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Open AccessJournal ArticleDOI

In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing

TLDR
Two easy-to-use Web tools for in silico detection and characterization of whole-genome sequence (WGS) and whole-plasmid sequence data from members of the family Enterobacteriaceae are designed and developed.
Abstract
In the work presented here, we designed and developed two easy-to-use Web tools for in silico detection and characterization of whole-genome sequence (WGS) and whole-plasmid sequence data from members of the family Enterobacteriaceae. These tools will facilitate bacterial typing based on draft genomes of multidrug-resistant Enterobacteriaceae species by the rapid detection of known plasmid types. Replicon sequences from 559 fully sequenced plasmids associated with the family Enterobacteriaceae in the NCBI nucleotide database were collected to build a consensus database for integration into a Web tool called PlasmidFinder that can be used for replicon sequence analysis of raw, contig group, or completely assembled and closed plasmid sequencing data. The PlasmidFinder database currently consists of 116 replicon sequences that match with at least at 80% nucleotide identity all replicon sequences identified in the 559 fully sequenced plasmids. For plasmid multilocus sequence typing (pMLST) analysis, a database that is updated weekly was generated from www.pubmlst.org and integrated into a Web tool called pMLST. Both databases were evaluated using draft genomes from a collection of Salmonella enterica serovar Typhimurium isolates. PlasmidFinder identified a total of 103 replicons and between zero and five different plasmid replicons within each of 49 S . Typhimurium draft genomes tested. The pMLST Web tool was able to subtype genomic sequencing data of plasmids, revealing both known plasmid sequence types (STs) and new alleles and ST variants. In conclusion, testing of the two Web tools using both fully assembled plasmid sequences and WGS-generated draft genomes showed them to be able to detect a broad variety of plasmids that are often associated with antimicrobial resistance in clinically relevant bacterial pathogens.

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Journal ArticleDOI

The Current Landscape of Antibiotic Resistance of Salmonella Infantis in Italy: The Expansion of Extended-Spectrum Beta-Lactamase Producers on a Local Scale

TL;DR: The analysis of strains from Abruzzo and Molise and the publicly available Italian S. Infantis sequences revealed a dramatic increase in the number of identified AMR genes in the strains isolated after 2011, likely due to the acquisition of the megaplasmid.
Journal ArticleDOI

Detection of a New Resistance-Mediating Plasmid Chimera in a bla(OXA-48)-Positive Klebsiella pneumoniae Strain at a German University Hospital

TL;DR: This study investigates the plasmid-resistome of seven blaOXA-48 gene-carrying Klebsiella pneumoniae isolates, which were isolated between 2013 and 2014 at the University Medical Center in Göttingen, Germany and contributes a piece in the puzzle of molecular epidemiology of resistance gene- Carrying plasmids in K. pneumoniae in Germany.
Journal ArticleDOI

Complete Genome Sequence of Avian Pathogenic Escherichia coli Strain APEC O2-211.

TL;DR: The genome sequence of APEC O2-211 is reported, a sequence type 117 (ST117) strain isolated from a diseased chicken that causes colibacillosis and leads to multimillion-dollar losses annually.
Dissertation

Dynamics of insertion sequences in bacterial genomes

Jane Hawkey
TL;DR: A novel method for detecting insertion sequences from short read sequencing data and applying it to examine the role of IS and antibiotic resistance in multiple bacterial pathogens, to demonstrate the utility of using ISMapper to track the movement of IS in bacterial genomes, and how IS can contribute to the spread of antibiotic resistance.
Journal ArticleDOI

Resistome Analysis of a Carbapenemase (OXA-48)-Producing and Colistin-Resistant Klebsiella pneumoniae Strain.

TL;DR: Carbapenemase-producing Klebsiella pneumoniae are increasingly reported worldwide and the number of cases is increasing.
References
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Journal ArticleDOI

Identification of acquired antimicrobial resistance genes

TL;DR: A web server providing a convenient way of identifying acquired antimicrobial resistance genes in completely sequenced isolates was created, and the method was evaluated on WGS chromosomes and plasmids of 30 isolates.
Journal ArticleDOI

Identification of plasmids by PCR-based replicon typing

TL;DR: Results indicated that the inc/rep PCR method demonstrates high specificity and sensitivity in detecting replicons on reference plasmids and also revealed the presence of recurrent and common plasmid in epidemiologically unrelated Salmonella isolates of different serotypes.
Journal ArticleDOI

BIGSdb: Scalable analysis of bacterial genome variation at the population level

TL;DR: The Bacterial Isolate Genome Sequence Database (BIGSDB) represents a freely available resource that will assist the broader community in the elucidation of the structure and function of bacteria by means of a population genomics approach.
Journal ArticleDOI

Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria

TL;DR: A Web-based method for MLST of 66 bacterial species based on whole-genome sequencing data that enables investigators to determine the sequence types of their isolates on the basis of WGS data.
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