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Clinical Review State of the Art Review

The role of pathogen genomics in assessing disease transmission

BMJ 2015; 350 doi: (Published 11 May 2015) Cite this as: BMJ 2015;350:h1314
  1. Vitali Sintchenko, associate professor, director12,
  2. Edward C Holmes, professor13
  1. 1Marie Bashir Institute for Infectious Diseases and Biosecurity and Sydney Medical School, University of Sydney, Sydney, Australia
  2. 2Centre for Infectious Diseases and Microbiology-Public Health, Institute of Clinical Pathology and Medical Research-Pathology West, Westmead Hospital, Sydney, NSW 2145, Australia
  3. 3School of Biological Sciences, Charles Perkins Centre, University of Sydney, Sydney, Australia
  1. Correspondence to: V Sintchenko vitali.sintchenko{at}


Whole genome sequencing (WGS) of pathogens enables the sources and patterns of transmission to be identified during specific disease outbreaks and promises to transform epidemiological research on communicable diseases. This review discusses new insights into disease spread and transmission that have come from the use of WGS, particularly when combined with genomic scale phylogenetic analyses. These include elucidation of the mechanisms of cross species transmission, the potential modes of pathogen transmission, and which people in the population contribute most to transmission. Particular attention is paid to the ability of WGS to resolve individual patient to patient transmission events. Importantly, WGS data seem to be sufficiently discriminatory to target cases linked to community or hospital contacts and hence prevent further spread, and to investigate genetically related cases without a clear epidemiological link. Approaches to combine evidence from epidemiological with genomic sequencing observations are summarised. Ongoing genomic surveillance can identify determinants of transmission, monitor pathogen evolution and adaptation, ensure the accurate and timely diagnosis of infections with epidemic potential, and refine strategies for their control.


  • Both authors were supported by the Australian National Health and Medical Research Council.

  • Contributors: Both authors had full access to the content of this review, wrote the manuscript, and are guarantors.

  • Competing interests: We have read and understood BMJ policy on declaration of interests and declare the following interests: none.

  • Provenance and peer review: Commissioned; externally peer reviewed.

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