The transmission of Streptococcus pneumoniae is not well understood despite its importance for evaluating the use case of pneumococcal vaccination schedules that rely on indirect protection. In Nha Trang, Vietnam, we have collected more than 30,000 nasopharyngeal swabs from young children and their care giver in 5 cross-sectional city-wide studies between 2017 and 2020. After covid-related delays during which the robustness of inference pipelines has been explored, all approvals are now in place to sequence about 3,000 of the 8,000 samples tested positive for S. pneumoniae. Whole genome and ultra-deep sequencing of these samples is expected to start in early 2022. All samples are linked to demographic, clinical and epidemiological information collected at the time of sampling. This provides a uniquely dense sampling frame for a single city that will allow the exploration of spatio-temporal transmission patterns of the pneumococcus and the identification of the pathogen’s prominent routes of transmission.

The PhD candidate will use this rich dataset to develop, test and implement a robust methodology to (i) infer pneumococcal transmission from genomic and epidemiological data, (ii) distinguish direct transmission events between recruited individuals from those involving an unsampled intermediary, (iii) identify who infects infants and toddlers with pneumococci using those techniques, and (iv) investigate the role of subdominantly carried serotypes in transmission.