Using genomic & human mobility data to elucidate long-range migration of Streptococcus pneumoniae
Channel: BSC CNS
Date: 2023-04-21

🗣Speaker: Sophie Belman, PhD candidate at the Wellcome Sanger Institute & University of Cambridge.

Streptococcus pneumoniae is a globally endemic, human obligate bacteria, and a leading cause child mortality by pneumonia and meningitis worldwide. Despite the enormous public health burden, the extent and mechanisms of pneumococcal spread across spatial scales remains largely unknown. We analysed 6910 geolocated pneumococcal genome sequences from patients, collected from 2000-2014 in South Africa. We develop mechanistic phylogeographic models to reconstruct pathogen spread, incorporating the generation time distribution, human mobility data provided by Meta, population size, and underlying heterogeneities in sampling. We found that pairs from the same province had 2.43 (95%CI 2.02-3.17) times the relative risk of having a recent common ancestor (within 5 years) than distal pairs . As the evolutionary time between isolates increases the relative probability of being from the same province decreases, however, it is only after around 50 years that the pneumococcus appeared to be well mixed throughout the country We were able to accurately recover this observed pattern of spatial-spread using our mechanistic model estimating that most transmission events were local with occasional long-distance transmissions. Our framework also showed the key role of travel to large cities in disease spread. We found that following an introduction, pneumococcus was 20 times more likely to have travelled to a major population hub than elsewhere after one year of sequential person-to-person transmission. We incorporated a fitness effect model to estimate the impact of non-vaccine serotype expansion after vaccination. The pneumococcus spreads slowly across South Africa, driven by limited long-distance human mobility and the long generation time of pneumococcus. Our framework provides an opportunity to explore whether similar patterns of spread are observed elsewhere with differing mobility patterns, or whether vaccine introduction results in different patterns of spread across pneumococcal serotypes.

Further information here: https://www.bsc.es/research-and-development/research-seminars/sorswomeninbsc-using-genomic-and-human-mobility-data-elucidate-the-long-range-migration