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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Ciprofloxacin facilitates the transfer of XDR plasmids from commensal E. coli into epidemic fluoroquinolone-resistant Shigella sonnei
P. T. Pham,To Nguyen Thi Nguyen,Duong Vu Thuy,F. Alcock,Christine J. Boinett,Ho Ngoc Dan Thanh,Ha Thanh Tuyen,G Thwaites,Maia A. Rabaa,Stephen Baker,Stephen Baker +10 more
TL;DR: In a setting with high antimicrobial use and a high prevalence of AMR commensals, cipR S. sonnei may be propelled towards pan-resistance by adherence to outdated international treatment guidelines and provides essential data to restrict the use of ciprofloxacin globally.
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High plasmidome diversity of extended-spectrum beta-lactam-resistant Escherichia coli isolates collected during one year in one community hospital.
TL;DR: In this paper , the authors combined 2nd and 3rd generation sequencing techniques to reconstruct the plasmidome of overall 97 clinical ESBL-E. coli isolates, highlighting the enormous plasmids diversity in respect to size, replicon-type and genetic content.
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ProkEvo: an automated, reproducible, and scalable framework for high-throughput bacterial population genomics analyses
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Draft genome sequences of PDR and XDR Klebsiella pneumoniae belonging to high-risk CG258 isolated from a Brazilian tertiary hospital.
Louise Cerdeira,Rafael Nakamura-Silva,Mariana Oliveira-Silva,Bruna Fuga,Quézia Moura,Eliana Carolina Vespero,Nilton Lincopan,André Pitondo-Silva +7 more
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Genomic Characterization of Multidrug-Resistant Escherichia coli BH100 Sub-strains.
Rodrigo Dias de Oliveira Carvalho,Flávia Figueira Aburjaile,Flávia Figueira Aburjaile,Marcus Vinicius Canário,Andréa M. A. Nascimento,Edmar Chartone-Souza,Luís Cláudio Lima de Jesus,Andrey A. Zamyatnin,Andrey A. Zamyatnin,Bertram Brenig,Debmalya Barh,Preetam Ghosh,Aristóteles Góes-Neto,Henrique César Pereira Figueiredo,Siomar de Castro Soares,Rommel Thiago Jucá Ramos,Anne Cybelle Pinto,Vasco Azevedo +17 more
TL;DR: In this paper, the authors attempted to unravel the factors involved in the mobilization of virulence and drug-resistance genes by assessing genomic rearrangements in four BH100 sub-strains.
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