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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Genomics for Molecular Epidemiology and Detecting Transmission of Carbapenemase-Producing Enterobacterales in Victoria, Australia, 2012 to 2016
Norelle L Sherry,Courtney R Lane,Jason C Kwong,Mark B. Schultz,Michelle Sait,Kerrie Stevens,Susan A Ballard,Anders Gonçalves da Silva,Torsten Seemann,Claire L. Gorrie,Timothy P. Stinear,Deborah A Williamson,Judith Brett,Annaliese van Diemen,Marion Easton,Benjamin P Howden +15 more
TL;DR: Systematic application of genomics has uncovered the emergence of polyclonal CPE as a significant threat in Australia, providing important insights to inform local public health guidelines and interventions.
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The phylogenetic landscape and nosocomial spread of the multidrug-resistant opportunist Stenotrophomonas maltophilia
Matthias I. Gröschel,Conor J. Meehan,Ivan Barilar,Margo Diricks,Aitor Gonzaga,Matthias Steglich,Oscar Conchillo-Solé,Isabell-Christin Scherer,Uwe Mamat,Christian F. Luz,Katrien De Bruyne,Christian Utpatel,Daniel Yero,Isidre Gibert,Xavier Daura,Xavier Daura,Stefanie Kampmeier,Nurdyana Binte Abdul Rahman,Michael Kresken,Tjip S. van der Werf,Ifey Alio,Wolfgang R. Streit,Kai Zhou,Kai Zhou,Thomas Schwartz,John W. A. Rossen,Maha R. Farhat,Ulrich E. Schaible,Ulrich Nübel,Jan Rupp,Joerg Steinmann,Stefan Niemann,Thomas Kohl +32 more
TL;DR: An international collection of the emerging, multidrug-resistant, opportunistic pathogen Stenotrophomonas maltophilia from 22 countries is analyzed to infer population structure and clonality at a global level and find evidence for intra-hospital transmission.
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Heterogeneous and Flexible Transmission of mcr-1 in Hospital-Associated Escherichia coli
Yingbo Shen,Zuowei Wu,Yang Wang,Rong Zhang,Hongwei Zhou,Shaolin Wang,Lei Lei,Mei Li,Mei Li,Jiachang Cai,Jonathan M. Tyrrell,Guo-Bao Tian,Congming Wu,Qijing Zhang,Jianzhong Shen,Timothy R. Walsh,Zhangqi Shen +16 more
TL;DR: It is indicated that mcr-1 is heterogeneously disseminated in both commensal and pathogenic strains of E. coli, suggest the high flexibility of this gene in its association with diverse genetic backgrounds of the hosts, and provide new insights into the genome epidemiology of mCR-1 among hospital-associated E.ccoli strains.
Journal ArticleDOI
Genomic and Molecular Characterization of Clinical Isolates of Enterobacteriaceae Harboring mcr-1 in Colombia, 2002 to 2016
Sandra Yamile Saavedra,Lorena Diaz,Lorena Diaz,Magdalena Wiesner,Adriana Correa,Stefany Alejandra Arévalo,Jinnethe Reyes,Jinnethe Reyes,Andrea Melissa Hidalgo,Elsa De La Cadena,Marcela Perenguez,Lucy Angeline Montaño,Javier Ardila,Rafael Rios,María Victoria Ovalle,Paula Lucía Díaz,Paola Porras,Maria V. Villegas,Cesar A. Arias,Cesar A. Arias,Mauricio Beltrán,Carolina Duarte +21 more
TL;DR: The results indicate that mcr-1 is circulating in clinical isolates of colistin-resistant Enterobacteriaceae in Colombia and is mainly harbored in transferable plasmids.
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Co-occurrence of Variants of mcr-3 and mcr - 8 Genes in a Klebsiella pneumoniae Isolate From Laos.
TL;DR: Five colistin-resistant Klebsiella pneumoniae strains from Laos and Thailand were analyzed by Next Generation Sequencing (NGS) approaches to determine theircolistin resistance mechanisms, resulting in the first description of the novel variants mcr-3.21, mcr -3.26, mCr-3-dgkA- ISKpn40, andmcr-8.3 genes.
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