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
In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing
Alessandra Carattoli,Ea Zankari,Aurora García-Fernández,Mette Voldby Larsen,Ole Lund,Laura Villa,Frank Møller Aarestrup,Henrik Hasman +7 more
TL;DR: Two easy-to-use Web tools for in silico detection and characterization of whole-genome sequence (WGS) and whole-plasmid sequence data from members of the family Enterobacteriaceae are designed and developed.
Journal ArticleDOI
CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database
Baofeng Jia,Amogelang R. Raphenya,Brian Alcock,Nicholas Waglechner,Peiyao Guo,Kara K. Tsang,Briony A. Lago,Biren M. Dave,Sheldon K. Pereira,Arjun N. Sharma,Sachin Doshi,Mélanie Courtot,Raymond Lo,Laura E. Williams,Jonathan G. Frye,Tariq Elsayegh,Daim Sardar,Erin L. Westman,Andrew C. Pawlowski,Timothy A. Johnson,Fiona S. L. Brinkman,Gerard D. Wright,Andrew G. McArthur +22 more
TL;DR: The Comprehensive Antibiotic Resistance Database (CARD) is a manually curated resource containing high quality reference data on the molecular basis of antimicrobial resistance (AMR), with an emphasis on the genes, proteins and mutations involved in AMR.
Journal ArticleDOI
CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database
Brian Alcock,Amogelang R. Raphenya,Tammy T. Y. Lau,Kara K. Tsang,Mégane Bouchard,Arman Edalatmand,William Huynh,Anna-Lisa V. Nguyen,Annie A. Cheng,Sihan Liu,Sally Y. Min,Anatoly Miroshnichenko,Hiu-Ki R Tran,Rafik El Werfalli,Jalees A. Nasir,Martins Oloni,David Speicher,Alexandra Florescu,Bhavya Singh,Mateusz Faltyn,Anastasia Hernández-Koutoucheva,Arjun N. Sharma,Emily Bordeleau,Andrew C. Pawlowski,Haley L. Zubyk,Damion M. Dooley,Emma Griffiths,Finlay Maguire,Geoffrey L. Winsor,Robert G. Beiko,Fiona S. L. Brinkman,William W. L. Hsiao,William W. L. Hsiao,Gary Van Domselaar,Gary Van Domselaar,Andrew G. McArthur +35 more
TL;DR: A new Resistomes & Variants module provides analysis and statistical summary of in silico predicted resistance variants from 82 pathogens and over 100 000 genomes, able to summarize predicted resistance using the information included in CARD, identify trends in AMR mobility and determine previously undescribed and novel resistance variants.
Journal ArticleDOI
The Comprehensive Antibiotic Resistance Database
Andrew G. McArthur,Nicholas Waglechner,Fazmin Nizam,Austin Yan,Marisa A. Azad,Alison J. Baylay,Kirandeep Bhullar,Marc J. Canova,Gianfranco De Pascale,Linda Ejim,Lindsay Kalan,Andrew M. King,Kalinka Koteva,Mariya Morar,Michael R. Mulvey,Jonathan S O'Brien,Andrew C. Pawlowski,Laura J. V. Piddock,Peter Spanogiannopoulos,Arlene D. Sutherland,Irene Tang,Patricia L. Taylor,Maulik N. Thaker,Wenliang Wang,Marie Yan,Tennison Yu,Gerard D. Wright +26 more
TL;DR: The CARD integrates disparate molecular and sequence data, provides a unique organizing principle in the form of the Antibiotic Resistance Ontology (ARO), and can quickly identify putative antibiotic resistance genes in new unannotated genome sequences.
Journal ArticleDOI
ResFinder 4.0 for predictions of phenotypes from genotypes.
Valeria Bortolaia,Rolf Sommer Kaas,Etienne Ruppé,Marilyn C. Roberts,Stefan Schwarz,Vincent Cattoir,Alain Philippon,Rosa Lundbye Allesøe,Rosa Lundbye Allesøe,Ana-Rita Rebelo,Alfred Ferrer Florensa,Linda Fagelhauer,Trinad Chakraborty,Bernd Neumann,Guido Werner,Jennifer K. Bender,Kerstin Stingl,Minh Ngoc Nguyen,Jasmine Coppens,Basil Britto Xavier,Surbhi Malhotra-Kumar,Henrik Westh,Henrik Westh,Mette Pinholt,Muna F. Anjum,Nicholas A. Duggett,Isabelle Kempf,Suvi Nykäsenoja,Satu Olkkola,Kinga Wieczorek,Ana Amaro,Lurdes Clemente,Joël Mossong,Serge Losch,Catherine Ragimbeau,Ole Lund,Frank Møller Aarestrup +36 more
TL;DR: WGS-based AST using ResFinder 4.0 provides in silico antibiograms as reliable as those obtained by phenotypic AST at least for the bacterial species/antimicrobial agents of major public health relevance considered.
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
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Journal ArticleDOI
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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
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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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