Supported MLST species (PUBMLST names)
This page lists the PUBMLST-format names used as keys for MLST databases. These
are the names you should use as the mlst_species keys in
bactscout_config.yml (the key itself is the local directory name under
bactscout_dbs/).
If you want to add MLST support for a species, create a directory in
bactscout_dbs/ named exactly as the key below and place the PUBMLST/ARIBA
formatted MLST database files there.
For more information about these species see https://pubmlst.org/organisms.
Full list (PUBMLST-format names)
- Achromobacter spp.
- Acinetobacter baumannii #1
- Acinetobacter baumannii #2
- Aeromonas spp.
- Aggregatibacter actinomycetemcomitans
- Anaplasma phagocytophilum
- Arcobacter spp.
- Aspergillus fumigatus
- Bacillus cereus
- Bacillus licheniformis
- Bacillus subtilis
- Bacteroides fragilis
- Bartonella bacilliformis
- Bartonella henselae
- Bartonella washoensis
- Bordetella spp.
- Borrelia spp.
- Brachyspira hampsonii
- Brachyspira hyodysenteriae
- Brachyspira intermedia
- Brachyspira pilosicoli
- Brachyspira spp.
- Brucella spp.
- Burkholderia cepacia complex
- Burkholderia pseudomallei
- Campylobacter concisus/curvus
- Campylobacter fetus
- Campylobacter helveticus
- Campylobacter hyointestinalis
- Campylobacter insulaenigrae
- Campylobacter jejuni
- Campylobacter lanienae
- Campylobacter lari
- Campylobacter sputorum
- Campylobacter upsaliensis
- Candida albicans
- Candida glabrata
- Candida krusei
- Candida tropicalis
- Candidatus Liberibacter solanacearum
- Carnobacterium maltaromaticum
- Chlamydiales spp.
- Citrobacter freundii
- Clonorchis sinensis
- Clostridioides difficile
- Clostridium botulinum
- Clostridium perfringens
- Clostridium septicum
- Corynebacterium diphtheriae
- Cronobacter spp.
- Cutibacterium acnes
- Dichelobacter nodosus
- Edwardsiella spp.
- Enterobacter cloacae
- Enterococcus faecalis
- Enterococcus faecium
- Escherichia coli #1
- Escherichia coli #2
- Flavobacterium psychrophilum
- Gallibacterium anatis
- Geotrichum spp.
- Glaesserella parasuis
- Haemophilus influenzae
- Helicobacter cinaedi
- Helicobacter pylori
- Helicobacter suis
- Kingella kingae
- Klebsiella aerogenes
- Klebsiella oxytoca
- Klebsiella pneumoniae
- Kudoa septempunctata
- Lactobacillus salivarius
- Lactococcus lactis bacteriophage
- Leptospira spp.
- Leptospira spp. #2
- Leptospira spp. #3
- Listeria monocytogenes
- Macrococcus canis
- Macrococcus caseolyticus
- Mammaliicoccus sciuri
- Mannheimia haemolytica
- Melissococcus plutonius
- Moraxella catarrhalis
- Mycobacteria spp.
- Mycobacteroides abscessus
- Mycoplasma agalactiae
- Mycoplasma anserisalpingitidis
- Mycoplasma bovis
- Mycoplasma flocculare
- Mycoplasma gallisepticum #1
- Mycoplasma gallisepticum #2
- Mycoplasma hominis
- Mycoplasma hyopneumoniae
- Mycoplasma hyorhinis
- Mycoplasma iowae
- Mycoplasma pneumoniae
- Mycoplasma synoviae
- Neisseria spp.
- Orientia tsutsugamushi
- Ornithobacterium rhinotracheale
- Paenibacillus larvae
- Pasteurella multocida #1
- Pasteurella multocida #2
- Pediococcus pentosaceus
- Photobacterium damselae
- Piscirickettsia salmonis
- Porphyromonas gingivalis
- Pseudomonas aeruginosa
- Pseudomonas fluorescens
- Pseudomonas putida
- Rhodococcus spp.
- Riemerella anatipestifer
- Salmonella enterica
- Saprolegnia parasitica
- Shewanella spp.
- Sinorhizobium spp.
- Staphylococcus aureus
- Staphylococcus chromogenes
- Staphylococcus epidermidis
- Staphylococcus haemolyticus
- Staphylococcus hominis
- Staphylococcus lugdunensis
- Staphylococcus pseudintermedius
- Stenotrophomonas maltophilia
- Streptococcus agalactiae
- Streptococcus bovis/equinus complex (SBSEC)
- Streptococcus canis
- Streptococcus dysgalactiae equisimilis
- Streptococcus gallolyticus
- Streptococcus oralis
- Streptococcus pneumoniae
- Streptococcus pyogenes
- Streptococcus suis
- Streptococcus thermophilus
- Streptococcus thermophilus #2
- Streptococcus uberis
- Streptococcus zooepidemicus
- Streptomyces spp.
- Taylorella spp.
- Tenacibaculum spp.
- Treponema pallidum
- Trichomonas vaginalis
- Ureaplasma spp.
- Vibrio cholerae
- Vibrio chole