PhD studentship
Estimating parameter distributions and developing epidemiological methods and tools to support
GI outbreak investigation.
Both parameters, such as incubation time, and analytical approaches used in outbreak investigation largely follow longstanding estimates and methods. Cited incubation time parameters for some infections are based on little evidence, for novel infections they are unknown, and factors affecting incubation time are poorly understood. In high profile outbreaks such as the STEC 104 outbreak in
Germany incubation times were longer than expected, complicating the collection of relevant exposure data. Improvement in the evidence base for both parameters and methods should improve the practice of public health epidemiology. This work aims to use the population laboratory approach afforded by systematic surveillance and the natural experiments afforded by outbreaks to define key epidemiological parameters and to develop and test epidemiological methods and approaches. The NIHR Health Protection Research Unit (HPRU) in GI infections combining Public
Health England (PHE) activity and data and both PHE and university expertise provides a framework to undertake work in this area. Other HPRUs such as modelling methodologies have both overlapping and complementary interests and capacity and are natural collaborators. Participation in this project will include GI HPRU staff in the University of Oxford (Noel McCarthy) and PHE Field
Epidemiology Service (Paul Cleary) and Centre for Infectious Disease Surveillance and Control
(Gordon Nichols) and collaborating HPRU staff (Modelling Methodologies and Emergency
Preparedness and Response) at PHE Porton Down (Ian Hall).
A DPhil studentship funded by the NIHR Health Protection Research unit in GI Infections is available offering a tax free stipend at the RCUK stipend rate of £14,057 per year and payment of university and college fees (home student rates) funded by the NIHR Health Protection Research Unit in
Gastrointestinal Infections. This studentship will be based at the Department of Zoology, University of Oxford which is part of the Mathematical, Physical and Life Sciences Division and has an active body of approximately 160 doctoral students at any time http://www.ox.ac.uk/admissions/graduate/courses/dphil-zoology .The student will also be part of the Health Protection Research Unit academy being established by Public Health England to support professional training of those undertaking doctorates across the full range of Health Protection
Research Unit themes.
The ideal candidate will be a mathematically strong graduate with interest in developing and translating mathematical approaches to support public health issues in the area of outbreaks of infectious disease. The project will involve working with a multidisciplinary team and across institutions and will require good personal and communication skills. The skills gained would provide a foundation for either an academic or service public health career in this area of work.
Informal enquiries can be made to noel.mccarthy@zoo.ox.ac.uk
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Project – fuller description if we can have a link to this
Estimating parameter distributions and developing epidemiological methods and tools to support
GI outbreak investigation.
Rationale and aims
Both parameters, such as incubation time, and analytical approaches used in outbreak investigation largely follow longstanding estimates and methods. Cited incubation time parameters for some infections are based on little evidence, for novel infections they are unknown, and factors affecting incubation time are poorly understood. In high profile outbreaks such as the STEC 104 outbreak in
Germany and Godstone Farm outbreak in England incubation times were longer than expected, complicating the collection of relevant exposure data. Improvement in the evidence base for both parameters and methods should improve the practice of public health epidemiology. The outputs of this work are expected to include:
1.
Identification of factors affecting the incubation period and estimates of incubation time distribution and associated related parameters.
2.
An application that will support synthesis of prior estimates of incubation time and information from accruing data in an outbreak on incubation time.
3.
Development and evaluation of epidemiological approaches to support the investigation of outbreaks of GI disease.
4.
A PHE held resource of outbreak datasets to support future research and analytical method development.
5.
Protocols to improve PHEs capacity to collate and jointly analyse datasets from future outbreaks of GI infection increasing the research resources generated by PHE.
Context and project participants
This work aims to use the population laboratory approach afforded by systematic surveillance and the natural experiments afforded by outbreaks to define key epidemiological parameters and to develop and test epidemiological methods and approaches. The NIHR Health Protection Research
Unit (HPRU) in GI infections combining Public Health England (PHE) activity and data and both PHE and university expertise provides a framework to undertake work in this area. Other HPRUs such as modelling methodologies have both overlapping and complementary interests and capacity and are natural collaborators. Participation in this project will include GI HPRU staff in the University of
Oxford (Noel McCarthy) and PHE Field Epidemiology Service (Paul Cleary) and Centre for Infectious
Disease Surveillance and Control (Gordon Nichols) and collaborating HPRU staff (Modelling
Methodologies and Emergency Preparedness and Response) at PHE Porton Down (Ian Hall).
Research approach:
1.
Secondary research to define the existing evidence base for epidemiological parameters identified as critical including incubation time distributions and factors affecting them.
2.
Collation of PHE outbreak data to develop a dataset for this project and to act as a research resource for PHE and the HPRU collaborators.
3.
Description of the distribution of incubation times and factors affecting these for GI pathogens integrating data from published literature and PHE datasets.

4.
Development of a model to integrate prior knowledge (e.g. a prior distribution of incubation time based on existing data for the pathogen or similar pathogen strains) and accruing data in an outbreak.
5.
Evaluation of the results of different analytical approaches to detecting disease – exposure associations within outbreak datasets e.g. case-control comparison compared with casecrossover where exposure histories cover longer time periods than the incubation time.
Initially his may involve analysis of simulated datasets as well as real data.
6.
Evaluation of the usefulness of existing outbreak datasets as a research resource with recommendations for how data collection during outbreak response could improve this.
7.
Development of research protocols for use in PHE during outbreak response to provide appropriate data to add to the evidence base for GI infections and outbreak investigation.