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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: 2016-07-27.

Organism Website and link to database Sequence types Isolates Applications to date Selected references
Achromobacter spp. http://pubmlst.org/achromobacter 333 * 757 * Isolate characterisation Spilker et al. (2012) J Clin Microbiol 50:3010-5.
Acinetobacter baumannii#1 http://pubmlst.org/abaumannii/ 1384 * 3227 * Isolate characterisation and population structure analysis Bartual et al. (2005) J Clin Microbiol 43:4382-90.
Acinetobacter baumannii#2 http://pubmlst.org/abaumannii/ 897 * 3227 * -
Aeromonas spp. http://pubmlst.org/aeromonas/ 398 * 455 * Strain characterization
Anaplasma phagocytophilum http://pubmlst.org/aphagocytophilum/ 118 * 339 * Strain characterization and population structure analysis
Arcobacter spp. http://pubmlst.org/arcobacter/ 563 * 786 * Isolate characterisation and population structure
Aspergillus fumigatus http://pubmlst.org/afumigatus/ 48 * 22 * Isolate characterisation
Bacillus cereus http://pubmlst.org/bcereus/ 1298 * 2059 * 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 * 504 * -
Borrelia spp. http://pubmlst.org/borrelia/ 675 * 1886 * Isolate characterisation and epidemiological analyses
Brachyspira hampsonii http://pubmlst.org/brachyspira/ 20 * 544 * Strain characterization and population structure analysis
Brachyspira hyodysenteriae http://pubmlst.org/brachyspira/ 195 * 544 * Molecular epidemiology and population structure analyses.
Brachyspira intermedia http://pubmlst.org/brachyspira/ 83 * 544 * Molecular epidemiology and population structure analyses.
Brachyspira pilosicoli http://pubmlst.org/brachyspira/ 124 * 544 * Strain characterization and population structure analysis
Brachyspira spp. http://pubmlst.org/brachyspira/ 36 * 544 * Isolate characterisation and population structure analysis
Burkholderia cepacia complex http://pubmlst.org/bcc/ 1082 * 2030 * Isolate characterisation and population structure analyses Baldwin et al. (2005) J Clin Microbiol 43:4665-73.
Burkholderia pseudomallei http://pubmlst.org/bpseudomallei 1479 * 4570 * 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 * 311 * 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)
68 * 311 * 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 * 311 * -
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 * 311 * 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 * 311 * Isolate characterisation and population structure analysis
Campylobacter jejuni http://pubmlst.org/campylobacter/ 8300 * 41888 * 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 * 311 * 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 * 311 * -
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 * 311 * 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 * 311 * -
Candida albicans http://pubmlst.org/calbicans 3114 * 4144 * 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/ 613 * 802 * 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 * 3979 * Isolate characterisation and population structure analysis Pannekoek et al. (2008) BMC Microbiol 8:42.
Citrobacter freundii http://pubmlst.org/cfreundii 114 * 70 * 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 356 * 1558 * 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/ 387 * 534 * -
Cronobacter spp. http://pubmlst.org/cronobacter/ 467 * 1600 * -
Enterobacter cloacae http://pubmlst.org/ecloacae/ 827 * - Strain characterization and population structure analysis
Enterococcus faecalis http://pubmlst.org/efaecalis/ 723 * 1431 * Isolate characterisation and population structure analysis
Enterococcus faecium http://pubmlst.org/efaecium/ 1187 * 2928 * Strain characterization and population structure analysis
Escherichia coli#1 http://mlst.warwick.ac.uk/mlst/dbs/Ecoli 6047 * 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/ 734 * 1032 * -
Flavobacterium psychrophilum http://pubmlst.org/fpsychrophilum/ 166 * 995 * Strain characterization and population structure analysis
Haemophilus influenzae http://pubmlst.org/hinfluenzae/ 1524 * 2507 * 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 * 2037 * 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/ 2372 * 3396 * 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 * 584 * Isolate characterisation and epidemiological analyses
Leptospira spp.#2 http://pubmlst.org/leptospira/ 102 * 584 * Strain characterization and population structure analysis Varni et al. (2014) Infect Genet Evol 22:216-22.
Leptospira spp.#3 http://pubmlst.org/leptospira 139 * 584 * Strain characterization and population structure analysis Ahmed et al. (2006) Ann Clin Microbiol Antimicrob 5:28.
Listeria monocytogenes http://bigsdb.web.pasteur.fr/listeria/ 1012 * 3161 * -
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/ 27 * 113 * Isolate characterisation and population structure analysis McAuliffe et al. (2011) J Med Microbiol 60:803-11.
Mycoplasma bovis http://pubmlst.org/mbovis 40 * 207 * Isolate characterisation and population structure analysis Register et al. (2015) Vet Microbiol 175:92-8.
Mycoplasma hyorhinis http://pubmlst.org/mhyorhinis/ 70 * 99 * Isolate characterisation and population structure analysis
Neisseria spp. http://pubmlst.org/neisseria/ 12187 * 39367 * 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/ 325 * 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/ 2334 * 5614 * 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 3238 * 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 3596 * 31418 * 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/ 705 * 793 * 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/ 896 * 1604 * Identification of clones associated with neonatal infections. Jones et al. (2003) J Clin Microbiol 41:2530-6.
Streptococcus bovis/equinus complex (SBSEC) http://pubmlst.org/sbsec/ 66 * 74 * Isolate characterisation and population structure analysis Jans et al. (2016) BMC Microbiol 16:117.
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 * 671 * Isolate characterisation and population structure analyses Do et al. (2009) Microbiology 155:2593-602.
Streptococcus pneumoniae http://pubmlst.org/spneumoniae/ 11972 * 32160 * 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 871 * 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 776 * 1612 * 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/ 363 * 1335 * 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/ 289 * 221 * Strain characterization and population structure analysis
Vibrio parahaemolyticus http://pubmlst.org/vparahaemolyticus/ 1551 * 2254 * -
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 265 * 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