The new study into air pollution comes from the Wellcome Sanger Institute, the National Institute for Communicable Diseases in Johannesburg, South Africa, the Barcelona Supercomputing Center – Centro Nacional de Supercomputación (BSC-CNS), and collaborators.
The team suggests that the subtype of the bacterium, Streptococcus pneumoniae (S. pneumoniae), together with air pollution exposure impacts the rate and timing of invasive disease — with some strains linked to immediate infection after air pollution exposure, and some taking several weeks.
Published in Nature Microbiology, the researchers also found that older adults and young children are more vulnerable during periods of high air pollution, and that improving air quality could lower disease risk. They also suggest that understanding what type of bacterial strains are circulating and how environmental factors shape infection rates could inform future public health policies, protect those most at risk, and prepare hospitals for outbreaks.
Understanding how environmental factors like pollution impact the respiratory microbiome
S. pneumoniae is found in the respiratory microbiome, the collection of microbes that live in the human nose and throat, in almost 20% per cent of adults globally1. While many adults and children carry the bacteria without any symptoms, when S. pneumoniae gets into the lower respiratory tract, or bloodstream, it can lead to invasive pneumococcal disease (IPD)2.
IPD includes bacterial sepsis, pneumonia and meningitis. It is a major cause of disease and death globally and often peaks during colder months2. In South Africa, there were over 1,800 reported cases of IPD in 20223. In England, the UK Health Security Agency reports that there are more than 5,000 cases per year, particularly impacting children under the age of five, people over 65 years old, and those with underlying conditions2. There are currently over 100 different serotypes, which are specific subtypes of S. pneumoniae4.
While it is known that different subtypes of S. pneumoniae can lead to varying infection rates in different populations, important gaps remain in our collective understanding of how things such as humidity, temperature, and air pollution impact the timing of disease, and how risks vary by individual age and bacterial subtype.
IPD risk increases significantly in the weeks after air pollution exposure
This new study examined around 59,000 cases of IPD across 19 years from South Africa’s national GERMS-SA surveillance programme. In South Africa, between 40-60% of children carry S. pneumoniae,5,6.
The researchers found that different subtypes of S. pneumoniae responded differently to higher air pollution exposure, noting three subtypes (14, 19A, and 8) were linked to the greatest risk of IPD following exposure.
Additionally, they found that different subtypes were linked to differences in the timing of disease risk. While the highest risk of IPD peaked roughly two weeks after air pollution exposure, in areas where subtypes 4, 8, 23F, and 19F were common, there was an immediate increase in disease risk, occurring within the same week.
Importantly, the team accounted for other factors including temperature, humidity, and population density to ensure that the effects were measured as accurately as possible. They also noted that high temperatures were associated with an immediate increase in disease risk, and cold temperatures led to a delayed rise in cases. The team suggests that cold weather slows bacterial transmission or that damage from seasonal viruses could make it easier for bacterial infections to follow.
The authors suggest that integrating environmental monitoring with genomic surveillance of S. pneumoniae could help predict infection spikes, inform vaccination strategies, and support healthcare providers prepare during periods of poor air quality. The study also provides further evidence that reducing air pollution may yield important benefits for infectious disease prevention, particularly in areas with high levels of exposure, such as cities.
“Invasive pneumococcal diseases are a significant public health issue in South Africa and globally, commented Professor Anne von Gottberg, co-senior author at the National Institute for Communicable Diseases in Johannesburg, South Africa. “This research adds to the ongoing evidence that air quality greatly impacts our health and shows that it has different effects depending on the strain of bacteria that is found in an area. We need to focus on monitoring and improving air quality in areas with high disease risk to prevent or reduce some of these infections.”
“Climate change and rapid urbanisation are fundamentally altering the environmental conditions that influence risk of infectious disease,” added Professor Rachel Lowe, co-senior author at the Barcelona Supercomputing Center and the Catalan Institution for Research & Advanced Studies “By linking long-term climate and air quality monitoring with health outcomes, this work highlights how shifting environmental patterns can amplify public health risks. Protecting communities most at risk will require cross-sector collaboration and adaptive health strategies that can keep pace with a changing environment.”
Dr Sophie Belman,first author previously at the Wellcome Sanger Institute, and Barcelona Supercomputing Center, currently Assistant Professor at Yale School of Public Health, concluded that: “While we found that temperature and air pollution generally increase the risk of invasive pneumococcal diseases, such as bacterial meningitis, our research also suggests that it is the bacterial subtypes a person is carrying that modulate infection rates. The strain of bacteria impacts the timing of disease and who might be more at risk depending on their respiratory microbiome, meaning that the risk is not the same in every situation or for every person. By extending our findings to other parts of the globe, we will better understand who has the highest health risk from environmental exposures, and what factors need to be addressed in different regions, such as improving air quality in cities.”
References
- Rosdiana, AM. Simanjuntak, NC. Ediwi, et al. (2025) Prevalence of Streptococcus pneumoniaecarriage among adults: Should we raise a concern? A systematic review and meta-analysis with geospatial analysis. Exploration of Medicine. DOI: 10.37349/emed.2025.1001354
- Pneumococcal disease: guidance, data and analysis. UK Health Security Agency. Available at: https://www.gov.uk/government/collections/pneumococcal-disease-guidance-data-and-analysis [Accessed August 2026]
- Lekhuleni, K. Ndlangisa, R.A. Gladstone, et al.(2024) Impact of pneumococcal conjugate vaccines on invasive pneumococcal disease-causing lineages among South African children. Nature Communications. DOI: 10.1038/s41467-024-52459-3
- Ganaie, et al. (2020) A New Pneumococcal Capsule Type, 10D, is the 100th Serotype and Has a Large cps Fragment from an Oral Streptococcus. mBio. DOI: 10.1128/mbio.00937-20
- S. Dube, et al. (2018) Longitudinal characterization of nasopharyngeal colonization with Streptococcus pneumoniae in a South African birth cohort post 13-valent pneumococcal conjugate vaccine implementation. Scientific Reports. DOI: 10.1038/s41598-018-30345-5
- L. Downs, et al. (2023) Streptococcus pneumoniae and other bacterial nasopharyngeal colonization seven years post-introduction of 13-valent pneumococcal conjugate vaccine in South African children. International Journal of Infectious Diseases. DOI: 10.1016/j.ijid.2023.05.016
Sophie Belman conducted this research as part of her Schmidt Science Fellowship at Barcelona Supercomputing Center (BSC). Surveillance for IPD in South Africa is funded by the National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, Johannesburg, South Africa. This research was supported in part by the Fogarty International Center, the Gates Foundation, Wellcome, and the Department of Health and Social Care. A full acknowledgement list can be found in the publication.
