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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A prolonged multispecies outbreak of IMP-6 carbapenemase-producing Enterobacterales due to horizontal transmission of the IncN plasmid
Takuya Yamagishi,Mari Matsui,Tsuyoshi Sekizuka,Hiroaki Ito,Munehisa Fukusumi,Tomoko Uehira,Miyuki Tsubokura,Yoshihiko Ogawa,Atsushi Miyamoto,Shoji Nakamori,Akio Tawa,Takahisa Yoshimura,Hideki Yoshida,Hidetetsu Hirokawa,Satowa Suzuki,Tamano Matsui,Keigo Shibayama,Makoto Kuroda,Kazunori Oishi +18 more
TL;DR: Plasmid analysis of isolates in an outbreak of IMP-6-CPE suggested interspecies gene transmission and helped to clarify hidden epidemiological links between cases.
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PhageLeads: Rapid Assessment of Phage Therapeutic Suitability Using an Ensemble Machine Learning Approach
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TL;DR: A tool capable of checking all three conditions required for the selection of suitable therapeutic phage candidates, including the presence of temperate markers, antimicrobial resistance genes, and virulence genes is developed.
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Antibiotic resistance plasmids cointegrated into a megaplasmid harbouring the blaOXA-427 carbapenemase gene
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Whole-Genome Sequencing and Concordance Between Antimicrobial Susceptibility Genotypes and Phenotypes of Bacterial Isolates Associated with Bovine Respiratory Disease
Joseph R. Owen,Noelle R. Noyes,Amy E. Young,Daniel J. Prince,Patricia C Blanchard,Terry W. Lehenbauer,Sharif S. Aly,Jessica H Davis,Sean O'Rourke,Zaid Abdo,Keith E. Belk,Michael R. Miller,Paul S. Morley,Alison L. Van Eenennaam +13 more
TL;DR: Antimicrobial susceptibility phenotypes are needed to complement genomically predicted antibiotic resistance gene genotypes to better understand how the presence of antibiotic resistance genes within a given bacterial species could potentially impact optimal bovine respiratory disease treatment and morbidity/mortality outcomes.
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Comparative genomic analysis reveals a high prevalence of inter-species in vivo transfer of carbapenem-resistance plasmids in patients with haematological malignancies.
Kaan Kocer,Sébastien Boutin,Alexander H. Dalpke,Alexander H. Dalpke,Klaus Heeg,Nico T. Mutters,Nico T. Mutters,Dennis Nurjadi +7 more
TL;DR: Better understanding of HGT will help optimizing containment measures and may guide antibiotic stewardship programs, and give insight into the occurrence of natural in vivo HGT in a clinical setting.
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