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
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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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Genomic analysis of Escherichia coli strains isolated from diseased chicken in the Czech Republic.
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TL;DR: The results support the concept of local spread of virulent APEC clones, as well as of zoonotic potential of specific poultry-associated lineages, and highlight the need to investigate the possible source of these pathogenic strains.
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Molecular Characterization by Using Next-Generation Sequencing of Plasmids Containing blaNDM-7 in Enterobacteriaceae from Calgary, Canada
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TL;DR: The findings may indicate horizontal transmission within the health region, or it may indicate contact with individuals from areas of endemicity within the hospital setting, as patients infected or colonized with bacteria containing blaNDM-7 IncX3 plasmids generate infection control challenges.
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Expansion of KPC-producing Klebsiella pneumoniae with various mgrB mutations giving rise to colistin resistance: the role of ISL3 on plasmids.
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TL;DR: Investigation of the expansion of mgrB-mutated KPC-KP isolates found that transposition of insertion sequences from plasmids and subsequent clonal expansion may contribute to the emerging colistin resistance in KPC -KP.
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Stepwise evolution and convergent recombination underlie the global dissemination of carbapenemase-producing Escherichia coli.
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TL;DR: Lineages of CP-Ec have started to disseminate globally, however, their selection is a multistep process involving mutations, recombination, acquisition of antibiotic resistance genes, and selection by β-lactams from diverse families.
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Extended-spectrum β-lactamase-encoding genes are spreading on a wide range of Escherichia coli plasmids existing prior to the use of third-generation cephalosporins.
Catherine Branger,Alice Ledda,Typhaine Billard-Pomares,Benoît Doublet,Stéphanie Fouteau,Valérie Barbe,David Roche,Stéphane Cruveiller,Claudine Médigue,Miguel Castellanos,Dominique Decré,Laurence Drieux-Rouze,Olivier Clermont,Jérémy Glodt,Olivier Tenaillon,Axel Cloeckaert,Guillaume Arlet,Erick Denamur +17 more
TL;DR: Findings showed that ESBL-encoding genes have arrived on wide range of pre-existing plasmids and that the successful spread of blaCTX-M-15 seems to be favoured by the presence of well-adapted IncF plasmid that carry a Tn2-blaTEM-1 transposon.
References
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