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 Potential of the Biocontrol Agent Pseudomonas brassicacearum (Formerly P. trivialis) 3Re2-7 Unraveled by Genome Sequencing and Mining, Comparative Genomics and Transcriptomics
Johanna Nelkner,Gonzalo Arturo Torres Tejerizo,Julia Hassa,Timo Wentong Lin,Julian Witte,Bart Verwaaijen,Anika Winkler,Boyke Bunk,Cathrin Spröer,Jörg Overmann,Rita Grosch,Alfred Pühler,Andreas Schlüter +12 more
TL;DR: The genome sequence of the strain Pseudomonas brassicacearum 3Re2-7 is provided, revealing a high collinearity with the representative genome for the species, P. brassic ACearum NFM421, and gene clusters that might encode specialized biocontrol mechanisms of strain 3Re 2-7 are revealed.
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Integrating multiple genomic technologies to investigate an outbreak of carbapenemase-producing Enterobacter hormaechei
Leah W. Roberts,Patrick N A Harris,Brian M. Forde,Nouri L. Ben Zakour,Elizabeth Catchpoole,Mitchell Stanton-Cook,Minh-Duy Phan,Hanna E. Sidjabat,Haakon Bergh,Claire Heney,Jayde A. Gawthorne,Jeffrey Lipman,Anthony M. Allworth,Kok-Gan Chan,Kok-Gan Chan,Teik Min Chong,Wai-Fong Yin,Mark A. Schembri,David L. Paterson,Scott A. Beatson +19 more
TL;DR: The application of several complementary whole-genome sequencing technologies to characterise a hospital outbreak of blaIMP-4 carbapenemase-producing E. hormaechei provided an in-depth analysis of the outbreak, and the true relationship of subsequent isolates to the initial outbreak was resolved.
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Benchmarking hybrid assembly approaches for genomic analyses of bacterial pathogens using Illumina and Oxford Nanopore sequencing
TL;DR: The hybrid assembly pipeline of Unicycler is demonstrated as a superior approach for genomic analyses of bacterial pathogens using Illumina and Oxford Nanopore sequencing.
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Multiple Klebsiella pneumoniae KPC Clones Contribute to an Extended Hospital Outbreak.
Carolina Ferrari,Marta Corbella,Stefano Gaiarsa,Francesco Comandatore,Erika Scaltriti,Claudio Bandi,Patrizia Cambieri,Piero Marone,Davide Sassera +8 more
TL;DR: This work characterized a subset of the CRKP isolates and reconstruct the spread of a multi-clone epidemic event that occurred in an Intensive Care Unit in a hospital in Northern Italy from August 2015 to May 2016, resulting in seven deaths.
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Novel linezolid resistance plasmids in Enterococcus from food animals in the USA.
Gregory H. Tyson,Jonathan L. Sabo,Maria Hoffmann,Chih-Hao Hsu,Sampa Mukherjee,Jacqueline Hernandez,Glenn E. Tillman,Jamie L. Wasilenko,Jovita Haro,Mustafa Simmons,Wanda Wilson Egbe,Patricia L. White,Uday Dessai,Patrick F. McDermott +13 more
TL;DR: The first identification of linezolid resistance in the USA in bacteria isolated from food animals is identified, indicating that there may be co-selection for these plasmids due to the use of different antimicrobials.
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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