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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A comprehensive and high-quality collection of Escherichia coli genomes and their genes
Gal Horesh,Grace A. Blackwell,Grace A. Blackwell,Gerry Tonkin-Hill,Jukka Corander,Jukka Corander,Jukka Corander,Eva Heinz,Nicholas R. Thomson,Nicholas R. Thomson +9 more
TL;DR: In this article, a collection of over 10,000 E. coli and Shigella genomes was curated to provide a single, uniform, high-quality dataset for analyzing the diversity of E coli.
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RFPlasmid: Predicting plasmid sequences from short read assembly data using machine learning
TL;DR: The newly developed prediction tool RFPlasmid uses a combination of multiple features, including k-mer composition and databases with plasmid and chromosomal marker proteins, to predict if the likely source of a contig is plasmids or chromosomal.
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Pre-vaccine serotype composition within a lineage signposts its serotype replacement - a carriage study over 7 years following pneumococcal conjugate vaccine use in the UK.
Rebecca A. Gladstone,Vanessa T Devine,Jessica Jones,David W. Cleary,Johanna M.C. Jefferies,Stephen D. Bentley,Saul N. Faust,Saul N. Faust,Stuart C. Clarke +8 more
TL;DR: The dynamics of serotype replacement, in this UK population, was preceded by the presence or absence of multiple serotypes within VT lineages, in the pre-PCV population, which could help predict which non-vaccine types (NVTs) may be involved in replacement in future PCV introductions here and elsewhere.
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Novel IS26-mediated hybrid plasmid harbouring tet(X4) in Escherichia coli
Pengcheng Du,Dejun Liu,Huangwei Song,Pei Zhang,Ruichao Li,Yulin Fu,Xiao Liu,Jinli Jia,Xiaodi Li,Séamus Fanning,Yang Wang,Li Bai,Hui Zeng +12 more
TL;DR: The recombination event that occurred during the conjugation process of a tet(X4)-bearing plasmid probably formed through IS26 homologous recombination and presumably play an important role in the dissemination of the tet( X4).
Journal ArticleDOI
Phylogeny, resistome and mobile genetic elements of emergent OXA-48 and OXA-245 Klebsiella pneumoniae clones circulating in Spain.
María Pérez-Vázquez,Jesús Oteo,Silvia García-Cobos,Belén Aracil,Simon R. Harris,Adriana Ortega,D. Fontanals,Juan Hernández,Sonia Solís,José Campos,Gordon Dougan,Robert A. Kingsley,Robert A. Kingsley +12 more
TL;DR: Investigation of the population structure of blaOXA-48-like-expressing K. pneumoniae using WGS and phylogenetic analysis of Spanish isolates found genome variation was generally lower in outbreak-associated isolates compared with those associated with sporadic infections and whole-genome sequence analysis enabled the discrimination of outbreak and sporadic isolates.
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
Molecular genetics of aminoglycoside resistance genes and familial relationships of the aminoglycoside-modifying enzymes.
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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.
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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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