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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Machine Learning Approaches for Epidemiological Investigations of Food-Borne Disease Outbreaks.
TL;DR: Whether ML or any other form of AI algorithms have already been proposed for the respective tasks and compare those with mechanistic model-based approaches are explored.
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Deterministic processes structure bacterial genetic communities across an urban landscape
James M. Hassell,James M. Hassell,Matthew Ward,Matthew Ward,Dishon Muloi,Dishon Muloi,Judy M. Bettridge,Judy M. Bettridge,H. Phan,H. Phan,Timothy P. Robinson,Allan Ogendo,Titus Imboma,John Kiiru,S. Kariuki,Michael Begon,Erastus K. Kang'ethe,Mark E. J. Woolhouse,Eric M. Fèvre,Eric M. Fèvre +19 more
TL;DR: It is suggested that it should be possible to forecast the effects of urban land-use change on microbial diversity by modelling the diversity of bacterial genes encoding virulence and antimicrobial resistance against ecological and anthropogenic forms of urban environmental change.
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Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid
Philipp Kirstahler,Søren Solborg Bjerrum,Alice Friis-Møller,Morten la Cour,Frank Møller Aarestrup,Henrik Westh,Sünje Johanna Pamp +6 more
TL;DR: Genomics-based analyses of human ocular body fluid specimens can provide actionable information relevant to infectious disease management as well as identify the sequence type of the microorganism and antibiotic resistance genes through analyses of whole genome sequence assemblies of isolates, and metagenomic assemblies.
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Virulence and resistance genes profiles and clonal relationships of non-typhoidal food-borne Salmonella strains isolated in Tunisia by whole genome sequencing.
Amal Ben Hassena,Julie Haendiges,Sonia Zormati,Sonda Guermazi,Radhouane Gdoura,Narjol Gonzalez-Escalona,Mariam Siala +6 more
TL;DR: This report is the first report of an application of WGS for genetic characterization of food-borne Tunisian strains using whole genome sequencing and subsequent data analysis to demonstrate that WGS provided an accurate tool for Genetic characterization of bacterial strains compared to usual molecular typing techniques.
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Phylogenetic Diversity and Antimicrobial Resistance of Campylobacter coli from Humans and Animals in Japan.
TL;DR: The first study to demonstrate the phylogenetic diversity and AMR profiles of C. coli in Japan suggests that poultry and cattle are major reservoirs, improving knowledge on the epidemiological and ecological traits of this pathogen.
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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