• Curr Opin Crit Care · Oct 2013

    Review

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

    • Vien Thi Minh Le and Binh An Diep.
    • aDivision of Infectious Diseases, Department of Medicine, University of California, San Francisco, California bDivision of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, USA.
    • Curr Opin Crit Care. 2013 Oct 1; 19 (5): 432-9.

    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.

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