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
Reads0
Chats0
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
More filters
Journal ArticleDOI
Evaluation of Whole Genome Sequencing for Outbreak Detection of Salmonella enterica
Pimlapas Leekitcharoenphon,Eva Møller Nielsen,Rolf Sommer Kaas,Ole Lund,Frank Møller Aarestrup +4 more
TL;DR: For S. Typhimurium, SNP analysis and nucleotide difference approach of WGS data seem to be the superior methods for epidemiological typing compared to other phylogenetic analytic approaches that may be used on WGS.
Journal ArticleDOI
Using Genomics to Track Global Antimicrobial Resistance.
Rene S. Hendriksen,Valeria Bortolaia,Heather Tate,Gregory H. Tyson,Frank Møller Aarestrup,Patrick F. McDermott +5 more
TL;DR: A scientific literature review is conducted and a description of examples of available tools and databases for antimicrobial resistance (AMR) detection and future perspectives and recommendations are presented.
Journal ArticleDOI
Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries.
Patrick Munk,Berith Elkær Knudsen,Oksana Lukjacenko,Ana Sofia Ribeiro Duarte,Liese Van Gompel,Roosmarijn E C Luiken,Lidwien A.M. Smit,Heike Schmitt,Alejandro Dorado Garcia,Rasmus Borup Hansen,Thomas Nordahl Petersen,Alex Bossers,Etienne Ruppé,Haitske Graveland,Alieda van Essen,Bruno Gonzalez-Zorn,Gabriel Moyano,Pascal Sanders,Claire Chauvin,Julie David,Antonio Battisti,Andrea Caprioli,Jeroen Dewulf,Thomas Blaha,Katharina Wadepohl,Maximiliane Brandt,Dariusz Wasyl,Magdalena Skarżyńska,Magdalena Zajac,H. Daskalov,Helmut W. Saatkamp,Katharina D.C. Stärk,Ole Lund,Tine Hald,Sünje Johanna Pamp,Håkan Vigre,Dick Heederik,Jaap A. Wagenaar,Dik Mevius,Frank Møller Aarestrup +39 more
TL;DR: The total acquired AMR level was associated with the overall country-specific antimicrobial usage in livestock and that countries with comparable usage patterns had similar resistomes, however, functionally determined AMR genes were not associated with total drug use.
Journal Article
The role of whole genome sequencing in antimicrobial susceptibility testing of bacteria
Matthew J. Ellington,Oskar Ekelund,Frank Møller Aarestrup,Rafael Cantón,Michel Doumith,Christian G. Giske,H. Grundman,Henrik Hasman,Matthew T. G. Holden,Katie L. Hopkins,J. Iredell,Gunnar Kahlmeter,Claudio U. Köser,Alasdair P. MacGowan,Dik Mevius,Michael R. Mulvey,Thierry Naas,Tim E. A. Peto,J.-M. Rolain,Samuelsen,Neil Woodford +20 more
TL;DR: For most bacterial species there is currently insufficient evidence to support the use of WGS-inferred AST to guide clinical decision making, so W GS-AST should be a funding priority if it is to become a rival to phenotypic AST.
Journal ArticleDOI
AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence.
Michael Feldgarden,Vyacheslav Brover,Narjol Gonzalez-Escalona,Jonathan G. Frye,Julie Haendiges,Daniel H. Haft,Maria Hoffmann,James B. Pettengill,Arjun B. Prasad,Glenn E. Tillman,Gregory H. Tyson,William Klimke +11 more
TL;DR: The Reference Gene Catalog (RGC) as discussed by the authors has been extended to include putative acid, biocide, metal, stress resistance genes, in addition to virulence genes and species-specific point mutations.
References
More filters
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.
Related Papers (5)
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
Trimmomatic: a flexible trimmer for Illumina sequence data
The RAST Server: Rapid Annotations using Subsystems Technology
Ramy K. Aziz,Ramy K. Aziz,Daniela Bartels,Aaron A. Best,Matthew DeJongh,Terrence Disz,Terrence Disz,Robert Edwards,Kevin Formsma,Svetlana Gerdes,Elizabeth M. Glass,Michael Kubal,Folker Meyer,Folker Meyer,Gary J. Olsen,Gary J. Olsen,Robert Olson,Robert Olson,Andrei L. Osterman,Ross Overbeek,Leslie Klis McNeil,Daniel Paarmann,Tobias Paczian,Bruce Parrello,Gordon D. Pusch,Claudia I. Reich,Rick Stevens,Rick Stevens,Olga Vassieva,Veronika Vonstein,Andreas Wilke,Olga Zagnitko +31 more