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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, 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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