Selected insights from application of whole-genome sequencing for outbreak investigations

被引：33

作者：

Vien Thi Minh Le ^{[1
]}

Diep, Binh An ^{[1
,2
]}

机构：

[1] Univ Calif San Francisco, Dept Med, Div Infect Dis, San Francisco, CA USA

[2] Univ Calif Berkeley, Sch Publ Hlth, Div Infect Dis & Vaccinol, Berkeley, CA 94720 USA

来源：

CURRENT OPINION IN CRITICAL CARE | 2013年 / 19卷 / 05期

关键词：

foodborne outbreaks; infection control; nosocomial infection; outbreak investigation; whole-genome sequencing; RESISTANT STAPHYLOCOCCUS-AUREUS; ESCHERICHIA-COLI; MYCOBACTERIUM-TUBERCULOSIS; MRSA; COLONIZATION; TRANSMISSION; VIRULENCE;

D O I：

10.1097/MCC.0b013e3283636b8c

中图分类号：

R4 [临床医学];

学科分类号：

1002 ; 100602 ;

摘要：

Purpose of reviewThe advent of high-throughput whole-genome sequencing has the potential to revolutionize the conduct of outbreak investigation. Because of its ultimate resolution power for differentiating between closely related pathogen strains, whole-genome sequencing could augment the traditional epidemiologic investigations of infectious disease outbreaks.Recent findingsThe combination of whole-genome sequencing and intensive epidemiologic analysis provided new insights on the sources and transmission dynamics of large-scale epidemics caused by Escherichia coli and Vibrio cholerae, nosocomial outbreaks caused by methicillin-resistant Staphylococcus aureus, Klebsiella pneumoniae, Mycobacterium abscessus, community-centered outbreaks caused by Mycobacterium tuberculosis, and natural disaster-associated outbreaks caused by environmentally acquired molds.SummaryWhen combined with traditional epidemiologic investigation, whole-genome sequencing has proven useful for elucidating the sources and transmission dynamics of disease outbreaks. Development of a fully automated bioinformatics pipeline for the analysis of whole-genome sequence data is much needed to make this powerful tool more widely accessible.

引用

页码：432 / 439

页数：8

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