Genomics and outbreak investigation: from sequence to consequence

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

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, 41–47]
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

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