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Protocols

pMLST specifications

Information


Unique identifier OMICS_22069
Name pMLST
Alternative name plasmid Multilocus Sequence Typing
Interface Web user interface
Restrictions to use None
Input data A sequence in one-letter nucleotide code or in a file.
Input format FASTA
Output data The sequence type (ST) that the server associated to the dna sequence you submitted, a table containing more detailed results for each gene and allele, a summary of the setting used in the executed, result files for download and an optional graphical description of the alignment for each of the loci against the allele on the selected mlst scheme that had the best alignment score.
Biological technology Illumina, Roche
Computer skills Basic
Version 1.4
Stability Stable
Maintained Yes

Maintainer


  • person_outline Henrik Hasman

Additional information


https://cge.cbs.dtu.dk/services/pMLST/instructions.php

Publication for plasmid Multilocus Sequence Typing

pMLST citations

 (78)
library_books

Draft Genome Sequence of Escherichia coli KL53

2018
Genome Announc
PMCID: 5876489
PMID: 29599162
DOI: 10.1128/genomeA.00220-18

[…] .93% identity] by PlasmidFinder (https://cge.cbs.dtu.dk/services/PlasmidFinder/). An exact match of IncI1 plasmid genes repl1-ardA-trbA-sogS-pilL with database alleles 1-4-17-1-3 was determined using pMLST (http://pubmlst.org/plasmid/).The KL53 strain includes multiple heavy metal resistance genes for zinc (znuC, znuB, zupT, and zntB), copper (copA to copD), a cation efflux system for silver and o […]

call_split

Draft Genome Sequence of the First New Delhi Metallo β Lactamase (NDM 1) Producing Escherichia coli Strain Isolated in Peru

2018
Genome Announc
PMCID: 5876490
PMID: 29599159
DOI: 10.1128/genomeA.00199-18
call_split See protocol

[…] me Annotation Pipeline (PGAP) v.3.2, whereas whole-genome sequence data were evaluated through bioinformatics tools (i.e., ResFinder v.3.0, VirulenceFinder v.1.5, MLST v.1.8, PlasmidFinder v.1.3, and pMLST v.1.4) available from the Center for Genomic Epidemiology (http://www.genomicepidemiology.org/).Multilocus sequence typing (MLST) showed that carbapenem-resistant E. coli 2ECMBL belongs to seque […]

library_books

Impact of human associated Escherichia coli clonal groups in Antarctic pinnipeds: presence of ST73, ST95, ST141 and ST131

2018
Sci Rep
PMCID: 5856829
PMID: 29549276
DOI: 10.1038/s41598-018-22943-0

[…] bitbucket.org/enterobase/enterobase-web/wiki/Escherichia%20Statistics. Antimicrobial resistances, plasmid detection and typing were in silico determined by using ResFinder V2.1 and PlasmidFinder 1.3./pMLST 1.4., respectively. […]

library_books

Complete Nucleotide Sequence of an Escherichia coli Sequence Type 410 Strain Carrying blaNDM 5 on an IncF Multidrug Resistance Plasmid and blaOXA 181 on an IncX3 Plasmid

2018
Genome Announc
PMCID: 5794949
PMID: 29437102
DOI: 10.1128/genomeA.01542-17

[…] tion using Subsystem Technology server (RAST [http://rast.nmpdr.org]).Plasmid replicons were detected using PlasmidFinder version 1.3, and incompatibility group F (IncF) subtyping was performed using pMLST version 1.4 (). blaNDM-5 was detected on a 110,959-bp plasmid (pAMA1167-NDM-5) belonging to IncF and pMLST type [F1:A1:B49]. Besides blaNDM-5, 16 other resistance genes were detected on pAMA1167 […]

library_books

Extended spectrum beta lactamase (ESBL) producing Escherichia coli and Acinetobacter baumannii among horses entering a veterinary teaching hospital: The contemporary 'Trojan Horse'

2018
PLoS One
PMCID: 5790241
PMID: 29381714
DOI: 10.1371/journal.pone.0191873

[…] mid replicon detection revealed a high variety of different types of plasmids including Inc/Rep types IncFIA/B and IncFII, which are commonly found in ESBL-producing E. coli. One IncFIA plasmid type (pMLST type F-:A8:B-) was present in 15 of the 41 tested E. coli assigned to 13 different STs, originating from 15 different animals. However, the genetic makeup of resistance genes differed between th […]

library_books

In Situ Analyses Directly in Diarrheal Stool Reveal Large Variations in Bacterial Load and Active Toxin Expression of Enterotoxigenic Escherichia coli and Vibrio cholerae

2018
PMCID: 5784243
PMID: 29404412
DOI: 10.1128/mSphere.00517-17

[…] To perform initial functional analysis, we used the CGE pipeline v 1.1 (), which performs resistance gene prediction using ResFinder, in silico MLST, plasmid prediction, and pMLST. Resistance gene prediction was also performed by ARG-annot (http://en.mediterranee-infection.com/article.php?laref=283%26titre=arg-annot).Whole-genome alignment was performed and visualized usi […]

Citations

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pMLST institution(s)
Department of Infectious, Parasitic and Immuno-Mediated Diseases, Istituto Superiore di Sanità, Rome, Italy; Danish Technical University, National Food Institute, Division for Epidemiology and Microbial Genomics, Lyngby, Denmark; Danish Technical University, Center for Biological Sequence Analysis, Department of Systems Biology, Lyngby, Denmark
pMLST funding source(s)
Supported by the Center for Genomic Epidemiology grant 09-067103/DSF, the Danish Council for Strategic Research, and the InterOmics project (PB.P05), funded by the Italian Ministry of Education, University and Research (MIUR).

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