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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: 2017-02-25.

Organism Website and link to database Sequence types Isolates Applications to date Selected references
Achromobacter spp. https://pubmlst.org/achromobacter 343 * 771 * Isolate characterisation Spilker et al. (2012) J Clin Microbiol 50:3010-5.
Acinetobacter baumannii#1 https://pubmlst.org/abaumannii/ 1489 * 3421 * Isolate characterisation and population structure analysis Bartual et al. (2005) J Clin Microbiol 43:4382-90.
Acinetobacter baumannii#2 https://pubmlst.org/abaumannii/ 957 * 3421 * -
Aeromonas spp. https://pubmlst.org/aeromonas/ 509 * 571 * Strain characterization
Anaplasma phagocytophilum https://pubmlst.org/aphagocytophilum/ 118 * 339 * Strain characterization and population structure analysis
Arcobacter spp. https://pubmlst.org/arcobacter/ 648 * 825 * Isolate characterisation and population structure
Aspergillus fumigatus https://pubmlst.org/afumigatus/ 48 * 22 * Isolate characterisation
Bacillus cereus https://pubmlst.org/bcereus/ 1332 * 2092 * Population and evolutionary analyses. Priest et al. (2004) J Bacteriol 186:7959-70.
Bacillus licheniformis https://pubmlst.org/blicheniformis/ 27 * 62 * Isolate characterisation and population structure analysis Madslien et al. (2012) BMC Microbiol 12:230.
Bacillus subtilis https://pubmlst.org/bsubtilis/ 155 * 332 * Isolate characterisation and population structure analysis
Bartonella henselae https://pubmlst.org/bhenselae 32 * 434 * Isolate characterisation and population structure analysis
Batrachochytrium dendrobatidis n/a 10 35 Population and evolutionary analyses.
Bordetella spp. https://pubmlst.org/bordetella/ 82 * 1616 * -
Borrelia spp. https://pubmlst.org/borrelia/ 683 * 1900 * Isolate characterisation and epidemiological analyses
Brachyspira hampsonii https://pubmlst.org/brachyspira/ 20 * 588 * Strain characterization and population structure analysis
Brachyspira hyodysenteriae https://pubmlst.org/brachyspira/ 218 * 588 * Molecular epidemiology and population structure analyses.
Brachyspira intermedia https://pubmlst.org/brachyspira/ 83 * 588 * Molecular epidemiology and population structure analyses.
Brachyspira pilosicoli https://pubmlst.org/brachyspira/ 124 * 588 * Strain characterization and population structure analysis
Brachyspira spp. https://pubmlst.org/brachyspira/ 36 * 588 * Isolate characterisation and population structure analysis
Brucella spp. https://pubmlst.org/brucella 73 * 754 * Isolate characterisation and population structure analysis
Burkholderia cepacia complex https://pubmlst.org/bcc/ 1297 * 2359 * Isolate characterisation and population structure analyses Baldwin et al. (2005) J Clin Microbiol 43:4665-73.
Burkholderia pseudomallei https://pubmlst.org/bpseudomallei 1521 * 4802 * Isolate characterisation and species identification. Godoy et al. (2003) J Clin Microbiol 41:2068-79.
Campylobacter concisus/curvus https://pubmlst.org/campylobacter/
(Isolate database contains other non-jejuni/coli Campylobacter species and the number of isolates reported reflect all of these together)
130 * 349 * Isolate characterisation and population structure analysis
Campylobacter fetus https://pubmlst.org/campylobacter/
(Isolate database contains other non-jejuni/coli Campylobacter species and the number of isolates reported reflect all of these together)
69 * 349 * Isolate characterisation and population structure analyses van Bergen et al. (2005) J Clin Microbiol 43:5888-98.
Campylobacter helveticus https://pubmlst.org/campylobacter/
(Isolate database contains other non-jejuni/coli Campylobacter species and the number of isolates reported reflect all of these together)
9 * 349 * -
Campylobacter hyointestinalis https://pubmlst.org/campylobacter/
(Isolate database contains other non-jejuni/coli Campylobacter species and the number of isolates reported reflect all of these together)
131 * 349 * Isolate characterisation and population structure analysis
Campylobacter insulaenigrae https://pubmlst.org/campylobacter/
(Isolate database contains other non-jejuni/coli Campylobacter species and the number of isolates reported reflect all of these together)
43 * 349 * Isolate characterisation and population structure analysis
Campylobacter jejuni https://pubmlst.org/campylobacter/ 8653 * 51095 * Epidemiological surveillance of food-borne infections, population structure analyses. Dingle et al. (2001) J Clin Microbiol 39:14-23.
Campylobacter lanienae https://pubmlst.org/campylobacter/
(Isolate database contains other non-jejuni/coli Campylobacter species and the number of isolates reported reflect all of these together)
171 * 349 * Isolate characterisation and population structure analysis
Campylobacter lari https://pubmlst.org/campylobacter/
(Isolate database contains other non-jejuni/coli Campylobacter species and the number of isolates reported reflect all of these together)
65 * 349 * -
Campylobacter sputorum https://pubmlst.org/campylobacter/
(Isolate database contains other non-jejuni/coli Campylobacter species and the number of isolates reported reflect all of these together)
16 * 349 * Isolate characterisation and population structure analysis
Campylobacter upsaliensis https://pubmlst.org/campylobacter/
(Isolate database contains other non-jejuni/coli Campylobacter species and the number of isolates reported reflect all of these together)
203 * 349 * -
Candida albicans https://pubmlst.org/calbicans 3267 * 4318 * Isolate characterisation and identification of nosocomial outbreaks Bougnoux et al. (2003) J Clin Microbiol 41:5265-6.
Candida glabrata https://pubmlst.org/cglabrata/ 77 * 231 * Isolate characterisation and population structure analyses Dodgson et al. (2003) J Clin Microbiol 41:5709-17.
Candida krusei https://pubmlst.org/ckrusei/ 188 * 245 * Isolate characterisation and population structure analyses Jacobsen et al. (2007) J Clin Microbiol 45:317-23.
Candida tropicalis https://pubmlst.org/ctropicalis/ 673 * 839 * Isolate characterisation and epidemiological analyses Tavanti et al. (2005) J Clin Microbiol 43:5593-600.
Carnobacterium maltaromaticum https://pubmlst.org/cmaltaromaticum 39 * 50 * Strain characterization and population structure analysis
Chlamydiales spp. https://pubmlst.org/chlamydiales/ 183 * 4012 * Isolate characterisation and population structure analysis Pannekoek et al. (2008) BMC Microbiol 8:42.
Citrobacter freundii https://pubmlst.org/cfreundii 124 * 82 * Isolate characterisation and population structure analysis Bai et al. (2012) PLoS One 7:e33054.
Clonorchis sinensis https://pubmlst.org/csinensis/ 254 * 256 * Strain characterization and population structure analysis
Clostridium botulinum https://pubmlst.org/cbotulinum/ 98 * 276 * Isolate characterisation and evolutionary analyses
Clostridium difficile https://pubmlst.org/cdifficile 396 * 1604 * Isolate characterisation and population structure analysis Griffiths et al. (2010) J Clin Microbiol 48:770-8.
Clostridium septicum https://pubmlst.org/csepticum/ 8 * - Isolate characterisation and evolutionary analyses
Corynebacterium diphtheriae https://pubmlst.org/cdiphtheriae/ 423 * 565 * -
Cronobacter spp. https://pubmlst.org/cronobacter/ 516 * 1762 * -
Enterobacter cloacae https://pubmlst.org/ecloacae/ 907 * - Strain characterization and population structure analysis
Enterococcus faecalis https://pubmlst.org/efaecalis/ 767 * 1690 * Isolate characterisation and population structure analysis
Enterococcus faecium https://pubmlst.org/efaecium/ 1291 * 3067 * Strain characterization and population structure analysis
Escherichia coli#1 http://mlst.warwick.ac.uk/mlst/dbs/Ecoli 6792 * 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/ 813 * 1032 * -
Flavobacterium psychrophilum https://pubmlst.org/fpsychrophilum/ 166 * 995 * Strain characterization and population structure analysis
Haemophilus influenzae https://pubmlst.org/hinfluenzae/ 1738 * 2698 * Isolate characterisation and population structure analysis Meats et al. (2003) J Clin Microbiol 41:1623-36.
Haemophilus parasuis https://pubmlst.org/hparasuis/ 254 * 281 * Population and evolutionary analyses.
Helicobacter cinaedi https://pubmlst.org/hcinaedi 18 * 68 * Molecular epidemiology and population structure analysis
Helicobacter pylori https://pubmlst.org/helicobacter/ 3137 * 2225 * Tracking the patterns of human migration. Wirth et al. (2004) Proc Natl Acad Sci U S A 101:4746-51.
Helicobacter suis https://pubmlst.org/hsuis/ 123 * 157 * Strain characterization and population structure analysis
Kingella kingae http://bigsdb.web.pasteur.fr/kingella/ 65 * 108 * -
Klebsiella oxytoca https://pubmlst.org/koxytoca/ 177 * 126 * Isolate characterisation and population structure analysis
Klebsiella pneumoniae http://bigsdb.web.pasteur.fr/klebsiella/ 2587 * 3531 * Isolate characterisation and epidemiological analyses
Kudoa septempunctata https://pubmlst.org/kseptempunctata/ 3 * 104 * Isolate characterisation
Lactobacillus salivarius https://pubmlst.org/lsalivarius/ 25 * 33 * Population and evolutionary analyses. Raftis et al. (2011) Appl Environ Microbiol 77:954-65.
Leptospira spp. https://pubmlst.org/leptospira/ 202 * 592 * Isolate characterisation and epidemiological analyses
Leptospira spp.#2 https://pubmlst.org/leptospira/ 106 * 592 * Strain characterization and population structure analysis Varni et al. (2014) Infect Genet Evol 22:216-22.
Leptospira spp.#3 https://pubmlst.org/leptospira 143 * 592 * Strain characterization and population structure analysis Ahmed et al. (2006) Ann Clin Microbiol Antimicrob 5:28.
Listeria monocytogenes http://bigsdb.web.pasteur.fr/listeria/ 1233 * 3285 * -
Macrococcus canis https://pubmlst.org/mcanis/ 21 * 24 * Isolate characterisation and population structure
Macrococcus caseolyticus https://pubmlst.org/mcaseolyticus/ 6 * 12 * Isolate characterisation and population structure
Mannheimia haemolytica https://pubmlst.org/mhaemolytica/ 36 * 115 * Isolate characterisation
Melissococcus plutonius https://pubmlst.org/mplutonius/ 34 * 379 * Isolate characterisation and population structure analysis
Moraxella catarrhalis http://mlst.warwick.ac.uk/mlst/dbs/Mcatarrhalis 349 * 346 * -
Mycobacterium abscessus https://pubmlst.org/mabscessus/ 26 * - Isolate characterisation and population structure analyses
Mycobacterium massiliense https://pubmlst.org/mabscessus/ 12 * - Isolate characterisation and population structure analyses
Mycoplasma agalactiae https://pubmlst.org/magalactiae/ 32 * 134 * Isolate characterisation and population structure analysis McAuliffe et al. (2011) J Med Microbiol 60:803-11.
Mycoplasma bovis https://pubmlst.org/mbovis 40 * 207 * Isolate characterisation and population structure analysis Register et al. (2015) Vet Microbiol 175:92-8.
Mycoplasma hyopneumoniae https://pubmlst.org/mhyopneumoniae/ 70 * 184 * Strain characterization and population structure analysis Mayor et al. (2008) Vet Microbiol 127:63-72.
Mycoplasma hyorhinis https://pubmlst.org/mhyorhinis/ 70 * 99 * Isolate characterisation and population structure analysis
Mycoplasma iowae https://pubmlst.org/miowae/ 23 * 47 * Isolate characterisation and population structure analysis Ghanem et al. (2016) Vet Microbiol 195:2-8.
Mycoplasma pneumoniae https://pubmlst.org/mpneumoniae/ 22 * 63 * Isolate characterisation and population structure Brown et al. (2015) J Clin Microbiol 53:3195-203.
Mycoplasma synoviae https://pubmlst.org/msynoviae/ 46 * 58 * Isolate characterisation and population structure analysis
Neisseria spp. https://pubmlst.org/neisseria/ 12818 * 42255 * 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 https://pubmlst.org/otsutsugamushi/ 92 * 163 * Population and evolutionary analyses
Ornithobacterium rhinotracheale https://pubmlst.org/orhinotracheale/ 31 * 108 * Isolate characterisation and population structure analysis Thieme et al. (2016) PLoS One 11:e0148158.
Paenibacillus larvae https://pubmlst.org/plarvae 23 * 383 * Isolate characterisation and population structure analysis
Pasteurella multocida#1 https://pubmlst.org/pmultocida/ 337 * 562 * Isolate characterisation and population structure analysis
Pasteurella multocida#2 https://pubmlst.org/pmultocida/ 64 * 125 * Evolutionary analyses between isolates from different host species
Pediococcus pentosaceus https://pubmlst.org/ppentosaceus/ 17 * 31 * Strain characterization and population structure analysis
Pencillium marneffei http://mlstdb.hku.hk:14206/MLST_index.html 35 44 -
Photobacterium damselae https://pubmlst.org/pdamselae/ 55 * 78 * Isolate characterisation and population structure analysis
Porphyromonas gingivalis https://pubmlst.org/pgingivalis/ 138 * 144 * Isolate characterisation and population structure analyses Enersen et al. (2006) J Clin Microbiol 44:35-41.
Propionibacterium acnes https://pubmlst.org/pacnes/ 123 * 5 * Isolate characterisation and population structure analyses
Pseudomonas aeruginosa https://pubmlst.org/paeruginosa/ 2415 * 5728 * Population and evolutionary analyses.
Pseudomonas fluorescens https://pubmlst.org/pfluorescens/ 102 * 114 * Strain characterization and population structure analysis
Riemerella anatipestifer https://pubmlst.org/ranatipestifer/ 17 * 54 * Isolate characterisation and populations structure analysis
Salmonella enterica http://mlst.warwick.ac.uk/mlst/dbs/Senterica 3481 * 6286 * -
Salmonella typhi n/a 4 26 Estimation of age and time of emergence of S. typhi.
Sinorhizobium spp. https://pubmlst.org/sinorhizobium/ 136 * 550 * -
Staphylococcus aureus https://pubmlst.org/saureus 3851 * 32210 * Identification of predominant epidemic MRSA isolates, species evolution, population analyses
Staphylococcus epidermidis https://pubmlst.org/sepidermidis/ 626 * 1068 * Isolate characterisation and population structure analysis Thomas et al. (2007) J Clin Microbiol 45:616-9.
Staphylococcus haemolyticus https://pubmlst.org/shaemolyticus/ 41 * 80 * Strain characterisation and population structure analysis
Staphylococcus lugdunensis http://bigsdb.web.pasteur.fr/staphlugdunensis/ 31 * 109 * -
Staphylococcus pseudintermedius https://pubmlst.org/spseudintermedius/ 732 * 827 * Strain characterization and population structure analysis Solyman et al. (2013) J Clin Microbiol 51:306-10.
Stapylococcus hominis https://pubmlst.org/shominis 40 * 108 * Isolate characterisation and population structure analysis
Stenotrophomonas maltophilia https://pubmlst.org/smaltophilia/ 188 * 277 * -
Streptococcus agalactiae https://pubmlst.org/sagalactiae/ 1084 * 2824 * Identification of clones associated with neonatal infections. Jones et al. (2003) J Clin Microbiol 41:2530-6.
Streptococcus bovis/equinus complex (SBSEC) https://pubmlst.org/sbsec/ 66 * 74 * Isolate characterisation and population structure analysis Jans et al. (2016) BMC Microbiol 16:117.
Streptococcus canis https://pubmlst.org/scanis/ 25 * 90 * Strain characterization and population structure analysis Pinho et al. (2013) J Clin Microbiol 51:1099-109.
Streptococcus dysgalactiae equisimilis https://pubmlst.org/sdysgalactiae/ 317 * 1285 * Isolate characterisation and population structure analysis McMillan et al. (2010) PLoS One 5:e11741.
Streptococcus gallolyticus https://pubmlst.org/sgallolyticus/ 109 * 364 * Strain characterization and population structure analysis Dumke et al. (2014) J Clin Microbiol 52:2472-8.
Streptococcus oralis https://pubmlst.org/soralis/ 78 * 672 * Isolate characterisation and population structure analyses Do et al. (2009) Microbiology 155:2593-602.
Streptococcus pneumoniae https://pubmlst.org/spneumoniae/ 13126 * 36268 * Identification of antibiotic resistant clones, epidemiological surveillance, population analyses. Enright et al. (1998) Microbiology 144 ( Pt 11):3049-60.
Streptococcus pyogenes https://pubmlst.org/spyogenes 906 * 2683 * Identification of relationships between emm-type and clonal complex Enright et al. (2001) Infect Immun 69:2416-27.
Streptococcus suis https://pubmlst.org/ssuis 833 * 1751 * Population characterisation and population structure analysis
Streptococcus thermophilus http://bigsdb.web.pasteur.fr/streptococcus/ 125 * 174 * -
Streptococcus thermophilus#2 https://pubmlst.org/sthermophilus 119 * 257 * Isolate characterisation and population structure analysis
Streptococcus uberis https://pubmlst.org/suberis/ 816 * 1034 * - Coffey et al. (2006) Appl Environ Microbiol 72:1420-8.
Streptococcus zooepidemicus https://pubmlst.org/szooepidemicus/ 366 * 1381 * Isolate characterisation and population structure analysis
Streptomyces spp https://pubmlst.org/streptomyces/ 234 * 270 * Species identification
Taylorella spp. https://pubmlst.org/taylorella/ 54 * 291 * Strain characterization and population structure analysis Duquesne et al. (2013) Vet Microbiol 167:609-18.
Tenacibaculum spp. https://pubmlst.org/tenacibaculum/ 125 * 114 * Isolate characterisation and populations structure analysis
Trichomonas vaginalis https://pubmlst.org/tvaginalis/ 60 * 68 * -
Vibrio cholerae https://pubmlst.org/vcholerae/ 513 * 519 * Strain characterization and population structure analysis
Vibrio parahaemolyticus https://pubmlst.org/vparahaemolyticus/ 1712 * 2520 * -
Vibrio spp. https://pubmlst.org/vibrio 149 * 182 * Species identification
Vibrio tapetis https://pubmlst.org/vtapetis/ 10 * 30 * Isolate characterisation and populaton structure
Vibrio vulnificus https://pubmlst.org/vvulnificus/ 349 * 457 * Isolate characterisation and epidemiological analyses. Bisharat et al. (2005) Emerg Infect Dis 11:30-5.
Wolbachia https://pubmlst.org/wolbachia/ 470 * 1826 * Isolate characterisation and population structure analyses Baldo et al. (2006) Appl Environ Microbiol 72:7098-110.
Xylella fastidiosa https://pubmlst.org/xfastidiosa/ 79 * 293 * Isolate characterisation and population structure.
Yersinia pseudotuberculosis http://mlst.warwick.ac.uk/mlst/dbs/Ypseudotuberculosis 272 * 748 * Population and evolutionary analyses.
Yersinia ruckeri https://pubmlst.org/yruckeri/ 30 * 103 * Population and evolutionary analyses.
Yersinia spp. https://pubmlst.org/yersinia/ 170 * 389 * Speciation and isolate characterisation