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Table 2 How whole-genome sequencing contributes to each step in outbreak investigation

From: Genomics and outbreak investigation: from sequence to consequence

Step Contribution of whole-genome sequencing (WGS) References
Confirming the existence of an outbreak Bench-top sequencing of whole bacterial genomes in near real time to confirm or refute the existence of outbreaks of MRSA or C. difficile [25]
  Open-ended diagnostic metagenomics to identify and characterize outbreak strain [30]
Case definition WGS and/or metagenomics leads to the development of diagnostic reagents then used in defining cases within an outbreak [3, 31, 32]
Descriptive study: collecting data and generating hypotheses Integration of WGS with geographical data to uncover modes of spread of typhoid [38]
  Reconstruction of routes of transmission, including hidden transmission events [25, 45, 59, 60]
  Identification of virulence factors and antimicrobial resistance [26, 34, 36]
Analysis and hypothesis testing Iterative refinements to assumptions and models [25, 27, 36, 4147]
Institution and verification of control measures Documenting effects of vaccination on pathogen populations [48, 49]
  Confirmation that infections are imported rather than locally transmitted [25, 27, 50]
Communication Need for user-friendly digital output easily transferred between laboratories and expert advice of clinical academics at home in research and clinical environments