Uemura Kojiro, Sato Toyotaka, Yamamoto Soh, Ogasawara Noriko, Toyting Jirachaya, Aoki Kotaro, Takasawa Akira, Koyama Masayuki, Saito Atsushi, Wada Takayuki, Okada Kaho, Yoshida Yurie, Kuronuma Koji, Nakajima Chie, Suzuki Yasuhiko, Horiuchi Motohiro, Takano Kenichi, Takahashi Satoshi, Chiba Hirofumi, Yokota Shin-Ichi
Department of Microbiology, Sapporo Medical University School of Medicine, Chuo-Ku, Sapporo, Japan.
Department of Respiratory Medicine, Sapporo Medical University School of Medicine, Chuo-Ku, Sapporo, Japan.
Nat Commun. 2025 Mar 25;16(1):2917. doi: 10.1038/s41467-025-58049-1.
Bacteria continually evolve. Previous studies have evaluated bacterial evolution in retrospect, but this approach is based on only speculation. Cohort studies are reliable but require a long duration. Additionally, identifying which genetic mutations that have emerged during bacterial evolution possess functions of interest to researchers is an exceptionally challenging task. Here, we establish a Rapid and Integrated Bacterial Evolution Analysis (RIBEA) based on serial passaging experiments using hypermutable strains, whole-genome and transposon-directed sequencing, and in vivo evaluations to monitor bacterial evolution in a cohort for one month. RIBEA reveals bacterial factors contributing to serum and antimicrobial resistance by identifying gene mutations that occurred during evolution in the major respiratory pathogen Klebsiella pneumoniae. RIBEA also enables the evaluation of the risk for the progression and the development of invasive ability from the lung to blood and antimicrobial resistance. Our results demonstrate that RIBEA enables the observation of bacterial evolution and the prediction and identification of clinically relevant high-risk bacterial strains, clarifying the associated pathogenicity and the development of antimicrobial resistance at genetic mutation level.
细菌不断进化。以往的研究都是事后评估细菌进化情况，但这种方法仅仅基于推测。队列研究很可靠，但需要很长时间。此外，确定在细菌进化过程中出现的哪些基因突变具有研究人员感兴趣的功能是一项极具挑战性的任务。在此，我们基于使用超突变菌株的连续传代实验、全基因组和转座子定向测序以及体内评估建立了一种快速综合细菌进化分析方法（RIBEA），以在一个月的队列研究中监测细菌进化。RIBEA通过鉴定主要呼吸道病原体肺炎克雷伯菌进化过程中发生的基因突变，揭示了导致血清抗性和抗菌抗性的细菌因素。RIBEA还能够评估从肺部到血液的侵袭能力进展和发展以及抗菌抗性的风险。我们的结果表明，RIBEA能够观察细菌进化，并预测和鉴定临床相关的高风险细菌菌株，在基因突变水平上阐明相关的致病性和抗菌抗性的发展。
