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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Global Epidemiology and Evolutionary History of Staphylococcus aureus ST45.
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TL;DR: The phylogenetic analyses suggest multiple acquisitions of the SCCmec element and key virulence factors throughout the evolution of the ST45 lineage.
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Emergence of High Level Carbapenem and Extensively Drug Resistant Escherichia coli ST746 Producing NDM-5 in Influent of Wastewater Treatment Plant, Seoul, South Korea.
TL;DR: In this article, high level carbapenem and extensively-drug resistant Escherichia coli strain N7, which produces a variant of New Delhi metallo--lactamase (NDM-5), was isolated from the influent of the Jungnang wastewater treatment plant located on Han river, Seoul, South Korea.
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Characterization of blaCTX-M-27/F1:A2:B20 Plasmids Harbored by Escherichia coli Sequence Type 131 Sublineage C1/H30R Isolates Spreading among Elderly Japanese in Nonacute-Care Settings.
Nao Matsuo,Rina Nonogaki,Michiko Hayashi,Jun-ichi Wachino,Masahiro Suzuki,Yoshichika Arakawa,Kumiko Kawamura +6 more
TL;DR: 29 blaCTX-M-27-harboring plasmids of Escherichia coli sequence type 131 (ST131) sublineage C1/H30R isolates from healthy individuals and long-term-care facility (LTCF) residents were characterized, suggesting their prevalence as a newly arising public health concern.
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Draft Genome Sequence of an Extended-Spectrum β-Lactamase-Producing Klebsiella oxytoca Strain Bearing mcr-9 from Qatar.
Clement K. M. Tsui,Clement K. M. Tsui,Clement K. M. Tsui,Sathyavathi Sundararaju,Hassan Al Mana,Hassan Al Mana,Mohammad Rubayet Hasan,Mohammad Rubayet Hasan,Patrick Tang,Patrick Tang,Andres Perez-Lopez,Andres Perez-Lopez +11 more
TL;DR: The draft genome of an extended-spectrum β-lactamase-producing K. oxytoca isolate harboring an mcr-9 gene, a recently discovered colistin resistance analog, from Qatar is reported and the sequence type and resistance mechanisms are predicted for the assembled genome.
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Transcriptional Landscape of a blaKPC-2 Plasmid and Response to Imipenem Exposure in Escherichia coli TOP10
Agnès B Jousset,Isabelle Rosinski-Chupin,Isabelle Rosinski-Chupin,Julie Takissian,Julie Takissian,Philippe Glaser,Philippe Glaser,Rémy A. Bonnin,Rémy A. Bonnin,Thierry Naas +9 more
TL;DR: Adaptive responses of E. coli to imipenem-induced stress are described, and plasmid-encoded genes that could be involved in resistance to stressful environments are identified.
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