Mustafa Abu Salim
Department of Microbiology, College of Medicine, Kuwait University, Kuwait City, Kuwait.
Med Princ Pract. 2024;33(3):185-197. doi: 10.1159/000538002. Epub 2024 Feb 23.
The success in determining the whole genome sequence of a bacterial pathogen was first achieved in 1995 by determining the complete nucleotide sequence of Haemophilus influenzae Rd using the chain-termination method established by Sanger et al. in 1977 and automated by Hood et al. in 1987. However, this technology was laborious, costly, and time-consuming. Since 2004, high-throughput next-generation sequencing technologies have been developed, which are highly efficient, require less time, and are cost-effective for whole genome sequencing (WGS) of all organisms, including bacterial pathogens. In recent years, the data obtained using WGS technologies coupled with bioinformatics analyses of the sequenced genomes have been projected to revolutionize clinical bacteriology. WGS technologies have been used in the identification of bacterial species, strains, and genotypes from cultured organisms and directly from clinical specimens. WGS has also helped in determining resistance to antibiotics by the detection of antimicrobial resistance genes and point mutations. Furthermore, WGS data have helped in the epidemiological tracking and surveillance of pathogenic bacteria in healthcare settings as well as in communities. This review focuses on the applications of WGS in clinical bacteriology.
1995年，通过使用1977年由桑格等人建立并于1987年由胡德等人实现自动化的链终止法，首次成功测定了细菌病原体的全基因组序列，即流感嗜血杆菌Rd的完整核苷酸序列。然而，这项技术费力、昂贵且耗时。自2004年以来，已开发出高通量的新一代测序技术，这些技术效率高、所需时间少，并且对于包括细菌病原体在内的所有生物体的全基因组测序（WGS）具有成本效益。近年来，使用WGS技术获得的数据以及对测序基因组的生物信息学分析预计将给临床细菌学带来变革。WGS技术已被用于从培养的生物体以及直接从临床标本中鉴定细菌种类、菌株和基因型。WGS还通过检测抗菌药物耐药基因和点突变，帮助确定对抗生素的耐药性。此外，WGS数据有助于在医疗机构以及社区中对病原菌进行流行病学追踪和监测。本综述重点关注WGS在临床细菌学中的应用。
