We published our paper in Nature Microbiology: Pneumococcal population structure influences the effects of air pollution on invasive disease risk in South Africa.
We published our paper in Nature Microbiology: Pneumococcal population structure influences the effects of air pollution on invasive disease risk in South Africa.
This work brought together over 59,000 epidemiological cases spanning 19 years from GERMS-SA and over 4,000 genome-sequenced isolates from the Global Pneumococcal Sequencing Project.
Using distributed lag non-linear models in a Bayesian hierarchical framework, we found that changes in weather and air pollution influence IPD risk, with variations by age, disease presentation, serotype, and lineage. Cold temperatures, moderate humidity, and high temperatures all increased risk with variable timing. Air pollution (specifically PM2.5) consistently increased disease risk, but response timing varied across serotypes (immediate heightened risk for NVT serotype 8 and PCV serotypes 4 and 23F), and lineages (such as GPSC21). Some of these different effects by strain could be explained by their gene prevalence (pangenome) and may suggest divergent serotype-specific invasion pathways. For example, the acute serotype 4 effect could be driven by its high prevalence of virulent psrP adhesion gene. Lots more to do! Looking forward to continuing this work towards identifying mechanisms and exploring different geographic and sociodemographic contexts over the coming years!
Huge thanks to the team at National Institute for Communicable Diseases (NICD) (NICD), especially Anne von Gottberg and my co-authors there Cebile Lekhuleni, Jackie Kleynhans, Meiring Susan, Mignon du Plessis without whom this work would not be possible. Thanks to Rachel Lowe and the GHR team at Barcelona Supercomputing Center for climate and health discussions throughout development of this project. Thanks to Stephanie LO and the GPS project and partners, especially at Wellcome Sanger Institute, for continuing support. Global collaborations like this are critical to answering such complex questions across massive microbial diversity. Thanks to Cristina Carnerero and Daniela Lührsen for lots of lessons about atmospheric composition and Giovenale Moirano for helping develop the method to incorporate the genomes into this analysis. Finally thanks to Schmidt Science Fellows without whom this wouldn’t have been possible.