Bacteria in airway shape air pollution health risk
Air pollution leads to different risk of bacterial pneumonia, sepsis, and meningitis, depending on the subtype of bacteria a person has, new research suggests.
The new study 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 today (14 September) 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.
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 blood stream, 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.
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 per cent 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.
Professor Anne von Gottberg, co-senior author at the National Institute for Communicable Diseases in Johannesburg, South Africa, said: “Invasive pneumococcal diseases are a significant public health issue in South Africa and globally. 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.”
Professor Rachel Lowe, co-senior author at the Barcelona Supercomputing Center and the Catalan Institution for Research & Advanced Studies, said: “Climate change and rapid urbanisation are fundamentally altering the environmental conditions that influence risk of infectious disease. 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, said: “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."
ENDS
Contact details:
Rachael Smith
Press Office
Wellcome Sanger Institute
Cambridge, CB10 1SA
07827979492
Email: press.office@sanger.ac.uk
Notes to Editors:
- D. Rosdiana, AM. Simanjuntak, NC. Ediwi, et al. (2025) Prevalence of Streptococcus pneumoniae carriage 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]
- C. 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
- F. 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
- F. 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
- S.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
Publication:
S. Belman, C. Lekhuleni, J. Kleynhans, et al. (2026) ‘Pneumococcal population structure influences the effects of air pollution on invasive disease risk in South Africa’. Nature Microbiology. DOI: 10.1038/s41564-026-02458-5
Funding:
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.
Selected websites:
The Wellcome Sanger Institute
The Wellcome Sanger Institute is a world leader in genomics research. We apply and explore genomic technologies at scale to advance understanding of biology and improve health. Making discoveries not easily made elsewhere, our research delivers insights across health, disease, evolution and pathogen biology. We are open and collaborative; our data, results, tools, technologies and training are freely shared across the globe to advance science.
Funded by Wellcome, we have the freedom to think long-term and push the boundaries of genomics. We take on the challenges of applying our research to the real world, where we aim to bring benefit to people and society.
Find out more at www.sanger.ac.uk or follow us on Bluesky, X, Instagram, Facebook, LinkedIn and on our Blog.
About Wellcome
Wellcome supports science to solve the urgent health challenges facing everyone. We support discovery research into life, health and wellbeing, and we’re taking on three worldwide health challenges: mental health, infectious disease and climate and health. https://wellcome.org/
National Institute for Communicable Diseases
The National Institute for Communicable Diseases (NICD) is South Africa’s leading public health institute responsible for disease surveillance, outbreak response, reference laboratory services, and public health research. GERMS-SA is its national laboratory-based surveillance programme that monitors invasive bacterial diseases, including invasive pneumococcal disease across South Africa. More information: https://www.nicd.ac.za
Barcelona Supercomputing Center
Barcelona Supercomputing Center (BSC) is one of the leading supercomputing centers in Europe and houses one of the most powerful supercomputers in the world, MareNostrum 5. The center specializes in High Performance Computing (HPC) and artificial intelligence (AI), serving a dual purpose: providing supercomputing infrastructure and services to Spanish and European scientists, and generating knowledge and technology to transfer to society.
BSC’s research focuses on the fields of computer science, life sciences, Earth sciences, computer applications in science and engineering, and computational social sciences and humanities.
Within BSC’s Earth Sciences Department, the Global Health Resilience (GHR) group works to strengthen preparedness for and response to emerging climate-sensitive health threats worldwide. GHR develops approaches to anticipate how climate extremes, environmental degradation and social inequalities interact to shape disease risk across regions and populations. More information: https://www.bsc.es/discover-bsc/organisation/research-departments/global-health-resilience
Journal
Nature Microbiology
Article Title
Pneumococcal population structure influences the effects of air pollution on invasive disease risk in South Africa
Article Publication Date
14-Sep-2026
Sleep app tracks link between air pollution and a bad night’s sleep
University of Cambridge
Has your partner ever woken you up at night with their coughing? Has your coughing ever woken them up? New research suggests it could be due to air pollution levels in your area, even if those levels are low.
Researchers from the University of Cambridge, Tsinghua University and the sleep technology company Sleep Cycle analysed coughing sounds from 32 cities in 12 countries over 500 days, and found that higher daily air pollution levels were strongly linked to nighttime coughing levels, even where local pollution levels were below the World Health Organization’s recommended daily exposure limit.
The researchers used cough sounds passively recorded by the mobile app via the phone’s microphone. Cough sounds were counted on individual devices and pooled by city to build an unprecedented dataset of this kind. The researchers accounted for external factors that could lead to an increase in coughing levels, such as weather conditions or influenza levels.
Analysis of the data, which was anonymised, also found that when pollution levels rose by 10 micrograms of particulate matter per metre cubed, there was a 2.4% rise in coughing levels.
In Los Angeles, one of the cities included in the dataset, coughing levels spiked at the same time as the January 2025 wildfires, acting as a quasi-natural experiment that further supported the short-term association between daytime pollution and nighttime coughing. The results are reported in the journal Communications Health.
Air pollution is a leading environmental risk for human health, leading to an estimated seven million premature deaths per year. Among airborne pollutants, tiny particles of less than 2.5 micrometres (PM2.5) are particularly dangerous, as they can penetrate deep into the lungs and into the bloodstream, potentially leading to inflammation throughout the body, heart disease or respiratory conditions such as asthma or chronic obstructive pulmonary disease (COPD).
“Everyone coughs from time to time, but coughing, whether it’s a one-off or more persistent, is a sign of irritation or inflammation in the lungs,” said lead author Dr Tong Xia from Tsinghua University. “A cough could be a sign of something that hasn’t become chronic yet, but might in future.”
Sleep Cycle is a mobile app that uses sounds – such as breathing, snoring or coughing – to track sleep quality. These sounds are recorded locally and analysed by an AI algorithm. The company’s technology has analysed more than four billion sleep sessions, making it a useful complement to traditional public health surveillance and epidemiological research.
“The dataset from Sleep Cycle is really valuable, because the app is widely used worldwide,” said Professor Cecilia Mascolo from Cambridge’s Department of Computer Science and Technology, who led the research. “Most public health studies only have data from one country, so having a dataset of this size gives it much more power.”
“Every night, Sleep Cycle’s technology turns millions of smartphones into precise sound analysis instruments,” said co-author Dr Mikael Kågebäck from Sleep Cycle. “Coughs are detected and counted directly on each user’s device, so no audio ever leaves the phone. The combination of scale and privacy lets researchers see the health effects of air pollution city by city, night by night, at a scale no sleep lab could match.”
The dataset – which included no personal identifiers – contained information on cough sounds from tens of thousands of users over 18 months. The researchers used data from the 32 cities worldwide where usage rates of the app were highest. The cities were from 12 countries: Australia, Brazil, Chile, China, France, Germany, Italy, Japan, South Africa, Sweden, the United Kingdom and the United States.
The researchers linked the cough data with city-level PM2.5 concentrations, meteorological variables and influenza surveillance data over a period of 18 months. Analysis of the data, even when accounting for the annual flu season when cough rates would normally be higher, showed a strong link between daytime pollution levels and nighttime cough frequency.
“I was surprised we could still see the signal at all,” said Tong, who was formerly a PhD student in Mascolo’s group. “I thought that adding in the confounding factor of flu season would make the link in the data disappear, but it didn’t.”
The link between pollution and coughing persisted in the data, even when pollution levels were below the WHO’s recommended safe daily exposure limit.
“This suggests that there may be no such thing as a safe threshold for exposure to air pollution, although our research is purely observational,” said Mascolo. “However, people may wish to consider how they might mitigate their own exposure to air pollution, by using masks or air filters, for example.”
The research was supported by the European Research Council, the Tsinghua University Vanke School of Public Health Fund, and the Engineering and Physical Sciences Research Council (EPSRC), part of UK Research and Innovation (UKRI). Cecilia Mascolo is a Fellow of Jesus College, Cambridge.
Article Title
Short-term associations between air pollutions and nocturnal cough frequency
Article Publication Date
15-Sep-2026
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