In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing
Alessandra Carattoli,Ea Zankari,Aurora García-Fernández,Mette Voldby Larsen,Ole Lund,Laura Villa,Frank Møller Aarestrup,Henrik Hasman +7 more
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.read more
Citations
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Acquisition of genomic elements were pivotal for the success of Escherichia coli ST410.
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Genomic investigation of a suspected Klebsiella pneumoniae outbreak in a neonatal care unit in sub-Saharan Africa.
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TL;DR: In this article, a suspected outbreak of multi-drug-resistant Klebsiella pneumoniae was investigated using genomic characterisation, and the strain sequence types, plasmid types, virulence and resistance genes were identified.
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Prevalence and characteristics of the mcr-1 gene in retail meat samples in Zhejiang Province, China
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Antimicrobial‐Resistant E. coli from Surface Waters in Southwest Ontario Dairy Farms
Gurleen Taggar,Muhammad Attiq Rehman,Xianhua Yin,Dion Lepp,Kim Ziebell,Patrick Handyside,Patrick Boerlin,Moussa S. Diarra +7 more
TL;DR: It is shown that untreated surface water sources contain antimicrobial-resistant which may serve as a reservoir of AMR that could be disseminated through horizontal gene transfer, which is another reason why effective water treatment before usage should be routinely done on dairy farm operations.
Book ChapterDOI
Plasmids and Their Hosts
Masaki Shintani,Haruo Suzuki +1 more
TL;DR: Factors that determine and affect the host ranges of plasmids are reviewed, including features of replication, maintenance, conjugative transfer, and the effects on host fitness caused by plasmid carriage.
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