Researchers have warned that air pollution levels in South Africa, and exposure to higher levels of fine particulate matter (PM2.5) – especially in Gauteng and KwaZulu-Natal – are placing residents at greater risk of invasive pneumococcal disease, reports IOL.
Their recent collaborative research, published in Nature Microbiology, examined cases recorded through South Africa’s national GERMS-SA surveillance programme and found that air pollution, temperature, and humidity were linked to changes in both the risk and timing of disease.
Invasive pneumococcal disease, or IPD, occurs when Streptococcus pneumoniae bacteria invade normally sterile parts of the body. It can cause bloodstream infections, meningitis and, in some cases, pneumonia associated with bloodstream infection.
The study teams from the National Institute for Communicable Diseases (NICD), the Wellcome Sanger Institute, the Barcelona Supercomputing Centre, and collaborating institutions examined 59 017 cases recorded at 531 hospitals between 2005 and 2023, including genetic information from 4 350 bacterial samples.
The main modelling covered 2005 to 2019 because of the sharp fall in recorded IPD cases during the Covid-19 pandemic.
At a weekly district-level average PM2.5 concentration of 50 micrograms per cubic metre, the model found that the cumulative risk of IPD was about 3.4% higher over the subsequent eight weeks.
This is a population-level estimate and does not mean every exposed person has a 3.4% chance of developing the disease, the scientists cautioned.
The study used weekly district-level averages, which are not directly comparable with 24-hour air-quality standards.
Under South Africa’s national PM2.5 standard applying from 2016 to the end of 2029, the 24-hour limit is 40 micrograms per cubic metre.
The World Health Organisation’s guideline is 15 micrograms per cubic metre over 24 hours and 5 micrograms per cubic metre annually.
Such pollution levels have been recorded in South Africa. Johannesburg had weekly PM2.5 averages above 100 micrograms per cubic metre during 32 weeks in 2023, while about 23 districts nationally recorded weekly averages of at least 50 micrograms per cubic metre in a typical year.
The pollution burden was not confined to Gauteng. The study identified several districts outside the province where PM2.5 levels exceeded the study’s threshold for more than 10 weeks, including Fezile Dabi in the Free State; Gert Sibande and Nkangala in Mpumalanga; Bojanala Platinum and Dr Kenneth Kaunda in North West; and eight KwaZulu-Natal districts – Amajuba, eThekwini, Harry Gwala, iLembe, Ugu, uMgungundlovu, uMzinyathi and uThukela.
KwaZulu-Natal was also among the provinces contributing a sizeable share of the invasive pneumococcal disease cases analysed, accounting for about 11% of the national total.
People aged 65 and older were the most vulnerable group. At the same pollution level, their cumulative risk over eight weeks was about 16% higher, substantially more than the increase seen across the population overall.
Professor Anne von Gottberg, co-senior author at the NICD, said the findings added to evidence of the health effects of poor air quality, and that invasive pneumococcal diseases were a significant public health issue in South Africa and globally.
“This research adds to ongoing evidence that air quality greatly impacts our health. and shows that it has different effects depending on the strain of bacteria in an area,” she said.
Many people carry S. pneumoniae in their nose or throat without becoming ill. In South Africa, an estimated 40% to 60% of children carry the bacteria.
The researchers found that bacterial subtypes, known as serotypes, responded differently to pollution exposure. Serotypes 14, 19A and 8 were among those showing the strongest increases in pollution-associated disease risk.
Timing also differed. While increased risk could emerge after exposure and persist for weeks, areas where serotypes 4, 8, 23F and 19F were common showed a more immediate increase.
Dr Sophie Belman, the study’s first author and now at Yale School of Public Health, said the bacterial subtype a person carried could affect both the timing of disease and who was most at risk.
“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,” she said.
The researchers accounted for temperature, humidity and population density. High temperatures were associated with an immediate increase in disease risk, while colder temperatures were followed by a delayed rise. Lower humidity was also associated with increased risk.
In a modelling exercise estimating what might have happened if pollution levels had been lower in Gauteng in 2019, the study recorded a mean PM2.5 concentration of 117 micrograms per cubic metre in its weekly exposure data.
Researchers estimated that about 16 of the 718 observed IPD cases might theoretically have been averted if weekly levels had remained at or below 40 micrograms per cubic metre, and about 25 at a threshold of 15 micrograms per cubic metre.
The authors cautioned that air-quality data had limitations, including sparse ground monitoring in parts of South Africa.
The study identified population-level associations and does not show that air pollution caused a person’s infection.
The researchers said combining air-quality monitoring with genetic surveillance of circulating pneumococcal strains could help health authorities anticipate increases in disease, prepare hospitals and inform vaccination strategies.
Study details
Pneumococcal population structure influences the effects of air pollution on invasive disease risk in South Africa
Sophie Belman, Cebile Lekhuleni, Jackie Kleynhans, Giovenale Moirano, Daniela Lührsen, Cristina Carnerero, Susan Meiring, Stephanie W. Lo, Mignon du Plessis, Anne von Gottberg & Rachel Lowe.
Published in Nature Microbiology on 14 September 2026
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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