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
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TLDR
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.Abstract:
Objectives
Identification of antimicrobial resistance genes is important for understanding the underlying mechanisms and the epidemiology of antimicrobial resistance. As the costs of whole-genome sequencing (WGS) continue to decline, it becomes increasingly available in routine diagnostic laboratories and is anticipated to substitute traditional methods for resistance gene identification. Thus, the current challenge is to extract the relevant information from the large amount of generated data.read more
Citations
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Journal ArticleDOI
Global phylogeography and evolutionary history of Shigella dysenteriae type 1.
Elisabeth Njamkepo,Nizar Fawal,Alicia Tran-Dien,Jane Hawkey,Nancy Strockbine,Claire Jenkins,Kaisar A. Talukder,Raymond Bercion,Konstantin V. Kuleshov,Renáta Kolínská,Julie E. Russell,Lidia Kaftyreva,Marie Accou-Demartin,Andreas Karas,Olivier Vandenberg,Alison E. Mather,Alison E. Mather,Carl J. Mason,Andrew J. Page,Thandavarayan Ramamurthy,Chantal Bizet,Andrzej Gamian,Isabelle Carle,Amy Gassama Sow,Christiane Bouchier,Astrid Louise Wester,Monique Lejay-Collin,Marie-Christine Fonkoua,Simon Le Hello,Martin J. Blaser,Cecilia Jernberg,Corinne Ruckly,Audrey Mérens,Anne-Laure Page,Martin Aslett,Peter Roggentin,Angelika Fruth,Erick Denamur,Malabi M. Venkatesan,Herve Bercovier,Ladaporn Bodhidatta,Chien-Shun Chiou,Dominique Clermont,Bianca Colonna,S. A. Egorova,Gururaja P. Pazhani,Analia V. Ezernitchi,Ghislaine Guigon,Simon R. Harris,Hidemasa Izumiya,Agnieszka Korzeniowska-Kowal,Anna Lutyńska,Malika Gouali,Francine Grimont,Céline Langendorf,Monika Marejková,Lorea A. M. Peterson,Guillermo I. Perez-Perez,Antoinette Ngandjio,Alexander Podkolzin,Erika Souche,M. A. Makarova,German A. Shipulin,Changyun Ye,Helena Žemličková,Mária Herpay,Patrick A. D. Grimont,Julian Parkhill,Philippe J. Sansonetti,Kathryn E. Holt,Sylvain Brisse,Sylvain Brisse,Nicholas R. Thomson,Nicholas R. Thomson,François-Xavier Weill,François-Xavier Weill +75 more
TL;DR: It is shown that Shigella dysenteriae type 1 has existed since at least the eighteenth century and that it swept the globe at the end of the nineteenth century, diversifying into distinct lineages associated with the First World War, Second World War and various conflicts or natural disasters across Africa, Asia and Central America.
Journal ArticleDOI
Characterization of antimicrobial resistance in lactobacilli and bifidobacteria used as probiotics or starter cultures based on integration of phenotypic and in silico data.
TL;DR: Insight is provided into AR of probiotics, probiotic candidates, and starter cultures with an emphasis on tetracycline and into the safety of these strains in the context of AR.
Journal ArticleDOI
Whole-Genome Sequencing-Based Characterization of 100 Listeria monocytogenes Isolates Collected from Food Processing Environments over a Four-Year Period
Daniel Hurley,Laura Luque-Sastre,Craig T. Parker,Steven Huynh,Athmanya K. Eshwar,Scott V. Nguyen,Nicholas Andrews,Alexandra Moura,Edward M. Fox,Kieran Jordan,Angelika Lehner,Roger Stephan,Séamus Fanning +12 more
TL;DR: WGS-based strategies facilitated tracking of this pathogen of importance to human health along the production chain while providing insights into the pathogenic potential for some of the L. monocytogenes isolates showing predicted pathogenic phenotypes inferred from virulence genotypes.
Journal ArticleDOI
The Promise of Whole Genome Pathogen Sequencing for the Molecular Epidemiology of Emerging Aquaculture Pathogens.
Sion C. Bayliss,David W. Verner-Jeffreys,Kerry L. Bartie,David M. Aanensen,Samuel K. Sheppard,Alexandra Adams,Edward J. Feil +6 more
TL;DR: The opportunities afforded by whole genome sequencing of bacterial and viral pathogens of aquaculture to mitigate disease emergence and spread are discussed.
Journal ArticleDOI
Plasmid-mediated colistin resistance in Escherichia coli from the Arabian Peninsula
Agnes Sonnevend,Akela Ghazawi,Manaf AlQahtani,Atef M. Shibl,Wafa Jamal,Rayhan Hashmey,Tibor Pál +6 more
TL;DR: This is the first report on the presence of the plasmid-coded mCr-1 gene in a variety of multi-resistant clinical isolates from the Arabian Peninsula indicating that several commonly used antibiotics can potentially facilitate the spread of mcr-1 carrying strains, or directly, mCR-1 containing plasmids.
References
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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.
Journal ArticleDOI
Molecular genetics of aminoglycoside resistance genes and familial relationships of the aminoglycoside-modifying enzymes.
TL;DR: A preliminary assessment of the amino acids which may be important in binding aminoglycosides was obtained from data and from the results of mutational analysis of several of the genes encoding am inoglycoside-modifying enzymes.
Journal ArticleDOI
Acquired Antibiotic Resistance Genes: An Overview
Angela H.A.M. van Hoek,Dik Mevius,Dik Mevius,Beatriz Guerra,Peter Mullany,Adam P. Roberts,Henk Aarts +6 more
TL;DR: Attention is paid to mobile genetic elements such as plasmids, transposons, and integrons, which are associated with AR genes, and involved in the dispersal of antimicrobial determinants between different bacteria.
Journal ArticleDOI
Staphylococcus aureus CC398: Host Adaptation and Emergence of Methicillin Resistance in Livestock
Lance B. Price,Marc Stegger,Henrik Hasman,Maliha Aziz,Jesper Larsen,Paal Skytt Andersen,Talima Pearson,Andrew E. Waters,Jeffrey T. Foster,James M. Schupp,John D. Gillece,Elizabeth M. Driebe,Cindy M. Liu,Cindy M. Liu,Burkhard Springer,Irena Zdovc,Antonio Battisti,Alessia Franco,Jacek Żmudzki,Stefan Schwarz,Patrick Butaye,Eric Jouy,Constança Pomba,M. Concepción Porrero,Raymond Ruimy,Tara C. Smith,D. Ashley Robinson,J. Scott Weese,Carmen Sofia Arriola,Fangyou Yu,Frédéric Laurent,Paul Keim,Paul Keim,Robert Skov,Frank Møller Aarestrup +34 more
TL;DR: The results strongly suggest that livestock-associated MRSA CC398 originated in humans as MSSA, which appears to have undergone a rapid radiation in conjunction with the jump from humans to livestock, where it subsequently acquired tetracycline and methicillin resistance.
Journal ArticleDOI
Comparison of antimicrobial resistance phenotypes and resistance genes in Enterococcus faecalis and Enterococcus faecium from humans in the community, broilers, and pigs in Denmark.
TL;DR: Differences in the occurrence of resistance and tetracycline resistance genes were observed among isolates from the different sources, however, similar resistance patterns and resistant genes were detected frequently indicating that transmission of resistant enterococci or resistance genes takes place between humans, broilers, and pigs.
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