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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Molecular mechanism of azithromycin resistance among typhoidal Salmonella strains in Bangladesh identified through passive pediatric surveillance.
Yogesh Hooda,Yogesh Hooda,Mohammad Saiful Islam Sajib,Hafizur Rahman,Stephen P. Luby,Joseph Bondy-Denomy,Mathuram Santosham,Jason R. Andrews,Samir K. Saha,Senjuti Saha,Senjuti Saha +10 more
TL;DR: This report confirms 12 azithromycin-resistant Salmonella Typhi strains and one Paratyphi A strain with molecular basis of macrolide resistance, and finds a non-synonymous single-point mutation exclusively in these 12 strains in the gene encoding AcrB, an efflux pump that removes small molecules from bacterial cells.
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Genomic Epidemiology of Global Carbapenemase-Producing Enterobacter spp., 2008-2014.
Gisele Peirano,Yasufumi Matsumura,Mark Raymond Adams,Patricia A. Bradford,Mary Motyl,Liang Chen,Barry N. Kreiswirth,Johann D.D. Pitout,Johann D.D. Pitout +8 more
TL;DR: The study highlights the importance of surveillance programs using whole-genome sequencing in providing insight into the molecular epidemiology of carbapenemase-producing Enterobacter spp.
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Zoonotic Transmission of mcr-1 Colistin Resistance Gene from Small-Scale Poultry Farms, Vietnam
Nguyen Vinh Trung,Sébastien Matamoros,Juan Carrique-Mas,Nguyen Huu Nghia,Nguyen Thi Nhung,Tran Thi Bich Chieu,Ho Huynh Mai,Willemien J. M. van Rooijen,James Campbell,Jaap A. Wagenaar,Anita Hardon,Nguyen Thi Nhu Mai,Thai Quoc Hieu,Guy E. Thwaites,Menno D. de Jong,Constance Schultsz,Ngo Thi Hoa +16 more
TL;DR: Investigation of the consequences of colistin use in backyard chicken farms in Vietnam by examining the prevalence of mcr-1 in fecal samples from chickens and humans found detection of mCR-1–carrying bacteria in chicken samples was associated with colistIn use and detection in human samples with exposure to mcr–1–positive chickens.
Journal ArticleDOI
The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa.
Se Eun Park,Se Eun Park,Duy Thanh Pham,Christine J. Boinett,Vanessa K. Wong,Gi Deok Pak,Ursula Panzner,Ligia Maria Cruz Espinoza,Vera von Kalckreuth,Justin Im,Heidi Schütt-Gerowitt,Heidi Schütt-Gerowitt,John A. Crump,Robert F. Breiman,Robert F. Breiman,Yaw Adu-Sarkodie,Ellis Owusu-Dabo,Raphaël Rakotozandrindrainy,Abdramane Bassiahi Soura,Abraham Aseffa,Nagla Gasmelseed,Karen H. Keddy,Jürgen May,Amy Gassama Sow,Amy Gassama Sow,Peter Aaby,Peter Aaby,Holly M. Biggs,Julian T. Hertz,Joel M. Montgomery,Leonard Cosmas,Beatrice Olack,Barry S. Fields,Nimako Sarpong,Tsiriniaina Jean Luco Razafindrabe,Tiana Mirana Raminosoa,Leon Parfait Kabore,Emmanuel Sampo,Mekonnen Teferi,Biruk Yeshitela,Muna Ahmed El Tayeb,Arvinda Sooka,Christian Meyer,Christian Meyer,Ralf Krumkamp,Denise Dekker,Anna Jaeger,Sven Poppert,Adama Tall,Aissatou Ahmet Niang,Morten Bjerregaard-Andersen,Morten Bjerregaard-Andersen,Sandra Valborg Løfberg,Sandra Valborg Løfberg,Hye Jin Seo,Hyon Jin Jeon,Jessica Fung Deerin,Jin Kyung Park,Frank Konings,Mohammad Ali,Mohammad Ali,John D. Clemens,John D. Clemens,John D. Clemens,Peter Hughes,Juliet Nsimire Sendagala,Tobias Vudriko,Robert Downing,Usman N. Ikumapayi,Grant A. Mackenzie,Stephen K. Obaro,Stephen K. Obaro,Stephen K. Obaro,Silvia Argimón,David M. Aanensen,Andrew J. Page,Jacqueline A. Keane,Sebastián Duchêne,Zoe A. Dyson,Kathryn E. Holt,Gordon Dougan,Florian Marks,Florian Marks,Stephen Baker,Stephen Baker +84 more
TL;DR: A phylogenetic reconstruction of whole genome sequenced 249 contemporaneous S. Typhi isolates from 11 sub-Saharan African countries is presented, identifying genes and plasmids associated with antibiotic resistance and showing that multi-drug resistance is highly pervasive inSub-Saharan Africa.
Journal ArticleDOI
Genomic epidemiology of global Klebsiella pneumoniae carbapenemase (KPC)-producing Escherichia coli.
Nicole Stoesser,Anna E. Sheppard,Gisele Peirano,LW Anson,Louise Pankhurst,Robert Sebra,H T T Phan,H T T Phan,Andrew Kasarskis,Amy J. Mathers,Tim E. A. Peto,Patricia A. Bradford,Mary Motyl,A S Walker,Derrick W. Crook,Johann D. D. Pitout +15 more
TL;DR: The association of blaKPC with a range of MGEs previously linked to the successful spread of widely endemic resistance mechanisms suggests that it may become similarly prevalent, and evidence of inter-species, regional and international plasmid spread is found.
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