Development of a quantitative model for comparing the genomic and epidemiological signal of foodborne pathogens : improving the application of whole-genome sequencing to infectious disease epidemiology

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Hetman, Benjamin M.
University of Lethbridge. Faculty of Arts and Science
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Lethbridge, Alta : University of Lethbridge, Dept. of Biological Sciences
Interpreting microbial whole genome sequencing data remains an ongoing challenge in the fields of public health and epidemiology. For this thesis, 274 isolates of the human bacterial pathogen Campylobacter jejuni were selected for sequencing on the basis of their genotype and sampling metadata. A novel core genome typing method revealed that the genomic signal of bacterial isolates is not always concordant with their underlying epidemiology. To systematically examine this relationship, I developed an analytical model for quantifying the epidemiological similarity of bacterial isolates based on their sampling metadata, allowing for direct comparison to their genomic similarities. Applying this model to my dataset highlighted certain genotypes that were present throughout several diverse ecologies in disproportionately high amounts. A competitive recovery experiment revealed that particular genotypes seen in high prevalence in national and international repositories display preferential growth under laboratory conditions, providing evidence for systematic bias in infectious disease surveillance systems.
bacterial isolates , Campylobacter jejuni , disease surveillance systems , systemic bias , whole genome sequence