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
Genetic Determinants of Resistance to Extended-Spectrum Cephalosporin and Fluoroquinolone in Escherichia coli Isolated from Diseased Pigs in the United States
Shivdeep S. Hayer,Shivdeep S. Hayer,Seunghyun Lim,Samuel L. Hong,Samuel L. Hong,Ehud Elnekave,Timothy J. Johnson,Albert Rovira,Fabio A. Vannucci,Jonathan B. Clayton,Jonathan B. Clayton,Andres M. Perez,Julio Alvarez,Julio Alvarez +13 more
TL;DR: The aim of the present study was to identify and characterize the genetic basis of resistance against fluoroquinolones and extended-spectrum cephalosporins (ceftiofur) in swine E. coli isolates using whole-genome sequencing (WGS).
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Genomic Surveillance of Streptococcus pyogenes Strains Causing Invasive Disease, United States, 2016-2017.
Yuan Li,Joy Rivers,Saundra Mathis,Zhongya Li,Srinivasan Velusamy,Srinivas Nanduri,Chris A. Van Beneden,Paula Snippes-Vagnone,Ruth Lynfield,Lesley McGee,Sopio Chochua,Benjamin J. Metcalf,Bernard Beall +12 more
TL;DR: While the overall population structure of invasive S. pyogenes isolates in the United States remained stable, some lineages, including several that were antibiotic-resistant, increased between 2016 and 2017.
Journal ArticleDOI
Plasmid diversity among genetically related Klebsiella pneumoniae bla KPC-2 and bla KPC-3 isolates collected in the Dutch national surveillance
Antoni P. A. Hendrickx,Fabian Landman,Angela de Haan,Dyogo Borst,Sandra Witteveen,Marga G van Santen-Verheuvel,Han G. J. van der Heide,Leo M. Schouls +7 more
TL;DR: Implementing long-read plasmid sequencing analysis for K. pneumoniae surveillance provided important insights in the transmission of a KpnCluster-019 blaKPC-2 strain between the Netherlands and the Caribbean.
Journal ArticleDOI
Plasmids of novel incompatibility group IncpRBL16 from Pseudomonas species.
Xiaoyuan Jiang,Yin Zhe,Min Yuan,Qiaoxiang Cheng,Lingfei Hu,Yanan Xu,Wenhui Yang,Huiying Yang,Yuee Zhao,Xiaodong Zhao,Bo Gao,Erhei Dai,Yajun Song,Dongsheng Zhou +13 more
TL;DR: Different IncpRBL16 plasmids contain different profiles of accessory modules and thus diverse collections of resistance genes, particularly in resistance to 15 categories of antibiotics and heavy metals.
Posted ContentDOI
INfrastructure for a PHAge REference Database: Identification of large-scale biases in the current collection of phage genomes
Ryan Cook,Nathan Brown,Tamsin Redgwell,Branko Rihtman,Megan Barnes,Martha R. J. Clokie,Dov J. Stekel,Jon L. Hobman,Michael Jones,Andrew D. Millard +9 more
TL;DR: In 2018, Cook et al. as mentioned in this paper developed an automated retrieval and analysis system for bacteriophage genomes, INPHARED (https://github.com/RyanCook94/inphared), that provides data in a consistent format.
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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