{
  "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.",
  "abstract_shown": true,
  "affiliations": [
    "Barcelona Supercomputing Center (BSC), Barcelona, Spain",
    "Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK",
    "Present Address: Environmental Health Sciences, Yale School of Public Health, New Haven, CT USA",
    "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa",
    "Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa",
    "School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa",
    "Department of Medical Sciences, University of Turin, Torino, Italy",
    "Division of Public Health Surveillance and Response, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa",
    "European Molecular Biology Laboratory–European Bioinformatics Institute, Cambridge, UK",
    "Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa",
    "Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain",
    "Centre on Climate Change and Planetary Health and Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK"
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 11,
  "authors": [
    {
      "affs": [
        0,
        1,
        2
      ],
      "name": "Sophie Belman",
      "orcid": "0000-0002-9778-7174"
    },
    {
      "affs": [
        3,
        4
      ],
      "name": "Cebile Lekhuleni",
      "orcid": "0000-0002-1264-2284"
    },
    {
      "affs": [
        3,
        5
      ],
      "name": "Jackie Kleynhans"
    },
    {
      "affs": [
        0,
        6
      ],
      "name": "Giovenale Moirano"
    },
    {
      "affs": [
        0
      ],
      "name": "Daniela Lührsen",
      "orcid": "0009-0002-6340-5964"
    },
    {
      "affs": [
        0
      ],
      "name": "Cristina Carnerero",
      "orcid": "0000-0002-9228-4092"
    },
    {
      "affs": [
        7
      ],
      "name": "Susan Meiring",
      "orcid": "0000-0003-4508-5469"
    },
    {
      "affs": [
        1,
        8
      ],
      "name": "Stephanie W. Lo",
      "orcid": "0000-0002-2182-0222"
    },
    {
      "affs": [
        3,
        4
      ],
      "name": "Mignon du Plessis",
      "orcid": "0000-0001-9186-0679"
    },
    {
      "affs": [
        3,
        4,
        9
      ],
      "name": "Anne von Gottberg",
      "orcid": "0000-0002-0243-7455"
    },
    {
      "affs": [
        0,
        10,
        11
      ],
      "name": "Rachel Lowe",
      "orcid": "0000-0003-3939-7343"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/a3kd1tkm180y6.bib",
  "cited_by": 1,
  "doi": "10.1038/s41564-026-02458-5",
  "fulltext_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13716828/",
  "id": "a3kd1tkm180y6",
  "issns": [
    "2058-5276"
  ],
  "landing_url": "https://doi.org/10.1038/s41564-026-02458-5",
  "language": "en",
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "Article"
    ],
    [
      "openalex",
      "2713|Pneumonia and Respiratory Infections"
    ]
  ],
  "openalex": "W7212722546",
  "pdf_url": null,
  "pmcid": "PMC13716828",
  "pmid": "42736433",
  "published": "2026-09-14",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/a3kd1tkm180y6.ris",
  "sources": [
    {
      "first_seen": "2026-11-01T12:24:01Z",
      "native_id": "PMC13716828",
      "source": "pmc",
      "url": "https://doi.org/10.1038/s41564-026-02458-5"
    }
  ],
  "subjects": [
    {
      "field": "medicine",
      "origin": "openalex:2713|Pneumonia and Respiratory Infections",
      "subfield": "epidemiology-public-health"
    }
  ],
  "title": "Pneumococcal population structure influences the effects of air pollution on invasive disease risk in South Africa",
  "title_text": "Pneumococcal population structure influences the effects of air pollution on invasive disease risk in South Africa",
  "type": "peer-reviewed",
  "updated_at": "2026-11-02T12:21:16Z",
  "url": "https://research.draconitic.com/paper/a3kd1tkm180y6",
  "venue": "Nature Microbiology",
  "versions": []
}