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
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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Metagenomic and viromic data mining reveals viral threats in biologically treated domestic wastewater
TL;DR: The persistent occurrence of pathogenic viruses, coupled with non-favorable virus removal by the AS treatment, reveals the hidden virus threats in biologically treated domestic wastewater.
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The Challenges of Implementing Next Generation Sequencing Across a Large Healthcare System, and the Molecular Epidemiology and Antibiotic Susceptibilities of Carbapenemase-Producing Bacteria in the Healthcare System of the U.S. Department of Defense
Emil Lesho,Robert J. Clifford,Fatma Onmus-Leone,Lakshmi Appalla,Erik Snesrud,Yoon I. Kwak,Ana Ong,Rosslyn Maybank,Paige E. Waterman,Patricia Rohrbeck,Michael Julius,Amanda L. Roth,Joshua Martinez,Lindsey Nielsen,Eric Steele,Patrick McGann,Mary Hinkle +16 more
TL;DR: An overview of the genomic epidemiology of an extensive collection of carbapenemase-producing bacteria collected in the U.S. Department of Defense health system is provided to illustrate challenges and offer mitigations for implementing next generation sequencing (NGS) across large health systems.
RFPlasmid: predicting plasmid sequences from short-read assembly data using machine learning.
TL;DR: RFPlasmid as discussed by the authors uses a combination of multiple features, including k-mer composition and databases with plasmid and chromosomal marker proteins, to predict whether the likely source of a contig is plasmids or chromosomal.
Posted ContentDOI
The distribution of plasmid fitness effects explains plasmid persistence in bacterial communities
Alonso-del Valle,Leon-Sampedro,Rodriguez-Beltran,DelaFuente,Hernandez-Garcia,Hernandez-Garcia,Ruiz-Garbajosa,Canton,Pena-Miller,San Millan +9 more
TL;DR: The results show that although pOXA-48 produced an overall reduction in bacterial fitness, the DFE was dominated by quasi-neutral effects, and beneficial effects were observed in several isolates, providing a simple and general explanation for plasmid persistence in natural bacterial communities.
Journal ArticleDOI
CTX-M-55-, MCR-1-, and FosA-Producing Multidrug-Resistant Escherichia coli Infection in a Child in France.
André Birgy,Fouad Madhi,Julien Hogan,Catherine Doit,Jean Gaschignard,Marion Caseris,Philippe Bidet,Robert M. Cohen,Stéphane Bonacorsi +8 more
TL;DR: Service de Pédiatrie Générale, Hôpital Robert Debré, AP-HP, Paris, France, andAssociation Clinique Thérapeutique Infantile du Val de Marne (ACTIV), Saint Maur des Fossés, France.
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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