Emerging and re-emerging infectious diseases represent a large and growing problem globally. Transmission within and between hospitals is an important mode of spread for many of the pathogens with the potential to cause major public health emergencies. For some pathogens, such as MERS-CoV and SARS-CoV, nosocomial transmission has been the dominant mode of spread. For COVID-19, the role of nosocomial transmission has so far been poorly defined, but it is clear that large numbers of healthcare workers have been infected. Multidrug-resistant bacterial pathogens also represent a major risk to patient health, particularly in resource-limited settings with high risk populations where antibiotics capable of treating such infections are not available.

The aims of this DPhil project are to characterize the role of hospitals and hospital networks in the transmission of emerging pathogens, and to develop mechanistic models of how hospital networks and their interactions with the wider community impact on epidemic dynamics for emerging pathogens. The work will consider health systems in different socio-economic settings and will make use of clinical, genomic and epidemiological data to calibrate models. Such mechanistic models will then be used to explore the potential effectiveness of different control measures including patient and healthcare worker screening, contact tracing, isolation and quarantine, ward and hospital closures, prophylaxis, vaccination, restrictions on movements between different hospitals and other infection control measures such as cleaning, hand hygiene and use of personal protective equipment.

This work will make use of existing data-sets (e.g. SARS-CoV-2, SARS-CoV and MERS-Cov) as well as data that are currently being collected for COVID-19. It is anticipated that available data for COVID-19 will include genomic as well as epidemiological data, and a major challenge will be to make use of diverse sources of data to inform the epidemiological models. The work will also make use of high resolution patient movement data which is available from some high income countries, and will require innovative approaches to characterizing patient movements within hospital networks in lower and middle income countries where such data are not available.