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
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Characterization of a pESI-like plasmid and analysis of multidrug-resistant Salmonella enterica Infantis isolates in England and Wales.
Winnie W Y Lee,Winnie W Y Lee,Jennifer Mattock,David R. Greig,David R. Greig,Gemma C. Langridge,David Baker,Samuel J. Bloomfield,Alison E. Mather,Alison E. Mather,John Wain,John Wain,Andrew M. Edwards,Hassan Hartman,Timothy J. Dallman,Timothy J. Dallman,Marie Anne Chattaway,Satheesh Nair +17 more
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Dynamics of extended-spectrum cephalosporin resistance genes in Escherichia coli from Europe and North America
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Genomic features of an Escherichia coli ST156 strain harboring chromosome-located mcr-1 and plasmid-mediated blaNDM-5
Yanfeng Lin,Lang Yang,Lanfen Lu,Kaiying Wang,Jinhui Li,Peihan Li,Yuqi Liu,Xuelin Liu,Peng Li,Hongbin Song +9 more
TL;DR: W Whole genome sequencing and analysis showed that GZEC065 belonged to sequence type ST156 and contained three different plasmids with multiple resistance genes, such as mcr-1, blaNDM-5 and blaTEM-1.
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