PubMLST available datasets

File data/PubMLST_datasets.csv contains information of the multiple datasets available for PubMLST profiles and sequences.

This needs manual curation of the list of species included and periodically updates.

Retrieve from PubMLST databases by viewing source and retrieve fields from html data.

Kingdom	name	Species
bacteria	achromobacter	Achromobacter
bacteria	abaumannii	Acinetobacter baumannii
bacteria	aeromonas	Aeromonas spp.
bacteria	aphagocytophilum	Anaplasma phagocytophilum
bacteria	arcobacter	Arcobacter spp.
bacteria	bcereus	Bacillus cereus
bacteria	blicheniformis	Bacillus licheniformis
bacteria	bsubtilis	Bacillus subtilis
bacteria	bordetella	Bordetella spp.
bacteria	borrelia	Borrelia spp.
bacteria	bbacilliformis	Bartonella bacilliformis
bacteria	bhenselae	Bartonella henselae
bacteria	brachyspira	Brachyspira spp.
bacteria	brucella	Brucella spp.
bacteria	bcc	Burkholderia cepacia complex
bacteria	bpseudomallei	Burkholderia pseudomallei
bacteria	campylobacter	Campylobacter spp.
bacteria	liberibacter	Liberibacter solanacearum
bacteria	cmaltaromaticum	Carnobacterium maltaromaticum
bacteria	chlamydiales	Chlamydiales spp.
bacteria	cfreundii	Citrobacter freundii
bacteria	cbotulinum	Clostridium botulinum
bacteria	cdifficile	Clostridium difficile
bacteria	csepticum	Clostridium septicum
bacteria	cdiphtheriae	Corynebacterium diphtheriae
bacteria	cronobacter	Cronobacter spp.
bacteria	dnodosus	Dichelobacter nodosus
bacteria	ecloacae	Enterobacter cloacae
bacteria	edwardsiella	Edwardsiella spp.
bacteria	efaecalis	Enterococcus faecalis
bacteria	efaecium	Enterococcus faecium
bacteria	escherichia	Escherichia spp.
bacteria	fpsychrophilum	Flavobacterium psychrophilum
bacteria	gallibacterium	Gallibacterium anatis
bacteria	hinfluenzae	Haemophilus influenzae
bacteria	hparasuis	Haemophilus parasuis
bacteria	hcinaedi	Helicobacter cinaedi
bacteria	helicobacter	Helicobacter pylori
bacteria	hsuis	Helicobacter suis
bacteria	kaerogenes	Klebsiella aerogenes
bacteria	koxytoca	Klebsiella oxytoca
bacteria	lsalivarius	Lactobacillus salivarius
bacteria	leptospira	Leptospira spp.
bacteria	mcanis	Macrococcus canis
bacteria	mcaseolyticus	Macrococcus caseolyticus
bacteria	mhaemolytica	Mannheimia haemolytica
bacteria	mplutonius	Melissococcus plutonius
bacteria	mycobacteria	Mycobacteria spp.
bacteria	mabscessus	Mycobacterium abscessus complex
bacteria	magalactiae	Mycoplasma agalactiae
bacteria	mbovis	Mycoplasma bovis
bacteria	mhyopneumoniae	Mycoplasma hyopneumoniae
bacteria	mhyorhinis	Mycoplasma hyorhinis
bacteria	miowae	Mycoplasma iowae
bacteria	mpneumoniae	Mycoplasma pneumoniae
bacteria	msynoviae	Mycoplasma synoviae
bacteria	neisseria	Neisseria spp.
bacteria	oralstrep	Oral Streptococcus spp.
bacteria	otsutsugamushi	Orientia tsutsugamushi
bacteria	orhinotracheale	Ornithobacterium rhinotracheale
bacteria	plarvae	Paenibacillus larvae
bacteria	pmultocida	Pasteurella multocida
bacteria	ppentosaceus	Pediococcus pentosaceus
bacteria	pdamselae	Photobacterium damselae
bacteria	psalmonis	Piscirickettsia salmonis
bacteria	pgingivalis	Porphyromonas gingivalis
bacteria	pacnes	Propionibacterium acnes
bacteria	paeruginosa	Pseudomonas aeruginosa
bacteria	pfluorescens	Pseudomonas fluorescens
bacteria	pputida	Pseudomonas putida
bacteria	rhodococcus	Rhodococcus equi
bacteria	ranatipestifer	Riemerella anatipestifer
bacteria	sinorhizobium	Sinorhizobium spp.
bacteria	salmonella	Salmonella spp.
bacteria	saureus	Staphylococcus aureus
bacteria	sepidermidis	Staphylococcus epidermidis
bacteria	shaemolyticus	Staphylococcus haemolyticus
bacteria	shominis	Staphylococcus hominis
bacteria	spseudintermedius	Staphylococcus pseudintermedius
bacteria	smaltophilia	Stenotrophomonas maltophilia
bacteria	sagalactiae	Streptococcus agalactiae
bacteria	sbsec	Streptococcus bovis/equinus complex
bacteria	scanis	Streptococcus canis
bacteria	sdysgalactiae	Streptococcus dysgalactiae
bacteria	sgallolyticus	Streptococcus gallolyticus
bacteria	spneumoniae	Streptococcus pneumoniae
bacteria	spyogenes	Streptococcus pyogenes
bacteria	ssuis	Streptococcus suis
bacteria	sthermophilus	Streptococcus thermophilus
bacteria	suberis	Streptococcus uberis
bacteria	szooepidemicus	Streptococcus zooepidemicus
bacteria	streptomyces	Streptomyces spp.
bacteria	taylorella	Taylorella spp.
bacteria	tenacibaculum	Tenacibaculum spp.
bacteria	tpallidum	Treponema pallidum subsp. pallidum
bacteria	ureaplasma	Ureaplasma spp.
bacteria	vibrio	Vibrio spp.
bacteria	vcholerae	Vibrio cholerae
bacteria	vparahaemolyticus	Vibrio parahaemolyticus
bacteria	vtapetis	Vibrio tapetis
bacteria	vvulnificus	Vibrio vulnificus
bacteria	wolbachia	Wolbachia spp.
bacteria	xfastidiosa	Xylella fastidiosa
bacteria	ypseudotuberculosis	Yersinia pseudotuberculosis
bacteria	yersinia	Yersinia spp.
bacteria	yruckeri	Yersinia ruckeri
eukarya	afumigatus	Aspergillus fumigatus
eukarya	blastocystis	Blastocystis sp.
eukarya	calbicans	Candida albicans
eukarya	cglabrata	Candida glabrata
eukarya	ckrusei	Candida krusei
eukarya	ctropicalis	Candida tropicalis
eukarya	csinensis	Clonorchis sinensis
eukarya	kseptempunctata	Kudoa septempunctata
eukarya	sparasitica	Saprolegnia parasitica
eukarya	tvaginalis	Trichomonas vaginalis
other	bacteriophages	Bacteriophage MLST
other	bburgdorferi	Borrelia burgdorferi MLSA
other	plasmid	Plasmid MLST