title: Selected insights from application of whole-genome sequencing for outbreak investigations.
abstract: OBJECTIVE
  The 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.
  
  
  RESULTS
  The 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.
  
  
  CONCLUSIONS
  When 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.
authors.affiliation: 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.
authors.forename: Vien Thi Minh
authors.initials: VT
authors.lastname: Le
authors.forename: Binh An
authors.initials: BA
authors.lastname: Diep
mesh_terms: D001427:Bacterial Toxins / Q000235:genetics; D015373:Bacterial Typing Techniques; D003428:Cross Infection / Q000235:genetics* / Q000382:microbiology*; D004190:Disasters; D004196:Disease Outbreaks; D005517:Foodborne Diseases / Q000235:genetics* / Q000382:microbiology*; D016680:Genome, Bacterial / Q000235:genetics*; D016681:Genome, Fungal / Q000235:genetics*; D006801:Humans; D008826:Microbial Sensitivity Tests; D009181:Mycoses / Q000235:genetics* / Q000382:microbiology*; D017422:Sequence Analysis, DNA
chemical_list: D001427:Bacterial Toxins