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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Characterization of an NDM-5 carbapenemase-producing Escherichia coli ST156 isolate from a poultry farm in Zhejiang, China
Biao Tang,Jiang Chang,Liujie Cao,Qixia Luo,Hao Xu,Lyu Wentao,Mingrong Qian,Xiaofeng Ji,Zhang Qiaoyan,Xiaodong Xia,Hua Yang +10 more
TL;DR: The results reflected the severe bacterial resistance in a poultry farm in Zhejiang province and increased the understanding of the presence and transmission of the blaNDM-5 gene.
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Whole Genome Sequence Analysis of CTX-M-15 Producing Klebsiella Isolates Allowed Dissecting a Polyclonal Outbreak Scenario.
Laura Becker,Stephan Fuchs,Yvonne Pfeifer,Torsten Semmler,Tim Eckmanns,Gerit Korr,Gerit Korr,Dagmar Sissolak,Michael Friedrichs,Edith Zill,Mei-Lin Tung,Christian Dohle,Martin Kaase,Sören Gatermann,Holger Rüssmann,Matthias Steglich,Sebastian Haller,Guido Werner +17 more
TL;DR: This work uses the rise of multidrug-resistant K. pneumoniae in a German neurorehabilitation center from April 2015 to April 2016 to dissect the benefit of whole genome sequencing for outbreak analyses, and introduces two novel open-source applications supporting reference genome selection and alignment-based SNP-filtering in NGS analyses.
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Characterization of cefotaxime resistant Escherichia coli isolated from broiler farms in Ecuador.
Christian Vinueza-Burgos,David Ortega-Paredes,Cristian Narváez,Lieven De Zutter,Jeannete Zurita +4 more
TL;DR: Poultry production systems represent a hotspot for AR in Ecuador, possibly mediated by the extensive use of antibiotics, and monitoring this sector in national and regional plans of AR surveillance should therefore be considered.
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Phenome-Genome Profiling of Single Bacterial Cell by Raman-Activated Gravity-Driven Encapsulation and Sequencing.
TL;DR: The ability to profile and correlate bacterial metabolic phenome and high-quality genome sequences at one-cell resolution suggests broad application of RAGE-Seq.
Journal ArticleDOI
Limited contribution of non-intensive chicken farming to ESBL-producing Escherichia coli colonization in humans in Vietnam: an epidemiological and genomic analysis.
Vinh Trung Nguyen,Dorota Jamrozy,Sébastien Matamoros,Juan Carrique-Mas,Huynh Mai Ho,Quoc Hieu Thai,Thi Nhu Mai Nguyen,Jaap A. Wagenaar,Jaap A. Wagenaar,Guy E. Thwaites,Julian Parkhill,Constance Schultsz,Thi Hoa Ngo +12 more
TL;DR: A limited contribution of non-intensive chicken farming to ESBL-Ec colonization in humans in Vietnam is demonstrated and further emphasizes the importance of reducing antimicrobial usage in both human and animal host reservoirs.
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.
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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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