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Peer-reviewedCC BY 4.0Nature Microbiology

Pneumococcal population structure influences the effects of air pollution on invasive disease risk in South Africa

  • Sophie Belman1,2,3
  • Cebile Lekhuleni4,5
  • Jackie Kleynhans4,6
  • Giovenale Moirano1,7
  • Daniela Lührsen1
  • Cristina Carnerero1
  • Susan Meiring8
  • Stephanie W. Lo2,9
  • Mignon du Plessis4,5
  • Anne von Gottberg4,5,10
  • Rachel Lowe1,11,12
12 affiliations
  1. 1Barcelona Supercomputing Center (BSC), Barcelona, Spain
  2. 2Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK
  3. 3Present Address: Environmental Health Sciences, Yale School of Public Health, New Haven, CT USA
  4. 4Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
  5. 5Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
  6. 6School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
  7. 7Department of Medical Sciences, University of Turin, Torino, Italy
  8. 8Division of Public Health Surveillance and Response, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
  9. 9European Molecular Biology Laboratory–European Bioinformatics Institute, Cambridge, UK
  10. 10Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
  11. 11Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
  12. 12Centre on Climate Change and Planetary Health and Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK
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Abstract

Streptococcus pneumoniae is highly diverse, comprising over 100 serotypes and hundreds of genomic lineages amid widespread vaccination. While it can cause invasive pneumococcal disease (IPD) which exhibits pronounced seasonal spikes, the interplay between pneumococcal diversity and environmental drivers remains unexplored. Here we analysed 59,017 IPD cases over 19 years from South Africa, incorporating 4,350 genome-sequenced isolates, using Bayesian spatiotemporal models to link environmental exposure and pneumococcal diversity. Cumulatively, across an 8-week period, moderate relative humidity (33–49%) and cold minimum temperatures (4–10 °C) increased IPD risk by 5% and 4%, respectively. Conversely, warm maximum temperatures (27–38 °C) were associated with up to a 10% increased risk within a week of exposure. There was a positive association between air pollution (PM2.5) and IPD, although it varied by age, disease presentation, and most notably serotype and lineage. Specifically, the lag time between PM2.5 exposure and disease onset varied by serotype, with only serotypes 4, 8 and 23F conferring an immediate IPD risk. High prevalence of GPSC21 lineage (serotype 19F) also modified the pollution response, shifting the lag structure to produce immediate risk of disease following high PM2.5 exposure. Our results demonstrate that pneumococcal population structure shapes air quality risk which in turn can shape the fitness landscape of microbial populations. Integration of these data may inform public health policy.

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Cite

BibTeXRIS
BibTeX
@article{belman2026pneumococcal,
  title = {{Pneumococcal population structure influences the effects of air pollution on invasive disease risk in South Africa}},
  author = {Sophie Belman and Cebile Lekhuleni and Jackie Kleynhans and Giovenale Moirano and Daniela Lührsen and Cristina Carnerero and Susan Meiring and Stephanie W. Lo and Mignon du Plessis and Anne von Gottberg and Rachel Lowe},
  journal = {Nature Microbiology},
  year = {2026},
  month = sep,
  doi = {10.1038/s41564-026-02458-5},
  url = {https://doi.org/10.1038/s41564-026-02458-5},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Pneumococcal population structure influences the effects of air pollution on invasive disease risk in South Africa
AU  - Sophie Belman
AU  - Cebile Lekhuleni
AU  - Jackie Kleynhans
AU  - Giovenale Moirano
AU  - Daniela Lührsen
AU  - Cristina Carnerero
AU  - Susan Meiring
AU  - Stephanie W. Lo
AU  - Mignon du Plessis
AU  - Anne von Gottberg
AU  - Rachel Lowe
PY  - 2026
DA  - 2026/09/14
JO  - Nature Microbiology
DO  - 10.1038/s41564-026-02458-5
UR  - https://doi.org/10.1038/s41564-026-02458-5
AB  - Streptococcus pneumoniae is highly diverse, comprising over 100 serotypes and hundreds of genomic lineages amid widespread vaccination. While it can cause invasive pneumococcal disease (IPD) which exhibits pronounced seasonal spikes, the interplay between pneumococcal diversity and environmental drivers remains unexplored. Here we analysed 59,017 IPD cases over 19 years from South Africa, incorporating 4,350 genome-sequenced isolates, using Bayesian spatiotemporal models to link environmental exposure and pneumococcal diversity. Cumulatively, across an 8-week period, moderate relative humidity (33–49%) and cold minimum temperatures (4–10 °C) increased IPD risk by 5% and 4%, respectively. Conversely, warm maximum temperatures (27–38 °C) were associated with up to a 10% increased risk within a week of exposure. There was a positive association between air pollution (PM2.5) and IPD, although it varied by age, disease presentation, and most notably serotype and lineage. Specifically, the lag time between PM2.5 exposure and disease onset varied by serotype, with only serotypes 4, 8 and 23F conferring an immediate IPD risk. High prevalence of GPSC21 lineage (serotype 19F) also modified the pollution response, shifting the lag structure to produce immediate risk of disease following high PM2.5 exposure. Our results demonstrate that pneumococcal population structure shapes air quality risk which in turn can shape the fitness landscape of microbial populations. Integration of these data may inform public health policy.
SN  - 2058-5276
ER  -