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
Citations
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Clonal Dissemination of Enterobacter cloacae Harboring blaKPC-3 in the Upper Midwestern United States
Melissa Hargreaves,Kristin M. Shaw,Ginette Dobbins,Paula Snippes Vagnone,Jane Harper,Dave Boxrud,Ruth Lynfield,Maliha Aziz,Maliha Aziz,Lance B. Price,Lance B. Price,Kevin A. T. Silverstein,Jessica L. Danzeisen,Bonnie P. Youmans,Kyle A. Case,Srinand Sreevatsan,Timothy J. Johnson +16 more
TL;DR: The spread of this clone throughout the upper midwestern United States is unprecedented for E. cloacae and highlights the importance of continued surveillance to identify such threats to human health.
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Characteristics of Carbapenemase-Producing Enterobacteriaceae in Wastewater Revealed by Genomic Analysis.
Ryota Gomi,Tomonari Matsuda,Masaki Yamamoto,Pei Hsin Chou,Michio Tanaka,Satoshi Ichiyama,Minoru Yoneda,Yasufumi Matsumura +7 more
TL;DR: It is indicated that CPE with various carbapenemase-encoding genes in different genetic contexts were present in biologically treated wastewater, highlighting the need to monitor for antibiotic resistance in wastewater.
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Detection of Plasmid-Mediated Colistin Resistance, mcr-1 and mcr-2 Genes, in Salmonella spp. Isolated from Food at Retail in Belgium from 2012 to 2015
Cristina Garcia-Graells,Sigrid C. J. De Keersmaecker,Kevin Vanneste,B Pochet,Katie Vermeersch,Nancy H. C. Roosens,Katelijne Dierick,Nadine Botteldoorn +7 more
TL;DR: The presence of mCr-1 and the first mcr-2 gene in Salmonella ever isolated in the Belgian food chain is reported, although present at retail since 2012, the occurrence is low and sporadic.
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Multidrug-Resistant Salmonella enterica 4,[5],12:i:- Sequence Type 34, New South Wales, Australia, 2016-2017.
Alicia Arnott,Qinning Wang,Nathan L. Bachmann,Rosemarie Sadsad,Chayanika Biswas,Cristina Sotomayor,Peter Howard,Rebecca Rockett,Agnieszka Wiklendt,Jon Iredell,Vitali Sintchenko +10 more
TL;DR: These findings highlight the public health benefits of genome sequencing–guided surveillance for monitoring the spread of multidrug-resistant mobile genes and isolates.
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Genomic characterisation of clinical and environmental Pseudomonas putida group strains and determination of their role in the transfer of antimicrobial resistance genes to Pseudomonas aeruginosa
Silke Peter,Philipp Oberhettinger,Leonard Schuele,Leonard Schuele,Ariane G Dinkelacker,Wichard Vogel,Daniela Dörfel,Daniela Dörfel,Daniela Bezdan,Stephan Ossowski,Stephan Ossowski,Matthias Marschal,Jan Liese,Matthias Willmann +13 more
TL;DR: Evidence is provided that no exchange of comprehensive ARG harbouring mobile genetic elements had occurred between P. aeruginosa and P. putida group strains during the study period, thus eliminating the need to implement enhanced infection control measures for high-risk patients colonized with a blaVIM positiv P.Putida group strain.
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