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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oriTfinder: a web-based tool for the identification of origin of transfers in DNA sequences of bacterial mobile genetic elements.
TL;DR: OriTfinder may contribute to meeting the increasing demands of re-annotations for bacterial conjugative, mobilizable or non-transferable elements and aid in the rapid risk accession of disease-relevant trait dissemination in pathogenic bacteria of interest.
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Plasmid classification in an era of whole-genome sequencing: application in studies of antibiotic resistance epidemiology.
Alex Orlek,Alex Orlek,Nicole Stoesser,Muna F. Anjum,Muna F. Anjum,Michel Doumith,Matthew J. Ellington,Matthew J. Ellington,Tim E. A. Peto,Tim E. A. Peto,Derrick W. Crook,Derrick W. Crook,Neil Woodford,Neil Woodford,A. Sarah Walker,A. Sarah Walker,Hang Phan,Hang Phan,Anna E. Sheppard,Anna E. Sheppard +19 more
TL;DR: The application of plasmid classification in WGS-based studies of antibiotic resistance epidemiology is discussed, and novel in silico plasmids analysis tools are highlighted.
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Genomic Epidemiology: Whole-Genome-Sequencing-Powered Surveillance and Outbreak Investigation of Foodborne Bacterial Pathogens.
TL;DR: Routine, real-time, and widespread application of whole-genome sequencing of foodborne bacterial pathogens a realistic and superior alternative to traditional subtyping methods is on the horizon.
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Linking the resistome and plasmidome to the microbiome.
TL;DR: It is demonstrated that the in vivo proximity-ligation method Hi-C can reconstruct a known plasmid-host association from a wastewater community, and identify the in situ host range of ARGs, plasmids, and integrons by physically linking them to their host chromosomes.
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Balancing mcr-1 expression and bacterial survival is a delicate equilibrium between essential cellular defence mechanisms.
Qiu E. Yang,Mei Li,Owen B. Spiller,Diego O. Andrey,Diego O. Andrey,Philip Hinchliffe,Hui Li,Craig MacLean,Pannika R. Niumsup,Lydia C. Powell,Manon F. Pritchard,Andrei Papkou,Yingbo Shen,Edward Portal,Kirsty Sands,James Spencer,Uttapoln Tansawai,David Thomas,Shaolin Wang,Yang Wang,Jianzhong Shen,Timothy R. Walsh +21 more
TL;DR: The results show that the bacterium is challenged to find a delicate equilibrium between expression of MCR-1-mediated colistin resistance and minimalizing toxicity and thus ensuring cell survival, and can reduce virulence in a Galleria mellonella infection model.
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