Multi-Locus Sequence Typing (MLST) is a method of identifying and characterizing isolates from sequence data. This method has been used for many years. As sequencing has become so common-place for microbial identification, tools to support those analyses continue to be of high importance.
At One Codex, when we classify your isolate sequence data, if we identify certain clinical and environmental species of interest, we automatically perform an MLST analysis to further characterize those organisms. In 2025, we updated this MLST workflow to include over 100 species, from open-source resources such as PubMLST [1]. We also added support for long-read sequencing technology such as Oxford Nanopore Technology (ONT) and PacBio sequence data.
Samples that contain a relevant sequence type will automatically be tagged, so that they are easier to find, and their sequence type is immediately identifiable. An example of such tags can be seen below.
Figure 1: Samples on the One Codex platform which have been analyzed for MLST, and tagged with their appropriate sequence type.
There is also a new results page where you can view details on the various sequence types that have been partially or fully identified in the sample. This results page shows details on the various marker alleles required in order to call a sequence type as present. Details on coverage, identity and depth of each marker are also provided.
Figure 2: Results page displaying the various sequence types that have been identified in a sample.
To view the details of the MLST results for a sample, you can switch between analyses that have been run on a sample by clicking "View Results" for the sample, and then clicking the database name at the top-right of the results page, which will provide you with a menu of the various workflows that have been run on the sample. You'll find more details on that here.
MLST markers are specific to certain species, genera, orders, and even one sup-species. The various taxa for which we currently assess MLST markers are listed below (taxon name and ID). If there are any organisms that are not listed but for which you'd like to assess the MLST of, reach out to our team!
Species-specific markers
Acinetobacter baumannii (470) | Aggregatibacter actinomycetemcomitans (714) | Anaplasma phagocytophilum (948) |
Aspergillus fumigatus (746128) | Avibacterium paragallinarum (728) | Bacillus cereus (1396) |
Bacillus licheniformis (1402) | Bacillus subtilis (1423) | Lactococcus lactis (1358) |
Bacteroides fragilis (817) | Bartonella bacilliformis (774) | Bartonella henselae (38323) |
Burkholderia cepacia (292) | Burkholderia mallei (13373) | Burkholderia pseudomallei (28450) |
Candida albicans (5476) | Nakaseomyces glabratus (5478) | Pichia kudriavzevii (4909) |
Candida tropicalis (5482) | Carnobacterium maltaromaticum (2751) | Clonorchis sinensis (79923) |
Clostridioides difficile (1496) | Clostridium botulinum (1491) | Clostridium chauvoei (46867) |
Clostridium perfringens (1502) | Clostridium septicum (1504) | Cutibacterium acnes (1747) |
Dichelobacter nodosus (870) | Enterococcus faecalis (1351) | Enterococcus faecium (1352) |
Escherichia coli (562) | Flavobacterium psychrophilum (96345) | Gallibacterium anatis (750) |
Glaesserella parasuis (738) | Haemophilus influenzae (727) | Helicobacter cinaedi (213) |
Helicobacter pylori (210) | Helicobacter suis (104628) | Klebsiella aerogenes (548) |
Klebsiella oxytoca (571) | Klebsiella pneumoniae (573) | Kudoa septempunctata (751907) |
Ligilactobacillus salivarius (1624) | Lactococcus garvieae (1363) | Macrococcoides canis (1855823) |
Macrococcoides caseolyticum (69966) | Mammaliicoccus sciuri (1296) | Mannheimia haemolytica (75985) |
Melissococcus plutonius (33970) | Mycobacteroides abscessus (36809) | Mycoplasma anserisalpingitidis (519450) |
Mycoplasmopsis bovis (28903) | Mycoplasmoides gallisepticum (2096) | Mycoplasmoides genitalium (2097) |
Mesomycoplasma hyopneumoniae (2099) | Mycoplasmopsis synoviae (2109) | Orientia tsutsugamushi (784) |
Ornithobacterium rhinotracheale (28251) | Paenibacillus larvae (1464) | Pasteurella multocida (747) |
Pediococcus pentosaceus (1255) | Photobacterium damselae (38293) | Piscirickettsia salmonis (1238) |
Porphyromonas gingivalis (837) | Pseudomonas aeruginosa (287) | Pseudomonas fluorescens (294) |
Pseudomonas putida (303) | Riemerella anatipestifer (34085) | Saprolegnia parasitica (101203) |
Stenotrophomonas maltophilia (40324) | Staphylococcus aureus (1280) | Staphylococcus chromogenes (46126) |
Staphylococcus epidermidis (1282) | Staphylococcus haemolyticus (1283) | Staphylococcus hominis (1290) |
Staphylococcus pseudintermedius (283734) | Streptococcus agalactiae (1311) | Streptococcus canis (1329) |
Streptococcus dysgalactiae (1334) | Streptococcus gallolyticus (315405) | Streptococcus iniae (1346) |
Streptococcus mitis (28037) | Streptococcus pneumoniae (1313) | Streptococcus pyogenes (1314) |
Streptococcus suis (1307) | Streptococcus thermophilus (1308) | Streptococcus uberis (1349) |
Treponema pallidum (160) | Vibrio cholerae (666) | Vibrio parahaemolyticus (670) |
Vibrio tapetis (52443) | Vibrio vulnificus (672) | Xanthomonas citri (346) |
Xylella fastidiosa (2371) | Yersinia ruckeri (29486) | Metamycoplasma hominis (2098) |
Subspecies-specific markers
Streptococcus equi subsp. zooepidemicus (40041) |
Genus-specific markers
Achromobacter (222) | Aeromonas (642) | Arcobacter (28196) |
Blastocystis (12967) | Borrelia (138) | Brachyspira (29521) |
Brucella (234) | Citrobacter (544) | Cronobacter (413496) |
Edwardsiella (132406) | Enterobacter (547) | Escherichia (561) |
Geotrichum (43987) | Leptospira (171) | Liberibacter (34019) |
Neisseria (482) | Proteus (210425) | Rhodococcus (1661425) |
Salmonella (590) | Serratia (2985502) | Shewanella (22) |
Sinorhizobium (28105) | Streptococcus (1301) | Taylorella (29574) |
Tenacibaculum (104267) | Ureaplasma (2129) | Vibrio (662) |
Wolbachia (953) |
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Order-specific markers
Chlamydiales (51291) |