Identification of acquired antimicrobial resistance genes

TY - JOUR

T1 - Identification of acquired antimicrobial resistance genes

AU - Zankari, Ea

AU - Hasman, Henrik

AU - Cosentino, Salvatore

AU - Vestergaard, Martin

AU - Rasmussen, Simon

AU - Lund, Ole

AU - Aarestrup, Frank Møller

AU - Larsen, Mette Voldby

PY - 2012/11

Y1 - 2012/11

N2 - 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. Methods: We developed a web-based method, ResFinder that uses BLAST for identification of acquired antimicrobial resistance genes in whole-genome data. As input, the method can use both pre-assembled, complete or partial genomes, and short sequence reads from four different sequencing platforms. The method was evaluated on 1862 GenBank files containing 1411 different resistance genes, as well as on 23 de-novo-sequenced isolates. Results: When testing the 1862 GenBank files, the method identified the resistance genes with an ID = 100% (100% identity) to the genes in ResFinder. Agreement between in silico predictions and phenotypic testing was found when the method was further tested on 23 isolates of five different bacterial species, with available phenotypes. Furthermore, ResFinder was evaluated on WGS chromosomes and plasmids of 30 isolates. Seven of these isolates were annotated to have antimicrobial resistance, and in all cases, annotations were compatible with the ResFinder results. Conclusions: A web server providing a convenient way of identifying acquired antimicrobial resistance genes in completely sequenced isolates was created. ResFinder can be accessed at. www.genomicepidemiology.org. ResFinder will continuously be updated as new resistance genes are identified.

AB - 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. Methods: We developed a web-based method, ResFinder that uses BLAST for identification of acquired antimicrobial resistance genes in whole-genome data. As input, the method can use both pre-assembled, complete or partial genomes, and short sequence reads from four different sequencing platforms. The method was evaluated on 1862 GenBank files containing 1411 different resistance genes, as well as on 23 de-novo-sequenced isolates. Results: When testing the 1862 GenBank files, the method identified the resistance genes with an ID = 100% (100% identity) to the genes in ResFinder. Agreement between in silico predictions and phenotypic testing was found when the method was further tested on 23 isolates of five different bacterial species, with available phenotypes. Furthermore, ResFinder was evaluated on WGS chromosomes and plasmids of 30 isolates. Seven of these isolates were annotated to have antimicrobial resistance, and in all cases, annotations were compatible with the ResFinder results. Conclusions: A web server providing a convenient way of identifying acquired antimicrobial resistance genes in completely sequenced isolates was created. ResFinder can be accessed at. www.genomicepidemiology.org. ResFinder will continuously be updated as new resistance genes are identified.

KW - Bacteria

KW - Bacterial Infections

KW - Computational Biology

KW - Drug Resistance, Bacterial

KW - Humans

KW - Internet

KW - Faculty of Health and Medical Sciences

KW - antibiotic resistance

KW - Genotype

KW - ResFinder

KW - resistance gene identification

U2 - 10.1093/jac/dks261

DO - 10.1093/jac/dks261

M3 - Journal article

C2 - 22782487

SN - 0305-7453

VL - 67

SP - 2640

EP - 2644

JO - Journal of Antimicrobial Chemotherapy

JF - Journal of Antimicrobial Chemotherapy

IS - 11

ER -