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 dissection of Klebsiella pneumoniae infections in hospital patients reveals insights into an opportunistic pathogen
Claire L. Gorrie,Mirjana Mirceta,Ryan R. Wick,Louise M. Judd,Margaret M. C. Lam,Ryota Gomi,Iain J. Abbott,Nicholas R. Thomson,Richard A. Strugnell,Nigel F. Pratt,Jill S. Garlick,Kerrie Watson,Peter Hunter,David Pilcher,Steven McGloughlin,Denis Spelman,Kelly L. Wyres,Adam Jenney,Kathryn E. Holt +18 more
TL;DR: In this paper , the authors conducted a year-long prospective surveillance study of K. pneumoniae clinical isolates in hospital patients and revealed a diverse pathogen population, including other species within the K pneumoniae species complex.
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Acquisition of Plasmid with Carbapenem-Resistance Gene blaKPC2 in Hypervirulent Klebsiella pneumoniae, Singapore.
Yahua Chen,Kalisvar Marimuthu,Jeanette W. P. Teo,Indumathi Venkatachalam,Benjamin Pei Zhi Cherng,Liang De Wang,Sai Rama Sridatta Prakki,Weizhen Xu,Yi Han Tan,Lan Chi Nguyen,Tse Hsien Koh,Oon Tek Ng,Yunn-Hwen Gan +12 more
TL;DR: The convergence of carbapenem-resistance and hypervirulence genes in Klebsiella pneumoniae has led to the emergence of highly drug-resistant superbugs capable of causing invasive disease, and isolates from patients in Singapore hospitals during 2010–2015 found 18 isolates also harbored hypervirulent features.
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Genomic Analysis of Factors Associated with Low Prevalence of Antibiotic Resistance in Extraintestinal Pathogenic Escherichia coli Sequence Type 95 Strains.
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Diversity and Antibiotic Susceptibility of Acinetobacter Strains From Milk Powder Produced in Germany
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TL;DR: The strains in this study were generally not resistant to the clinically relevant antibiotics, especially tobramycin, ciprofloxacin, cefepime, and meropenem, suggesting that the food route probably poses only a low risk for multidrug resistant Acinetobacter strains or resistance genes.
Journal ArticleDOI
Elucidation of quantitative structural diversity of remarkable rearrangement regions, shufflons, in IncI2 plasmids.
Tsuyoshi Sekizuka,Michiko Kawanishi,Mamoru Ohnishi,Ayaka Shima,Kengo Kato,Akifumi Yamashita,Mari Matsui,Satowa Suzuki,Makoto Kuroda +8 more
TL;DR: Findings indicate that remarkable rearrangement regions should be validated using both long-read and short-read sequencing data and that the structural variation of PilV in the shufflon might be closely related to phenotypic heterogeneity of plasmid-mediated transconjugation involved in horizontal gene transfer even in bacterial clonal populations.
References
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