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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Journal ArticleDOI
Characterization of antimicrobial resistance genes in Enterobacteriaceae carried by suburban mesocarnivores and locally owned and stray dogs.
Katherine E. L. Worsley-Tonks,Elizabeth Miller,Stanley D. Gehrt,Shane C. McKenzie,Dominic A. Travis,Timothy J. Johnson,Meggan E. Craft +6 more
TL;DR: Findings from this pilot investigation suggest that the microbial communities of suburban mesocarnivores and stray dogs can host ARGs that can confer resistance to several antimicrobials used in human and veterinary medicine.
Journal ArticleDOI
Conjugal Transfer, Whole-Genome Sequencing, and Plasmid Analysis of Four mcr-1-Bearing Isolates from U.S. Patients.
Wenming Zhu,Adrian Lawsin,Rebecca L. Lindsey,Dhwani Batra,Kristen Knipe,Byong Kwon Yoo,K. Allison Perry,Lori A. Rowe,David Lonsway,Maroya Spalding Walters,J. Kamile Rasheed,Alison Laufer Halpin +11 more
TL;DR: Results indicate that the mcr-1-bearing plasmids in this study were highly transferable in vitro and stable in the recipients.
Journal ArticleDOI
Characterization of blaNDM-1- and blaSHV-12-Positive IncX3 Plasmid in an Enterobacter Hormaechei New Sequence Type 1000 from China.
Peihan Li,Peihan Li,Yanfeng Lin,Yanfeng Lin,Xiaofeng Hu,Yuqi Liu,Yuqi Liu,Mei Xue,Lang Yang,Lang Yang,Jinhui Li,Lei Zha,Kaiying Wang,Kezong Qi,Shaofu Qiu,Peng Li,Hongbin Song +16 more
TL;DR: The rapid spread of the recurrent IncX3 plasmid highlights the need for continuous surveillance of the NDM-1 dissemination and the presence of mutations in existing carbapenem-resistant genes may generate potential new variants and raise serious challenges for clinical treatment.
Journal ArticleDOI
Whole-Genome Sequence of Pseudomonas xanthomarina Strain UASWS0955, a Potential Biological Agent for Agricultural and Environmental Uses
Julien Crovadore,Bastien Cochard,Gautier Calmin,Romain Chablais,Torsten Schulz,François Lefort +5 more
TL;DR: The whole-genome shotgun sequence of the strain UASWS0955 of the species Pseudomonas xanthomarina, isolated from sewage sludge is reported, which is the second genome registered for this species, considered as a promising resource for agriculture and bioremediation of contaminated soils.
References
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