Whole Genome Sequencing—Implications for Infection Prevention and Outbreak Investigations

  • Kyle J. PopovichEmail author
  • Evan S. Snitkin
Healthcare Associated Infections (G Bearman and D. Morgan, Section Editors)
Part of the following topical collections:
  1. Topical Collection on Healthcare Associated Infections


Purpose of Review

Whole genome sequencing (WGS) is a laboratory method that has emerged as a promising tool for epidemiologic investigations.

Recent Findings

Genomic epidemiology approaches have been utilized in outbreak settings, community settings, within acute care hospitals, and across healthcare facilities to better understand transmission and spread of potential pathogens. These studies have highlighted how essential robust epidemiologic data is in these analyses as well as how results can be translated into clinical practice and infection control and prevention.


Existing studies have highlighted both the promise and challenges of using WGS as an epidemiologic tool in a community and healthcare setting and across a region. Costs for performing and interpreting WGS analyses are decreasing, and availability of and experience with WGS analyses in healthcare epidemiology are increasing. With these favorable trends, this laboratory method soon could emerge as the gold standard for epidemiologic evaluations.


Whole genome sequencing (WGS) Genomic epidemiology Infection prevention Outbreaks 


Compliance with Ethical Standards

Conflict of Interest

Drs. Popovich and Snitkin declare no conflicts of interest.

Human and Animal Rights and Informed Consent

This article does not contain any studies with human or animal subjects performed by any of the authors.


Papers of particular interest, published recently, have been highlighted as: • Of importance •• Of major importance

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Copyright information

© Springer Science+Business Media New York 2017

Authors and Affiliations

  1. 1.Department of Internal Medicine, University Infectious DiseasesRush University Medical Center, Stroger Hospital of Cook CountyChicagoUSA
  2. 2.Department of Microbiology and Immunology, Department of Medicine, Division of Infectious Diseases, Center for Microbial SystemsUniversity of MichiganAnn ArborUSA

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