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O029 - ELUCIDATING THE SPATIOTEMPORAL DYNAMICS OF STREPTOCOCCUS PNEUMONIAE IN SOUTH AFRICA USING GENETIC AND HUMAN MOBILITY DATA (ID 132)
Abstract
Background
Streptococcus pneumoniae is a globally endemic, human obligate bacteria, and a leading cause of pneumonia and meningitis worldwide. Despite the enormous public health burden, the extent and mechanisms of pneumococcal spread across spatial scales remains largely unknown.
Methods
We analyze 5970 geolocated pneumococcal genome sequences from pneumococcal disease 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 Facebook, population size, and underlying heterogeneities in sampling.
Results
We found that sequence pairs from the same genotype and the same province had 4.7[3.4-7.4] times the probability of having a MRCA within 3 years compared to sequence pairs from >1000km apart. Pneumococci become homogenously mixed across South Africa after 50 years (relative-risk=1). We were able to accurately recover this observed pattern of spatial-spread using our mechanistic model estimating that most transmission events were local (77% within municipality), 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 (population >3-million) than elsewhere after one year of sequential person-to-person transmission.
Conclusions
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.