http://pubmlst.org/wolbachia/ 469 * 1825 * Isolate characterisation and population structure analyses Baldo et al. (2006) Appl Environ Microbiol 72:7098-110.
Xylella fastidiosa http://pubmlst.org/xfastidiosa/ 76 * 293 * Isolate characterisation and population structure.
Yersinia pseudotuberculosis http://mlst.warwick.ac.uk/mlst/dbs/Ypseudotuberculosis 257 * 748 * Population and evolutionary analyses.
Yersinia ruckeri http://pubmlst.org/yruckeri/ 30 * 103 * Population and evolutionary analyses.
Yersinia spp. http://pubmlst.org/yersinia/ 170 * 389 * Speciation and isolate characterisation