Infectious diseases remain a leading cause of morbidity and mortality worldwide, and antimicrobial resistance (AMR) continues to erode the effectiveness of standard treatment pathways. Against this backdrop, whole-genome sequencing (WGS) has shifted from being a specialized research capability to a practical engine for clinical decision support, outbreak investigation, and pathogen surveillance. The review by the distinguished Japanese scholar Professor Takashi Takahashi [1], “Whole-genome sequencing applications for evolution of clinical microbiology,” arrives at a timely moment, capturing not only what WGS can do today but also how rapidly its laboratory and analytic ecosystems are evolving.

The major strength of the review is its clear laboratory-facing structure. It systematically walks readers through major next-generation sequencing (NGS) platforms, workflows for generating genomes, comparative genomics, RNA-seq, genome-based typing, genome-based AMR detection, and identification of integrative and conjugative elements that mobilize resistance, supported by four figures and three tables that anchor key concepts in practice. Such arrangement makes the review useful both as an introduction for newcomers and as a reference for established laboratories refining their pipelines.

The review is particularly meaningful because it is written from the perspective of a researcher who has repeatedly implemented whole-genome and transcriptome methods in real laboratory workflows and not merely summarized them. Throughout the review, the methodological discussion is anchored in first-hand bench-to-bioinformatics experience, from generating pathogen genomes using short-read sequencing and hybrid long/short-read assembly to applying pan-genome and comparative genomics to clinically relevant questions, as well as extending these approaches to transcriptomic analyses of host-entry environments. The same practical lens shapes the treatment of mobile genetic elements and the spread of AMR, drawing on recent characterizations of integrative and conjugative elements carrying resistance determinants in streptococci. Overall, the review reads as guidance distilled from hands-on experience in conducting, troubleshooting, and interpreting results in clinical and “One Health” contexts.

The review is an invited comprehensive lecture, and we express our sincere gratitude for Professor Takahashi’s generous contribution. We also thank Professor Sunjoo Kim for arranging and facilitating this invitation. The friendship and sustained academic exchanges between the two professors are truly exemplary, and they offer a model that younger scholars should respect, emulate, and carry forward. Looking ahead, Annals of Clinical Microbiology (ACM) will continue to promote and expand activities that strengthen international academic collaboration, encourage meaningful cross-border dialogue, and build enduring research partnerships across disciplines and institutions.