University of Texas Health Science Center at Houston - School of Public Health.
Center for Antimicrobial Resistance and Microbial Genomics.
Curr Opin Infect Dis. 2021 Aug 1;34(4):339-345. doi: 10.1097/QCO.0000000000000743.
The advancement of molecular techniques such as whole-genome sequencing (WGS) has revolutionized the field of bacterial strain typing, with important implications for epidemiological surveillance and outbreak investigations. This review summarizes state-of-the-art techniques in strain typing and examines barriers faced by clinical and public health laboratories in implementing these new methodologies.
WGS-based methodologies are on track to become the new 'gold standards' in bacterial strain typing, replacing traditional methods like pulsed-field gel electrophoresis and multilocus sequence typing. These new techniques have an improved ability to identify genetic relationships among organisms of interest. Further, advances in long-read sequencing approaches will likely provide a highly discriminatory tool to perform pangenome analyses and characterize relevant accessory genome elements, including mobile genetic elements carrying antibiotic resistance determinants in real time. Barriers to widespread integration of these approaches include a lack of standardized workflows and technical training.
Genomic bacterial strain typing has facilitated a paradigm shift in clinical and molecular epidemiology. The increased resolution that these new techniques provide, along with epidemiological data, will facilitate the rapid identification of transmission routes with high confidence, leading to timely and effective deployment of infection control and public health interventions in outbreak settings.
全基因组测序（WGS）等分子技术的进步彻底改变了细菌株分型领域，对流行病学监测和暴发调查具有重要意义。本综述总结了目前的菌株分型技术，并探讨了临床和公共卫生实验室在实施这些新方法时所面临的障碍。
基于 WGS 的方法有望成为细菌株分型的新“金标准”，取代传统方法，如脉冲场凝胶电泳和多位点序列分型。这些新技术能够更好地识别目标生物之间的遗传关系。此外，长读测序方法的进步可能提供一种高度区分的工具，实时进行泛基因组分析和描述相关的辅助基因组元件，包括携带抗生素耐药决定因素的移动遗传元件。广泛整合这些方法的障碍包括缺乏标准化的工作流程和技术培训。
基因组细菌株分型促进了临床和分子流行病学的范式转变。这些新技术提供的更高分辨率以及流行病学数据将有助于高度置信地快速识别传播途径，从而及时有效地在暴发环境中部署感染控制和公共卫生干预措施。
