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 | |
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 | |
 | Identification of virulence factors and antimicrobial resistance | |
Analysis and hypothesis testing | Iterative refinements to assumptions and models | |
Institution and verification of control measures | Documenting effects of vaccination on pathogen populations | |
 | Confirmation that infections are imported rather than locally transmitted | |
Communication | Need for user-friendly digital output easily transferred between laboratories and expert advice of clinical academics at home in research and clinical environments | Â |