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
Genomic Epidemiology of Vancomycin-Resistant Enterococcus faecium (VREfm) in Latin America: Revisiting The Global VRE Population Structure.
Rafael Rios,Jinnethe Reyes,Jinnethe Reyes,Lina P Carvajal,Sandra Rincon,Diana Panesso,Diana Panesso,Aura M Echeverri,An Dinh,Sergios-Orestis Kolokotronis,Apurva Narechania,Truc T. Tran,Jose M. Munita,Barbara E. Murray,Paul J. Planet,Paul J. Planet,Cesar A. Arias,Lorena Diaz,Lorena Diaz +18 more
TL;DR: The results show an early branching of animal related isolates and a further split of clinical isolates into two sub-clades within clade A and the overall phylogenomic structure was highly dependent on recombination.
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Genomic investigation of Staphylococcus aureus isolates from bulk tank milk and dairy cows with clinical mastitis
Troels Ronco,Ilka Christine Klaas,Marc Stegger,Line Svennesen,Lærke Boye Astrup,Michael Farre,Karl Pedersen +6 more
TL;DR: Dairy cows are natural carriers of the S. aureus subtypes that cause clinical mastitis if the right conditions are present and that a broad range of subtypes cause mastitis, according to a phylogenetic tree based on single nucleotide polymorphisms.
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Elucidation of quantitative structural diversity of remarkable rearrangement regions, shufflons, in IncI2 plasmids.
Tsuyoshi Sekizuka,Michiko Kawanishi,Mamoru Ohnishi,Ayaka Shima,Kengo Kato,Akifumi Yamashita,Mari Matsui,Satowa Suzuki,Makoto Kuroda +8 more
TL;DR: Findings indicate that remarkable rearrangement regions should be validated using both long-read and short-read sequencing data and that the structural variation of PilV in the shufflon might be closely related to phenotypic heterogeneity of plasmid-mediated transconjugation involved in horizontal gene transfer even in bacterial clonal populations.
Journal ArticleDOI
Real time application of whole genome sequencing for outbreak investigation - What is an achievable turnaround time?
Patrick McGann,Jessica Bunin,Erik Snesrud,Seema Singh,Rosslyn Maybank,Ana C. Ong,Yoon I. Kwak,Scott Seronello,Robert J. Clifford,Mary Hinkle,Stephen Yamada,Jason Barnhill,Emil Lesho +12 more
TL;DR: Whole genome sequencing was used to investigate an unfolding outbreak of vancomycin resistant Enterococcus faecium among 3 patients in the ICU of a tertiary care hospital and suggested nosocomial transmission involved two separate events from patient 1 to patient 2 and 3, and not a linear transmission suspected by the time line.
Journal ArticleDOI
Complete Genome Sequence of Klebsiella quasipneumoniae subsp. similipneumoniae Strain ATCC 700603
TL;DR: The complete genome of strain ATCC 700603 is reported and it is shown that the ESBL genes are plasmid-encoded, resulting in resistance to these drugs.
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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