Title:
Are bacterial enteric pathogens detectable in the healthy stool microbiome?
Summary:
Diarrhoeal disease is a leading cause of death and malnutrition in young children worldwide. In addition to common viral infections such as norovirus and rotavirus, major bacterial causes of diarrhoea include Vibrio cholerae, Shigella spp., Salmonella enterica, Campylobacter spp. and certain E. coli. Despite causing what can be life-threatening acute diarrhoea, household studies suggest that 40-80% of infections with diarrhoea-causing bacteria may be asymptomatic. Although asymptomatic carriers might shed lower levels of bacteria in the stool than those with symptoms, they may be more likely to travel and contribute to long-range transmission. However it is unclear how common asymptomatic carriers are in a healthy population, and whether carriage can be detected by shotgun stool metagenomics.
In this project, the student will map stool metagenomic data to the reference genomes of bacterial diarrhoeal pathogens such as Vibrio cholerae, Salmonella enterica and Shigella spp., as well as to the DNA sequences encoding the E. coli, Shigella and cholera toxins. This will give preliminary insight into the frequency of asymptomatic carriage and the feasibility of detecting carriers from stool metagenomics.
Required knowledge:
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Previous experience in bash scripting and R/python would be advantageous but not essential.
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The project would suit a student with an interest in data science, bioinformatics and/or infectious disease research.