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Protocols

PubMLST specifications

Information


Unique identifier OMICS_20683
Name PubMLST
Alternative name Public MultiLocus Sequence Typing
Restrictions to use None
Community driven No
Data access File download, Browse, Application programming interface
User data submission Allowed
Maintained Yes

Subtools


  • BIGSdb
  • Tpallidum

Maintainer


  • person_outline Keith Jolley

Publications for Public MultiLocus Sequence Typing

PubMLST citations

 (522)
library_books

Acquisition and dissemination of cephalosporin resistant E. coli in migratory birds sampled at an Alaska landfill as inferred through genomic analysis

2018
Sci Rep
PMCID: 5943298
PMID: 29743625
DOI: 10.1038/s41598-018-25474-w

[…] typing scheme, was performed using a previously described methodology. The program SRST2 (v0.2.0) was used to identify MLST types by matching reads to the Escherichia coli #1 database downloaded from pubmlst.org. […]

library_books

Genome based analysis of Carbapenemase producing Klebsiella pneumoniae isolates from German hospital patients, 2008 2014

2018
PMCID: 5930415
PMID: 29744043
DOI: 10.1186/s13756-018-0352-y

[…] strains was conducted by wzi gene sequencing extracted from contigs derived from de novo assembly [] and using the websites of the Pasteur Institute (http://bigsdb.pasteur.fr/perl/bigsdb/bigsdb.pl?db=pubmlst_klebsiella_seqdef_public&page=downloadAlleles&scheme_id=4&render=1; last access 25/04/2018). Furthermore, all sequenced genomes were screened for the presence of the following virulence genes […]

library_books

Heavy Metal Susceptibility of Escherichia coli Isolated from Urine Samples from Sweden, Germany, and Spain

2018
Antimicrob Agents Chemother
PMCID: 5923176
PMID: 29530862
DOI: 10.1128/AAC.00209-18

[…] d using FastQC software (v0.11.4; http://www.bioinformatics.babraham.ac.uk) according to the developers' recommendations. Species identification was performed using the rMLST tool available at http://pubmlst.org/rmlst. This tool searches for exact matches to sequences defined in the rMLST allele library, which are derived from more than 7,000 bacterial species. Allelic matches are cross-referenced […]

library_books

A Natural Mouse Model for Neisseria Colonization

2018
Infect Immun
PMCID: 5913851
PMID: 29440372
DOI: 10.1128/IAI.00839-17

[…] Tblastn searches were conducted using TBLASTN 2.7.1+ (, ). Protein query sequences from N. meningitidis and N. gonorrhoeae were used to search N. musculi strain AP2031's genome sequence (PubMLST identifier [ID], 29520 []). Many N. meningitidis queries used for the analysis were retrieved from the Protegen protective antigen database (). The accession numbers for the commensal human-dw […]

call_split

Draft Genome Sequence of a Highly Resistant Streptococcus pneumoniae Serotype 15A Strain Isolated from Blood

2018
Genome Announc
PMCID: 5908931
PMID: 29674530
DOI: 10.1128/genomeA.00167-18
call_split See protocol

[…] in SS40_16 isolated in 2016 from a blood sample from a 19-month-old female from a government hospital in Malaysia. The strain belongs to serotype 15A and sequence type 1591 (ST1591) (as determined by PubMLST [https://pubmlst.org/]). SS40_16 is a multidrug-resistant strain with resistance to penicillin (MIC, ≥2 µg/ml), tetracycline, and trimethoprim-sulfamethoxazole.The genome was sequenced using a […]

library_books

Emergence of Vancomycin Resistant Enterococcus faecium at an Australian Hospital: A Whole Genome Sequencing Analysis

2018
Sci Rep
PMCID: 5908837
PMID: 29674657
DOI: 10.1038/s41598-018-24614-6

[…] e 4 consisted of isolates which belonged to ST203 (n = 4). The 10 isolates in Phylogenetic Clade 5, which lack the pstS gene, were assigned to a recently-designated MLST sequence type, ST1421, by the PubMLST database (https://pubmlst.org/efaecium/). […]

Citations

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PubMLST institution(s)
Department of Zoology, Peter Medawar Building for Pathogen Research, University of Oxford, South Parks Road, Oxford, UK
PubMLST funding source(s)
Supported by a Wellcome Trust Biomedical Resource Grant (104992) and the European Community grant FP7-278864-2 (PathoNgenTrace).

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