Vol.68 No.2 March 2020
Detection of antimicrobial resistance determinants using whole genome sequencing
1)Departments of Clinical Laboratory, Infection Control and Prevention, Kyoto University Hospital, 54 Shogoin-kawahara, Sakyo-ku, Kyoto, Japan
2)Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine
Abstract
Whole genome sequencing (WGS) is a technology that can obtain genetic information on the entire microbial genome swiftly by the use of next-generation sequencers. The use of WGS has been rapidly increasing in research fields. WGS provides all nucleotide sequences including chromosomes and plasmids. We therefore do not need to predefine target genes before experiments in contrast to PCR or microarray methods. WGS can provide not only data on antimicrobial resistance (AMR) genes but also species identification, multilocus sequence types, plasmid types, and virulence genes. WGS analysis consists of a next-generation sequence reaction and a bioinformatics analysis. Bioinformatics analyses utilize public AMR genes databases after draft genome assembly. Studies have already reported a high accuracy for resistance phenotype prediction among clinical Enterobacteriaceae isolates. However, AMR prediction using WGS still has issues to be solved: high cost, long turn-around time, lack of skilled technicians, technical limitations in analysis methods, lack of international standards for analysis and quality control. Further technical advances and standardization will enhance the possibility of introduction of WGS in clinical microbiology laboratories.
Key word
whole genome sequencing, next-generation sequencer, resistance gene, drug-resistant bacteria
Received
July 2, 2019
Accepted
August 29, 2019
Jpn. J. Chemother. 68 (2): 198-203, 2020
