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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High-resolution characterisation of ESBL/pAmpC-producing Escherichia coli isolated from the broiler production pyramid
Ilias Apostolakos,Claudia Feudi,Inga Eichhorn,Nicola Palmieri,Luca Fasolato,Stefan Schwarz,Alessandra Piccirillo +6 more
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Struggle To Survive: the Choir of Target Alteration, Hydrolyzing Enzyme, and Plasmid Expression as a Novel Aztreonam-Avibactam Resistance Mechanism.
TL;DR: A choir of target modification, hydrolyzing enzyme, and plasmid expression represents a novel, coordinated, complex antimicrobial resistance mechanism and also reflects the struggle of bacteria to survive under selection pressure imposed by antimicrobial agents.
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ESBL-Producing Klebsiella pneumoniae in the Broiler Production Chain and the First Description of ST3128.
TL;DR: In this paper, identical clones of SHV-2 -producing Klebsiella pneumoniae were detected in different stages of the industrial broiler production in one out of seven investigated broiler chains.
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Plasmid-Mediated Colistin Resistance Gene mcr-1 in an Escherichia coli ST10 Bloodstream Isolate in the Sultanate of Oman.
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TL;DR: To identify plasmid-mediated colistin resistance in clinical Enterobacteriaceae isolates in Oman, where this resistance mechanism has not been encountered yet, a single E. coli isolate (OM97) carrying mcr-1 gene was identified, while no strains carrying the mCr-2 gene was found.
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Genomic epidemiology of campylobacter jejuni associated with asymptomatic pediatric infection in the peruvian amazon
Ben Pascoe,Ben Pascoe,Francesca Schiaffino,Francesca Schiaffino,Susan Murray,Susan Murray,Guillaume Méric,Sion C. Bayliss,Matthew D. Hitchings,Evangelos Mourkas,Jessica K. Calland,Rosa Burga,Pablo Peñataro Yori,Keith A. Jolley,Kerry K. Cooper,Craig T. Parker,Maribel Paredes Olortegui,Margaret Kosek,Samuel K. Sheppard,Samuel K. Sheppard,Samuel K. Sheppard +20 more
TL;DR: As in many other countries, poultry-associated strains were likely a major source of human infection but almost half of local disease cases were attributable to genotypes that are rare outside of Peru, suggesting an important role for host factors in the cryptic epidemiology of campylobacteriosis in LMICs.
References
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