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
Metagenomic characterization of the effect of feed additives on the gut microbiome and antibiotic resistome of feedlot cattle
Milton Thomas,M. J. Webb,Sudeep Ghimire,Amanda D. Blair,Kenneth C. Olson,Gavin J. Fenske,Alex Thomas Fonder,Jane Christopher-Hennings,Derek Brake,Joy Scaria +9 more
TL;DR: The results indicate that use of antibiotic feed additives does not produce discernable changes at the phylum level, however, treated cattle had reduced abundance of gram-positive bacteria at the genus level and functional analysis of the data indicates that there was only minimal impact due to the treatment in the rumen.
Journal ArticleDOI
Rapid Nanopore Sequencing of Plasmids and Resistance Gene Detection in Clinical Isolates.
TL;DR: Evaluated workflows and turnaround times for a benchtop long-read sequencing approach in the clinical microbiology laboratory using the Oxford Nanopore Technologies MinION sequencer found full annotation of plasmid resistance gene content could be obtained in under 6 h from a subcultured isolate, less time than traditional phenotypic susceptibility testing.
Journal ArticleDOI
In-depth resistome analysis by targeted metagenomics
Val F. Lanza,Fernando Baquero,José L. Martínez,Ricardo Ramos-Ruiz,Bruno Gonzalez-Zorn,Antoine Andremont,Antonio Sánchez-Valenzuela,Dusko Ehrlich,Dusko Ehrlich,Sean Kennedy,Sean Kennedy,Etienne Ruppé,Etienne Ruppé,Willem van Schaik,Willem van Schaik,Rob J. L. Willems,Fernando de la Cruz,Fernando de la Cruz,Teresa M. Coque +18 more
TL;DR: ResCap, the first targeted sequence capture platform specifically developed to analyze resistomes, greatly enhances the sensitivity and specificity of available metagenomic methods and offers the possibility to analyze genes related to the selection and transfer of antimicrobial resistance (biocides, heavy metals, plasmids).
Journal ArticleDOI
Characterization of the resistome in manure, soil and wastewater from dairy and beef production systems
Noelle R. Noyes,Xiang Yang,Lyndsey M. Linke,Roberta J. Magnuson,Shaun R. Cook,Rahat Zaheer,Hua Yang,Dale R. Woerner,Ifigenia Geornaras,Jessica A.A. McArt,Sheryl P. Gow,Jaime Ruiz,Kenneth L. Jones,Christina Boucher,Tim A. McAllister,Keith E. Belk,Paul S. Morley +16 more
TL;DR: It is found that the ranch samples contained significantly fewer resistance mechanisms than dairy and feedlot samples, and that the resistome of dairy operations differed significantly from that of feedlots, suggesting that management of these effluents should be tailored appropriately.
Journal ArticleDOI
Genomics of KPC-Producing Klebsiella pneumoniae Sequence Type 512 Clone Highlights the Role of RamR and Ribosomal S10 Protein Mutations in Conferring Tigecycline Resistance
TL;DR: A PCR-based approach was devised to amplify the potential resistance mechanisms identified by genomics and applied to two additional ST512 strains showing resistance to tigecycline, allowing us to identify mutations in the ramR gene.
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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