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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Comparative Genomics and Characterization of Hybrid Shigatoxigenic and Enterotoxigenic Escherichia coli (STEC/ETEC) Strains
Outi Nyholm,Jani Halkilahti,Gudrun Wiklund,Uche Godfrey Okeke,Lars Paulin,Petri Auvinen,Kaisa Haukka,Anja Siitonen +7 more
TL;DR: This study shows that pathogroup-associated virulence genes of different E. coli can co-exist in strains originating from different phylogenetic lineages and should be taken into account in strain typing and in epidemiological surveillance.
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Combining short and long read sequencing to characterize antimicrobial resistance genes on plasmids applied to an unauthorized genetically modified Bacillus.
Bas Berbers,Assia Saltykova,Cristina Garcia-Graells,Patrick Philipp,Fabrice Arella,Kathleen Marchal,Raf Winand,Kevin Vanneste,Nancy H. C. Roosens,Sigrid C. J. De Keersmaecker +9 more
TL;DR: The added value of long read sequencing is illustrated in addressing the challenges of plasmid reconstruction within the context of evaluating the risk of AMR spread, and several plasmids, containing AMR genes, are against critically important antibiotics.
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Faecal carriage, risk factors, acquisition and persistence of ESBL-producing Enterobacteriaceae in dogs and cats and co-carriage with humans belonging to the same household
G van den Bunt,Ad C. Fluit,Mirlin P. Spaninks,Arjen J. Timmerman,Yvon Geurts,Arie Kant,Jelle Scharringa,Dik Mevius,Jaap A. Wagenaar,Marc J. M. Bonten,W van Pelt,Joost Hordijk +11 more
TL;DR: ESBL-E prevalence was higher in dogs than in humans and lowest in cats, and co-carriage in human–pet pairs belonging to the same household was uncommon.
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New Variant of Multidrug-Resistant Salmonella enterica Serovar Typhimurium Associated with Invasive Disease in Immunocompromised Patients in Vietnam
Alison E. Mather,Tu Le Thi Phuong,Tu Le Thi Phuong,Yunfeng Gao,Simon Clare,Subhankar Mukhopadhyay,David Goulding,Nhu Tran Do Hoang,Ha Thanh Tuyen,Nguyen Phu Huong Lan,Corinne N. Thompson,Nguyen Hoang Thu Trang,Juan Carrique-Mas,Ngo Tri Tue,James Campbell,Maia A. Rabaa,Duy Pham Thanh,Katherine Harcourt,Ngo Thi Hoa,Nguyen Vinh Trung,Nguyen Vinh Trung,Constance Schultsz,Gabriel G. Perron,J.E. Coia,Derek J. Brown,Chinyere K. Okoro,Julian Parkhill,Nicholas R. Thomson,Nicholas R. Thomson,Nguyen Van Vinh Chau,Guy E. Thwaites,Duncan J. Maskell,Gordon Dougan,Gordon Dougan,Linda J. Kenney,Linda J. Kenney,Stephen Baker,Stephen Baker +37 more
TL;DR: A chain of events where a pandemic monophasic variant of S. Typhimurium (serovar I:4,[5],12:i:− sequence type 34] has been introduced into Vietnam, reacquired a phase 2 flagellum, and acquired an IncHI2 multidrug-resistant plasmid is described.
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mcr-Colistin Resistance Genes Mobilized by IncX4, IncHI2, and IncI2 Plasmids in Escherichia coli of Pigs and White Stork in Spain.
Lourdes Migura-Garcia,Juan José González-López,Jaime Martinez-Urtaza,J. R. Aguirre Sánchez,Albert Moreno-Mingorance,A. Perez de Rozas,Ursula Höfle,Yolanda Ramiro,Narjol Gonzalez-Escalona +8 more
TL;DR: This is the first report of the presence of the mcr-1 gene in isolates from white storks in Spain, highlighting the potential importance of wildlife that forage at urban household waste landfills in the transmission and spread of colistin resistance genes.
References
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Journal ArticleDOI
Identification of acquired antimicrobial resistance genes
Ea Zankari,Henrik Hasman,Salvatore Cosentino,Martin Vestergaard,Simon Rasmussen,Ole Lund,Frank Møller Aarestrup,Mette Voldby Larsen +7 more
TL;DR: A web server providing a convenient way of identifying acquired antimicrobial resistance genes in completely sequenced isolates was created, and the method was evaluated on WGS chromosomes and plasmids of 30 isolates.
Journal ArticleDOI
CDD: a Conserved Domain Database for the functional annotation of proteins
Aron Marchler-Bauer,Shennan Lu,John B. Anderson,Farideh Chitsaz,Myra K. Derbyshire,Carol DeWeese-Scott,Jessica H. Fong,Lewis Y. Geer,Renata C. Geer,Noreen R. Gonzales,Marc Gwadz,David I. Hurwitz,John D. Jackson,Zhaoxi Ke,Christopher J. Lanczycki,Fu-Ping Lu,Gabriele H. Marchler,Mikhail Mullokandov,Marina V. Omelchenko,Cynthia L. Robertson,James S. Song,Narmada Thanki,Roxanne A. Yamashita,Dachuan Zhang,Naigong Zhang,Chanjuan Zheng,Stephen H. Bryant +26 more
TL;DR: NCBI’s Conserved Domain Database (CDD) is a resource for the annotation of protein sequences with the location of conserved domain footprints, and functional sites inferred from these footprints.
Journal ArticleDOI
Identification of plasmids by PCR-based replicon typing
Alessandra Carattoli,Alessia Bertini,Laura Villa,Vincenzo Falbo,Katie L. Hopkins,E. John Threlfall +5 more
TL;DR: Results indicated that the inc/rep PCR method demonstrates high specificity and sensitivity in detecting replicons on reference plasmids and also revealed the presence of recurrent and common plasmid in epidemiologically unrelated Salmonella isolates of different serotypes.
Journal ArticleDOI
BIGSdb: Scalable analysis of bacterial genome variation at the population level
TL;DR: The Bacterial Isolate Genome Sequence Database (BIGSDB) represents a freely available resource that will assist the broader community in the elucidation of the structure and function of bacteria by means of a population genomics approach.
Journal ArticleDOI
Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria
Mette Voldby Larsen,Salvatore Cosentino,Simon Rasmussen,Carsten Friis,Henrik Hasman,Rasmus L. Marvig,Lars Jelsbak,Thomas Sicheritz-Pontén,David W. Ussery,Frank Møller Aarestrup,Ole Lund +10 more
TL;DR: A Web-based method for MLST of 66 bacterial species based on whole-genome sequencing data that enables investigators to determine the sequence types of their isolates on the basis of WGS data.