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Title: Estimating parameter distributions and developing epidemiological methods and tools to support gastrointestinal outbreak investigation
Author: Awofisayo-Okuyelu, Adedoyin
ISNI:       0000 0004 7971 5454
Awarding Body: University of Oxford
Current Institution: University of Oxford
Date of Award: 2018
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Incubation periods of common gastrointestinal pathogens are cited inconsistently without a solid evidence base for these distributions or factors affecting incubation time. In some high-profile outbreaks, such as the STEC O104 outbreak in Germany or the large 2009 STEC O157 outbreak in South East England, incubation periods were longer than expected complicating the collection of exposure data and the outbreak investigation process. This research aimed to use observational and experimental data to understand the incubation period distribution of some common gastrointestinal pathogens and identify factors that influence these distributions. I conducted systematic reviews on the incubation period of Campylobacter, STEC and Salmonella Typhi. In addition to using traditional methods for testing and describing the pattern of heterogeneity, I developed methods for analysing data from observational studies which involved using Kolmogorov-Smirnov test and hierarchical cluster analysis. I also extracted and analysed individual patient data of cases associated with outbreaks of STEC reported in England and Wales. Finally, I developed a within-host mathematical model that simulated the process of Salmonella Typhi infection and conducted a sensitivity analysis to identify influencing parameters. The systematic reviews and meta-analysis of individual patient data indicated the presence of heterogeneity across outbreaks which could not be explained by chance alone. Some factors associated with the distribution of incubation period were age, food vehicle, mode of transmission, attack rate and vaccine history. The mathematical model estimated an incubation period of 9.6 days for Salmonella Typhi, and parameters strongly correlated with incubation period included the net population of bacteria in the colon and bacterial growth during systemic infection. Outputs of this research will inform the development of policies and public health interventions that contribute towards reducing the burden of disease due to gastrointestinal infections. Further research, developing a stochastic model of the incubation period of Salmonella Typhi, is recommended.
Supervisor: McCarthy, Noel ; Hall, Ian Sponsor: NIHR Health Protection Research Unit in Gastrointestinal Infections
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available