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
Antimicrobial use and production system shape the fecal, environmental, and slurry resistomes of pig farms.
Óscar Mencía-Ares,Raul Cabrera-Rubio,Raul Cabrera-Rubio,José F. Cobo-Díaz,Avelino Alvarez-Ordóñez,Manuel Gómez-García,Héctor Puente,Paul D. Cotter,Paul D. Cotter,Fiona Crispie,Fiona Crispie,Ana Carvajal,Pedro Rubio,Héctor Argüello +13 more
TL;DR: This study shows how AMU, production system, and sample type influence, mainly through MGEs, the profile and dispersion of ARGs in pig production, as compared to that of industrialized intensive pig farming.
Journal ArticleDOI
Whole Genome Sequencing for Surveillance of Antimicrobial Resistance in Actinobacillus pleuropneumoniae.
Janine T. Bossé,Yanwen Li,Jon Rogers,Roberto Fernandez Crespo,Yinghui Li,Roy R. Chaudhuri,Matthew T. G. Holden,Duncan J. Maskell,Alexander W. Tucker,Brendan W. Wren,Andrew N. Rycroft,Paul R. Langford +11 more
TL;DR: Results indicate that, with the exception of macrolides, wgs data can be used to accurately predict resistance of A. pleuropneumoniae to the tested antimicrobial agents and provides added value for routine surveillance.
Posted ContentDOI
CRISPR-Cas systems restrict horizontal gene transfer in Pseudomonas aeruginosa
TL;DR: It is found that CRISPR-Cas acts as an important constraint to horizontal gene transfer, suggesting that the ability of this pathogen to adapt to new niches and stressors may be constrain.
Journal ArticleDOI
Genomic and metagenomic technologies to explore the antibiotic resistance mobilome
TL;DR: How current genomic methodologies can serve to analyze the resistance mobilome and its linkage with different bacterial genomes and metagenomes is discussed and the possibility of implementing novel tools to improve the current metagenomic toolbox is discussed.
Posted ContentDOI
Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: An inter-laboratory study
Ronan Doyle,Ronan Doyle,Denise M. O'Sullivan,Sean D Aller,Sebastian Bruchmann,Taane G. Clark,Andreu Coello Pelegrin,Andreu Coello Pelegrin,Martin Cormican,Ernest Diez Benavente,Matthew J. Ellington,Elaine McGrath,Yair Motro,Thi Phuong Thuy Nguyen,Jody Phelan,Liam P. Shaw,Richard A. Stabler,Alex van Belkum,Lucy van Dorp,Neil Woodford,Jacob Moran-Gilad,Jim F. Huggett,Kathryn A. Harris +22 more
TL;DR: This paper performed an inter-laboratory study providing sets of participating researchers with identical short-read whole-genome sequencing (WGS) data sequenced from clinical isolates, allowing them to assess the reproducibility of the bioinformatic prediction of AMR between participants and identify problem cases and factors that lead to discordant results.
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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