Whole-genome sequencing applications for evolution of clinical microbiology
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In the present review, we systematically examine the diverse applications of whole-genome sequencing (WGS) and next-generation sequencing (NGS) to elucidate the evolution of clinical microbiology. The review aims to provide novel insight and to improve understanding of the applications of WGS in clinical microbiology laboratories. It is organized into the following sections: (1) the various types of NGS machines; (2) NGS workflows for obtaining genome sequences; (3) comparative genomic analysis; (4) RNA-seq (transcriptome) analysis; (5) genome-based bacterial typing; (6) genome-based antimicrobial resistance (AMR) detection; and (7) identification of integrative and conjugative elements carrying AMR gene(s). Four figures and three tables are provided to illustrate this information. The discussion focuses on WGS applications using several genera of microorganisms (Streptococcus, Enterococcus, Staphylococcus, Pasteurella, and Mycobacterium). Overall, WGS and related NGS technologies provide innovative clinical microbiology laboratory studies based on high-throughput genomic results for pathogen identification, tracking, and AMR/virulence profiling. In line with the concept of “One Health,” human and animal microbiology laboratories should pay careful attention to the drastically dynamic evolution of WGS and related NGS technologies.
Abstract
In the present review, we systematically examine the diverse applications of whole-genome sequencing (WGS) and next-generation sequencing (NGS) to elucidate the evolution of clinical microbiology. The review aims to provide novel insight and to improve understanding of the applications of WGS in clinical microbiology laboratories. It is organized into the following sections: (1) the various types of NGS machines; (2) NGS workflows for obtaining genome sequences; (3) comparative genomic analysis; (4) RNA-seq (transcriptome) analysis; (5) genome-based bacterial typing; (6) genome-based antimicrobial resistance (AMR) detection; and (7) identification of integrative and conjugative elements carrying AMR gene(s). Four figures and three tables are provided to illustrate this information. The discussion focuses on WGS applications using several genera of microorganisms (Streptococcus, Enterococcus, Staphylococcus, Pasteurella, and Mycobacterium). Overall, WGS and related NGS technologies provide innovative clinical microbiology laboratory studies based on high-throughput genomic results for pathogen identification, tracking, and AMR/virulence profiling. In line with the concept of “One Health,” human and animal microbiology laboratories should pay careful attention to the drastically dynamic evolution of WGS and related NGS technologies.