Microbial diversity mediates the impact of air pollution on pneumococcal disease risk

Streptococcus pneumoniae (pneumococcus) remains a major global cause of invasive human disease with clear seasonal variation suggesting a role for environmental factors. The pneumococcus includes >100 serotypes and many lineages with different disease patterns. Interactions between microbial diversity, environmental factors, and invasive pneumococcal disease (IPD) remain unclear. We examined the effects of air pollution and meteorological factors on 59,017 IPD cases over 15 years, including 4,350 genome-sequenced isolates, using Bayesian spatio-temporal hierarchical models that link environmental exposures to bacterial diversity. Humidity and air pollution conferred the highest disease risk. In South Africa low humidity increased risk while high humidity was protective. Weekly PM_2.5 50 μg/m³ was associated with 4% cumulative risk increase with diversity-specific lag structures suggesting partially vaccine-mitigated risk. PM_2.5 risk was greatest in adults ≥65 and varied by disease type. Understanding these relationships may refine vaccine-impact models and inform air pollution policy targets.