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
More filters
Journal ArticleDOI
Multidrug-resistant Escherichia coli isolated from canine faeces in a public park in Quito, Ecuador.
David Ortega-Paredes,David Ortega-Paredes,Marco Haro,Paula Leoro-Garzón,Pedro Barba,Karen Loaiza,Francisco X Mora,Martha Fors,Christian Vinueza-Burgos,Esteban Fernandez-Moreira +9 more
TL;DR: The finding of multidrug resistant E. coli in dog feces found in a city park illustrates the importance of analyzing canine feces in public settings as part of MDR E. Escherichia coli surveillance programs.
Journal ArticleDOI
Identification of virulence factors and antibiotic resistance markers using bacterial genomics
Sofiane Bakour,S.A. Sankar,J. Rathored,Philippe Biagini,Didier Raoult,Pierre-Edouard Fournier +5 more
TL;DR: The usefulness of whole-genome sequencing for the detection of virulence and antibiotic resistance associated genes is reviewed.
Journal ArticleDOI
Multistate population and whole genome sequence-based strain surveillance of invasive pneumococci recovered in the USA during 2017.
Jasmine Varghese,Sopio Chochua,Theresa Tran,Hollis Walker,Zhongya Li,P.M. Snippes Vagnone,Ruth Lynfield,Lesley McGee,Yanping Li,Benjamin J. Metcalf,Tamara Pilishvili,Bernard Beall +11 more
TL;DR: This well-annotated year 2017 WGS/strain dataset will prove useful for a broad variety of analyses and improved the understanding of IPD-causing strains in the post-PCV13 era.
Journal ArticleDOI
Protective role of the vulture facial skin and gut microbiomes aid adaptation to scavenging.
Marie Lisandra Zepeda Mendoza,Michael Roggenbuck,Karla Vargas,Karla Vargas,Lars Hestbjerg Hansen,Søren Brunak,Søren Brunak,M. Thomas P. Gilbert,M. Thomas P. Gilbert,Thomas Sicheritz-Pontén,Thomas Sicheritz-Pontén +10 more
TL;DR: The results highlight the importance of complementing genomic analyses with metagenomics in order to obtain a clearer understanding of the host-microbial alliance and show the need of microbiome-mediated health protection for adaptation to extreme diets, such as scavenging.
Posted ContentDOI
One Health genomic surveillance of Escherichia coli demonstrates distinct lineages and mobile genetic elements in isolates from humans versus livestock
Catherine Ludden,Kathy E. Raven,Dorota Jamrozy,Theodore Gouliouris,Beth Blane,Francesc Coll,Marcus C. de Goffau,Plamena Naydenova,Carolyne Horner,Juan Hernandez-Garcia,Paul Wood,Nazreen F. Hadjirin,Milorad Radakovic,Nicholas M. Brown,Mark A. Holmes,Julian Parkhill,Sharon J. Peacock +16 more
TL;DR: There was limited evidence to support the suggestion that antimicrobial resistant pathogens that cause serious infection in humans originate from livestock, and genomic epidemiology in a One Health study conducted in the East of England concluded that the idea that E. coli causing invasive disease or their resistance genes are commonly acquired from livestock was wrong.
References
More filters
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.
Related Papers (5)
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
Trimmomatic: a flexible trimmer for Illumina sequence data
The RAST Server: Rapid Annotations using Subsystems Technology
Ramy K. Aziz,Ramy K. Aziz,Daniela Bartels,Aaron A. Best,Matthew DeJongh,Terrence Disz,Terrence Disz,Robert Edwards,Kevin Formsma,Svetlana Gerdes,Elizabeth M. Glass,Michael Kubal,Folker Meyer,Folker Meyer,Gary J. Olsen,Gary J. Olsen,Robert Olson,Robert Olson,Andrei L. Osterman,Ross Overbeek,Leslie Klis McNeil,Daniel Paarmann,Tobias Paczian,Bruce Parrello,Gordon D. Pusch,Claudia I. Reich,Rick Stevens,Rick Stevens,Olga Vassieva,Veronika Vonstein,Andreas Wilke,Olga Zagnitko +31 more