Table 1 Examples of precision epidemiology

MRSA⁵⁰

Cambridge, UK

Whole-genome bacterial sequencing was used to help reconstruct transmission chains and identify a likely source for a sustained outbreak of MRSA within a hospital ward. This investigation led to targeted decolonization.

Ebola virus^36,37,67

West Africa

Whole-genome virus sequencing was used to help reconstruct transmission chains and confirm the first documented case of sexual transmission of Ebola virus. This investigation led to immediate changes to guidance for male survivors that included a recommendation to have semen tested for presence of viral RNA.

HIV²²

USA

Next-generation sequencing was used to identify low frequency drug resistance variants (≥1–3%) within individual patients. Baseline presence of a resistance variant, even at low frequency, increased probability of virologic failure.

HIV⁶⁸

British Columbia, Canada

An automated phylogenetic system was established for monitoring HIV outbreaks using routinely collected virus genetic data. This system was used to identify case clusters in near real time, thus directing public health interventions.

Candida auris ⁶⁹

Oxford, UK

Whole-genome fungal sequencing of patient and environmental isolates was used to help identify contaminated equipment as the source of many infections acquired within a hospital intensive care unit.

Yellow fever⁷⁰

Brazil

Whole-genome virus sequencing was used to show that the recent Yellow fever outbreak in Brazil was caused by repeated sylvatic (‘jungle’) spillover and not urban transmission. As sylvatic transmission involves different mosquito species than urban, this finding informs vector control strategies.

Zika virus⁴⁷

Florida, USA

Sequencing of virus genomes from cases and mosquitoes infected with Zika virus in Florida showed that multiple introductions of the virus from the Caribbean (perhaps hundreds) were required to sustain the outbreak, suggesting that traveler education and surveillance could reduce future outbreaks.

Lujo virus⁷¹

Zambia and South Africa

One of the earliest studies to use metagenomic sequencing of human samples to discover a novel virus responsible for a cluster of fatal hemorrhagic fever.

Listeria monocytogenes ⁴⁴

USA

By using whole-genome sequence data, investigators were able to substantially improve their ability to identify the source and cause of Listeria monocytogenes outbreaks.

Influenza virus⁷²

Worldwide

This paper shows that serological changes of influenza virus can be captured by studying virus genomic sequences. Such findings can be used to direct selection and design of seasonal influenza vaccines.

E. coli O104:H4 (ref. ⁷³)

Germany and France

Whole-genome sequencing of E. coli isolates was used to dissect a European outbreak of bloody diarrhea and hemolytic uremic syndrome caused by Shiga-toxin-producing E. coli.