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
Antibiotic Resistance Genes in the Human-Impacted Environment:A One Health Perspective
James M. Tiedje,Fang Wang,Célia M. Manaia,Marko Virta,Hongjie Sheng,Liping Ma,Tong Zhang,Edward Topp +7 more
TL;DR: This prospectus presents the status and issues relevant to the environmental component of antibiotic resistance, namely, the needs for advancing surveillance methodology: the environmental reservoirs and sources of resistance, including, urban wastewater treatment plants, aquaculture production systems, soil receiving manure and biosolid, and the atmosphere which includes longer range dispersal.
Journal ArticleDOI
Deciphering the Resistome of the Widespread Pseudomonas aeruginosa Sequence Type 175 International High-Risk Clone through Whole-Genome Sequencing.
Gabriel Cabot,Carla López-Causapé,Alain A. Ocampo-Sosa,Lea Mette Madsen Sommer,María Ángeles Domínguez,Laura Zamorano,Carlos Juan,Fe Tubau,Cristina Rodríguez,Bartolomé Moyá,Carmen Peña,Luis Martínez-Martínez,Patrick Plésiat,Antonio Oliver +13 more
TL;DR: Several unique resistance mutations were detected in single isolates; particularly interesting were those in genes encoding penicillin-binding proteins (PBP1A, PBP3, and PBP4).
Journal ArticleDOI
Using metagenomics to investigate human and environmental resistomes.
TL;DR: The current state of methods for sequence handling, mapping to databases of resistance genes, statistical analysis and metagenomic assembly are outlined, and some of the currently used tools and methods that are best equipped to inform research and clinical practice related to antibiotic resistance are recommended.
Journal ArticleDOI
Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.
Martin Hunt,Martin Hunt,Phelim Bradley,Simon Grandjean Lapierre,Simon Heys,Mark Thomsit,Michael B Hall,Kerri M. Malone,Penelope Wintringer,Timothy M Walker,Daniela Maria Cirillo,Iñaki Comas,Maha R. Farhat,Phillip Fowler,Jennifer L. Gardy,Nazir Ahmed Ismail,Thomas Kohl,Vanessa Mathys,Matthias Merker,Stefan Niemann,Shaheed V. Omar,Vitali Sintchenko,Grace Smith,Dick van Soolingen,Philip Supply,Sabira Tahseen,Mark H. Wilcox,Irena Arandjelovic,Tim E. A. Peto,Derrick W. Crook,Derrick W. Crook,Zamin Iqbal +31 more
TL;DR: The ability of Mykrobe-based DST to guide personalized therapeutic regimen design in the context of complex drug susceptibility profiles is measured, showing 94% concordance of implied regimen with that driven by phenotypic DST, higher than all other benchmarked tools.
Journal ArticleDOI
Tetracycline-inactivating enzymes from environmental, human commensal, and pathogenic bacteria cause broad-spectrum tetracycline resistance
Andrew J. Gasparrini,Jana L. Markley,Hirdesh Kumar,Hirdesh Kumar,Bin Wang,Luting Fang,Sidra Irum,Sidra Irum,Chanez T. Symister,Meghan A. Wallace,Carey-Ann D. Burnham,Saadia Andleeb,Niraj H. Tolia,Niraj H. Tolia,Timothy A. Wencewicz,Gautam Dantas +15 more
TL;DR: This work identifies and characterize an expanded pool of tet(X) -like genes in environmental and human commensal metagenomes via inactivation by antibiotic selection of metagenomic libraries and shows that Tet(X7) contributes to tetracycline resistance in a clinical Pseudomonas aeruginosa isolate and demonstrates the use of a Tet( X) inhibitor to circumvent resistance.
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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