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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Rapid identification of pathogens, antibiotic resistance genes and plasmids in blood cultures by nanopore sequencing.
TL;DR: This is the first study to gather the above-mentioned information from nanopore sequencing and conduct a comprehensive analysis for diagnostic purposes in real-time, and hold great promise for future applications in clinical microbiology and for health care surveillance purposes.
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Molecular epidemiology of Klebsiella pneumoniae invasive infections over a decade at Kilifi County Hospital in Kenya
Sonal P. Henson,Sonal P. Henson,Christine J. Boinett,Christine J. Boinett,Matthew J. Ellington,Ngure Kagia,Salim Mwarumba,Sammy Nyongesa,Neema Mturi,Samuel Kariuki,Samuel Kariuki,J. Anthony G. Scott,J. Anthony G. Scott,Nicholas R. Thomson,Nicholas R. Thomson,Susan C. Morpeth,Susan C. Morpeth +16 more
TL;DR: The data suggests that isolates that encode NDM-1 could be present in the population; should carbapenems be introduced as treatment in public hospitals in Kenya, resistance is likely to ensue rapidly.
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Plasmid- and strain-specific factors drive variation in ESBL-plasmid spread in vitro and in vivo.
Fabienne Benz,Jana S. Huisman,Jana S. Huisman,Erik Bakkeren,Joana A. Herter,Tanja Stadler,Tanja Stadler,Martin Ackermann,Martin Ackermann,Médéric Diard,Adrian Egli,Adrian Egli,Alex R. Hall,Wolf-Dietrich Hardt,Sebastian Bonhoeffer +14 more
TL;DR: Investigating the spread of clinical Extended Spectrum Beta-Lactamase-producing plasmids in the absence of antibiotics in vitro and in the mouse intestine suggests that plasmid spread in the complex gut environment of animals and humans can be predicted based on in vitro testing and genetic data.
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Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing.
Noelle R. Noyes,Maggie E. Weinroth,Jennifer K. Parker,Christopher J Dean,Steven M. Lakin,Robert Raymond,Pablo Rovira,Enrique Doster,Zaid Abdo,Jennifer N. Martin,Kenneth L. Jones,Jaime Ruiz,Christina Boucher,Keith E. Belk,Paul S. Morley +14 more
TL;DR: The extent and composition of the low-abundance portion of the resistome-virulome is described, using a bait-capture and enrichment system that incorporates unique molecular indices to count DNA molecules and correct for enrichment bias, to demonstrate that the rare resistomes contains valuable and unique information that can be utilized for both surveillance and population genetic investigations of resistance.
Journal ArticleDOI
Pan-genome analysis of Aeromonas hydrophila, Aeromonas veronii and Aeromonas caviae indicates phylogenomic diversity and greater pathogenic potential for Aeromonas hydrophila
Sandeep Ghatak,Jochen Blom,Samir Das,Rajkumari Sanjukta,K. Puro,Michael Mawlong,I. Shakuntala,Arnab Sen,Alexander Goesmann,Ashok Kumar,S. V. Ngachan +10 more
TL;DR: The usefulness of whole genome analyses to infer evolutionary cues for Aeromonas species which indicated considerable phylogenomic diversity for A. hydrophila and hitherto unknown genomic evidence for pathogenic potential of A. caviae is highlighted.
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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