{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,29]],"date-time":"2026-10-29T12:04:26Z","timestamp":1793275466546,"version":"4.5.0"},"reference-count":94,"publisher":"Springer Science and Business Media LLC","issue":"10","license":[{"start":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T00:00:00Z","timestamp":1789344000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T00:00:00Z","timestamp":1789344000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Microbiol"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    <jats:italic>Streptococcus pneumoniae<\/jats:italic>\n                    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\u2009years 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\u201349%) and cold minimum temperatures (4\u201310\u2009\u00b0C) increased IPD risk by 5% and 4%, respectively. Conversely, warm maximum temperatures (27\u201338\u2009\u00b0C) were associated with up to a 10% increased risk within a week of exposure. There was a positive association between air pollution (PM\n                    <jats:sub>2.5<\/jats:sub>\n                    ) and IPD, although it varied by age, disease presentation, and most notably serotype and lineage. Specifically, the lag time between PM\n                    <jats:sub>2.5<\/jats:sub>\n                    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 PM\n                    <jats:sub>2.5<\/jats:sub>\n                    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.\n                  <\/jats:p>","DOI":"10.1038\/s41564-026-02458-5","type":"journal-article","created":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T09:03:14Z","timestamp":1789376594000},"page":"2723-2737","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Pneumococcal population structure influences the effects of air pollution on invasive disease risk in South Africa"],"prefix":"10.1038","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9778-7174","authenticated-orcid":false,"given":"Sophie","family":"Belman","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1264-2284","authenticated-orcid":false,"given":"Cebile","family":"Lekhuleni","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jackie","family":"Kleynhans","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giovenale","family":"Moirano","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-6340-5964","authenticated-orcid":false,"given":"Daniela","family":"L\u00fchrsen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9228-4092","authenticated-orcid":false,"given":"Cristina","family":"Carnerero","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4508-5469","authenticated-orcid":false,"given":"Susan","family":"Meiring","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2182-0222","authenticated-orcid":false,"given":"Stephanie W.","family":"Lo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9186-0679","authenticated-orcid":false,"given":"Mignon","family":"du Plessis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0243-7455","authenticated-orcid":false,"given":"Anne","family":"von Gottberg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3939-7343","authenticated-orcid":false,"given":"Rachel","family":"Lowe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,9,14]]},"reference":[{"key":"2458_CR1","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1038\/s41579-018-0001-8","volume":"16","author":"JN Weiser","year":"2018","unstructured":"Weiser, J. N., Ferreira, D. M. & Paton, J. C. Streptococcus pneumoniae: transmission, colonization and invasion. Nat. Rev. Microbiol. 16, 355\u2013367 (2018).","journal-title":"Nat. Rev. Microbiol."},{"key":"2458_CR2","doi-asserted-by":"publisher","first-page":"304","DOI":"10.1101\/gr.241455.118","volume":"29","author":"JA Lees","year":"2019","unstructured":"Lees, J. A. et al. Fast and flexible bacterial genomic epidemiology with PopPUNK. Genome Res. 29, 304\u2013316 (2019).","journal-title":"Genome Res."},{"key":"2458_CR3","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.00937-20","volume":"11","author":"F Ganaie","year":"2020","unstructured":"Ganaie, F. et al. A new pneumococcal capsule type, 10D, is the 100th serotype and has a large cps fragment from an oral Streptococcus. mBio 11, e00937-20 (2020).","journal-title":"mBio"},{"key":"2458_CR4","doi-asserted-by":"publisher","first-page":"338","DOI":"10.1016\/j.ebiom.2019.04.021","volume":"43","author":"RA Gladstone","year":"2019","unstructured":"Gladstone, R. A. et al. International genomic definition of pneumococcal lineages, to contextualise disease, antibiotic resistance and vaccine impact. EBioMedicine 43, 338\u2013346 (2019).","journal-title":"EBioMedicine"},{"key":"2458_CR5","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-52459-3","volume":"15","author":"C Lekhuleni","year":"2024","unstructured":"Lekhuleni, C. et al. Impact of pneumococcal conjugate vaccines on invasive pneumococcal disease-causing lineages among South African children. Nat. Commun. 15, 8401 (2024).","journal-title":"Nat. Commun."},{"key":"2458_CR6","doi-asserted-by":"publisher","first-page":"759","DOI":"10.1016\/S1473-3099(19)30297-X","volume":"19","author":"SW Lo","year":"2019","unstructured":"Lo, S. W. et al. Pneumococcal lineages associated with serotype replacement and antibiotic resistance in childhood invasive pneumococcal disease in the post-PCV13 era: an international whole-genome sequencing study. Lancet Infect. Dis. 19, 759\u2013769 (2019).","journal-title":"Lancet Infect. Dis."},{"key":"2458_CR7","doi-asserted-by":"publisher","first-page":"e735","DOI":"10.1016\/S2666-5247(22)00158-6","volume":"3","author":"SW Lo","year":"2022","unstructured":"Lo, S. W. et al. Emergence of a multidrug-resistant and virulent Streptococcus pneumoniae lineage mediates serotype replacement after PCV13: an international whole-genome sequencing study. Lancet Microbe 3, e735\u2013e743 (2022).","journal-title":"Lancet Microbe"},{"key":"2458_CR8","doi-asserted-by":"publisher","first-page":"386","DOI":"10.1038\/s41586-024-07626-3","volume":"631","author":"S Belman","year":"2024","unstructured":"Belman, S. et al. Geographical migration and fitness dynamics of Streptococcus pneumoniae. Nature 631, 386\u2013392 (2024).","journal-title":"Nature"},{"key":"2458_CR9","doi-asserted-by":"publisher","first-page":"3953","DOI":"10.1016\/j.vaccine.2019.05.080","volume":"37","author":"EL German","year":"2019","unstructured":"German, E. L. et al. Protective effect of PCV vaccine against experimental pneumococcal challenge in adults is primarily mediated by controlling colonisation density. Vaccine 37, 3953\u20133956 (2019).","journal-title":"Vaccine"},{"key":"2458_CR10","doi-asserted-by":"publisher","first-page":"e0305892","DOI":"10.1371\/journal.pone.0305892","volume":"20","author":"TM Malik","year":"2025","unstructured":"Malik, T. M. et al. A dynamic transmission model for assessing the impact of pneumococcal vaccination in the United States. PLoS ONE 20, e0305892 (2025).","journal-title":"PLoS ONE"},{"key":"2458_CR11","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-39797-4","volume":"14","author":"J Rentschler","year":"2023","unstructured":"Rentschler, J. & Leonova, N. Global air pollution exposure and poverty. Nat. Commun. 14, 4432 (2023).","journal-title":"Nat. Commun."},{"key":"2458_CR12","doi-asserted-by":"publisher","unstructured":"Belman, S. et al. Environmental exposures and pneumococcal dynamics: a scoping review of meteorological factors and air pollution. SSRN https:\/\/doi.org\/10.2139\/ssrn.6400926 (2026).","DOI":"10.2139\/ssrn.6400926"},{"key":"2458_CR13","doi-asserted-by":"publisher","first-page":"977","DOI":"10.1016\/j.jaci.2016.04.062","volume":"139","author":"J-F Jusot","year":"2017","unstructured":"Jusot, J.-F. et al. Airborne dust and high temperatures are risk factors for invasive bacterial disease. J. Allergy Clin. Immunol. 139, 977\u2013986.e2 (2017).","journal-title":"J. Allergy Clin. Immunol."},{"key":"2458_CR14","doi-asserted-by":"publisher","first-page":"465","DOI":"10.1093\/jac\/dkh375","volume":"54","author":"C Garc\u00eda-Rey","year":"2004","unstructured":"Garc\u00eda-Rey, C., Fenoll, A., Aguilar, L. & Casal, J. Effect of social and climatological factors on antimicrobial use and Streptococcus pneumoniae resistance in different provinces in Spain. J. Antimicrob. Chemother. 54, 465\u2013471 (2004).","journal-title":"J. Antimicrob. Chemother."},{"key":"2458_CR15","doi-asserted-by":"publisher","first-page":"922","DOI":"10.1016\/j.jiph.2024.03.020","volume":"17","author":"FS Diouf","year":"2024","unstructured":"Diouf, F. S. et al. Seasonal variation of asymptomatic viral and bacterial nasopharyngeal carriage in rural Senegal. J. Infect. Public Health 17, 922\u2013928 (2024).","journal-title":"J. Infect. Public Health"},{"key":"2458_CR16","doi-asserted-by":"publisher","DOI":"10.1016\/j.jinf.2008.10.011","volume":"58","author":"DR Murdoch","year":"2009","unstructured":"Murdoch, D. R. & Jennings, L. C. Association of respiratory virus activity and environmental factors with the incidence of invasive pneumococcal disease. J. Infect. 58, 37\u201346 (2009.","journal-title":"J. Infect."},{"key":"2458_CR17","doi-asserted-by":"publisher","first-page":"1070","DOI":"10.1164\/rccm.202112-2668TR","volume":"206","author":"D Beentjes","year":"2022","unstructured":"Beentjes, D., Shears, R. K., French, N., Neill, D. R. & Kadioglu, A. Mechanistic insights into the impact of air pollution on pneumococcal pathogenesis and transmission. Am. J. Respir. Crit. Care Med. 206, 1070\u20131080 (2022).","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"2458_CR18","doi-asserted-by":"publisher","first-page":"125","DOI":"10.1186\/s13756-019-0574-7","volume":"8","author":"YJ Choe","year":"2019","unstructured":"Choe, Y. J., Smit, M. A. & Mermel, L. A. Seasonality of respiratory viruses and bacterial pathogens. Antimicrob. Resist. Infect. Control 8, 125 (2019).","journal-title":"Antimicrob. Resist. Infect. Control"},{"key":"2458_CR19","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1093\/clinids\/22.1.100","volume":"22","author":"PE Kim","year":"1996","unstructured":"Kim, P. E. et al. Association of invasive pneumococcal disease with season, atmospheric conditions, air pollution, and the isolation of respiratory viruses. Clin. Infect. Dis. 22, 100\u2013106 (1996).","journal-title":"Clin. Infect. Dis."},{"key":"2458_CR20","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-018-30345-5","volume":"8","author":"FS Dube","year":"2018","unstructured":"Dube, F. S. et al. Longitudinal characterization of nasopharyngeal colonization with Streptococcus pneumoniae in a South African birth cohort post 13-valent pneumococcal conjugate vaccine implementation. Sci. Rep. 8, 12497 (2018).","journal-title":"Sci. Rep."},{"key":"2458_CR21","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1016\/j.ijid.2023.05.016","volume":"134","author":"SL Downs","year":"2023","unstructured":"Downs, S. L. et al. Streptococcus pneumoniae and other bacterial nasopharyngeal colonization seven years post-introduction of 13-valent pneumococcal conjugate vaccine in South African children. Int. J. Infect. Dis. 134, 45\u201352 (2023).","journal-title":"Int. J. Infect. Dis."},{"key":"2458_CR22","unstructured":"National Environmental Management: Air Quality Act: National Ambient Air Quality Standard for Particulate Matter with Aerodynamic Diameter Less than 2.5 Micron Metres (PM 2.5) https:\/\/www.gov.za\/documents\/national-environmental-management-air-quality-act-national-ambient-air-quality-standard-0 (South African Government, 2012)."},{"key":"2458_CR23","doi-asserted-by":"publisher","first-page":"431","DOI":"10.1007\/s11869-020-00947-y","volume":"14","author":"J Williams","year":"2021","unstructured":"Williams, J., Petrik, L. & Wichmann, J. PM2.5 chemical composition and geographical origin of air masses in Cape Town, South Africa. Air Qual. Atmos. Health 14, 431\u2013442 (2021).","journal-title":"Air Qual. Atmos. Health"},{"key":"2458_CR24","first-page":"100","volume":"9","author":"M Mathuthu","year":"2019","unstructured":"Mathuthu, M., Dudu, V. P. & Manjoro, M. Source apportionment of air particulates in South Africa: a review. Atmos. Clim. Sci. 9, 100\u2013113 (2019).","journal-title":"Atmos. Clim. Sci."},{"key":"2458_CR25","unstructured":"PM2.5 Chemical Composition, Source Apportionment and Geographical Origin of Air Masses in Pretoria, South Africa (Univ. Pretoria, 2020)."},{"key":"2458_CR26","doi-asserted-by":"publisher","first-page":"e0149104","DOI":"10.1371\/journal.pone.0149104","volume":"11","author":"S Meiring","year":"2016","unstructured":"Meiring, S. et al. HIV infection and the epidemiology of invasive pneumococcal disease (IPD) in South African adults and older children prior to the introduction of a pneumococcal conjugate vaccine (PCV). PLoS ONE 11, e0149104 (2016).","journal-title":"PLoS ONE"},{"key":"2458_CR27","doi-asserted-by":"publisher","first-page":"1360","DOI":"10.1093\/infdis\/jir052","volume":"203","author":"BW Beall","year":"2011","unstructured":"Beall, B. W. et al. Shifting genetic structure of invasive serotype 19A pneumococci in the United States. J. Infect. Dis. 203, 1360\u20131368 (2011).","journal-title":"J. Infect. Dis."},{"key":"2458_CR28","doi-asserted-by":"publisher","first-page":"e246","DOI":"10.1016\/S2214-109X(21)00405-8","volume":"10","author":"MK Dherani","year":"2022","unstructured":"Dherani, M. K. et al. Association between household air pollution and nasopharyngeal pneumococcal carriage in Malawian infants (MSCAPE): a nested, prospective, observational study. Lancet Glob. Health 10, e246\u2013e256 (2022).","journal-title":"Lancet Glob. Health"},{"key":"2458_CR29","doi-asserted-by":"publisher","first-page":"2261","DOI":"10.2147\/IDR.S468419","volume":"17","author":"C Li","year":"2024","unstructured":"Li, C. et al. Investigating the distribution and antibiotic resistance of bacterial pathogens in clinical specimens from a Chinese maternal and child hospital: the role of environmental factors. Infect. Drug Resist. 17, 2261\u20132272 (2024).","journal-title":"Infect. Drug Resist."},{"key":"2458_CR30","doi-asserted-by":"publisher","first-page":"230259","DOI":"10.1183\/16000617.0259-2023","volume":"33","author":"J Ma","year":"2024","unstructured":"Ma, J. et al. Fine particulate matter manipulates immune response to exacerbate microbial pathogenesis in the respiratory tract. Eur. Respir. Rev. 33, 230259 (2024).","journal-title":"Eur. Respir. Rev."},{"key":"2458_CR31","doi-asserted-by":"publisher","first-page":"128376","DOI":"10.1016\/j.chemosphere.2020.128376","volume":"262","author":"J Gonz\u00e1lez-Mart\u00edn","year":"2021","unstructured":"Gonz\u00e1lez-Mart\u00edn, J., Kraakman, N. J. R., P\u00e9rez, C., Lebrero, R. & Mu\u00f1oz, R. A state-of-the-art review on indoor air pollution and strategies for indoor air pollution control. Chemosphere 262, 128376 (2021).","journal-title":"Chemosphere"},{"key":"2458_CR32","doi-asserted-by":"publisher","first-page":"934","DOI":"10.1007\/s11270-025-08562-2","volume":"236","author":"PP Somboonsin","year":"2025","unstructured":"Somboonsin, P. P. & Baffour, B. Spatial inequities in women\u2019s health: the global impact of household air pollution from solid fuels. Water Air Soil Pollut. 236, 934 (2025).","journal-title":"Water Air Soil Pollut."},{"key":"2458_CR33","doi-asserted-by":"crossref","unstructured":"Darkwah, S., Somda, N. S., Mahazu, S. & Donkor, E. S. Pneumococcal serotypes and their association with death risk in invasive pneumococcal disease: a systematic review and meta-analysis. Front. Med. 12, 1566502 (2025).","DOI":"10.3389\/fmed.2025.1566502"},{"key":"2458_CR34","doi-asserted-by":"publisher","first-page":"457","DOI":"10.1016\/S1473-3099(24)00665-0","volume":"25","author":"JC Bennett","year":"2025","unstructured":"Bennett, J. C. et al. Global impact of ten-valent and 13-valent pneumococcal conjugate vaccines on invasive pneumococcal disease in all ages (the PSERENADE project): a global surveillance analysis. Lancet Infect. Dis. 25, 457\u2013470 (2025).","journal-title":"Lancet Infect. Dis."},{"key":"2458_CR35","doi-asserted-by":"publisher","first-page":"1271","DOI":"10.1093\/infdis\/174.6.1271","volume":"174","author":"R Dagan","year":"1996","unstructured":"Dagan, R. et al. Reduction of nasopharyngeal carriage of pneumococci during the second year of life by a heptavalent conjugate pneumococcal vaccine. J. Infect. Dis. 174, 1271\u20131278 (1996).","journal-title":"J. Infect. Dis."},{"key":"2458_CR36","doi-asserted-by":"crossref","unstructured":"Cheliotis, K. S. et al. Influence of sex, season and environmental air quality on experimental human pneumococcal carriage acquisition: a retrospective cohort analysis. ERJ Open Res. 8, 00586-2021 (2022).","DOI":"10.1183\/23120541.00586-2021"},{"key":"2458_CR37","doi-asserted-by":"publisher","first-page":"706","DOI":"10.6061\/clinics\/2015(10)09","volume":"70","author":"R Carvalho-Oliveira","year":"2015","unstructured":"Carvalho-Oliveira, R. et al. Chemical composition modulates the adverse effects of particles on the mucociliary epithelium. Clinics 70, 706\u2013713 (2015).","journal-title":"Clinics"},{"key":"2458_CR38","doi-asserted-by":"publisher","first-page":"e20200028","DOI":"10.1590\/1678-4685-gmb-2020-0028","volume":"44","author":"JD de Oliveira","year":"2020","unstructured":"de Oliveira, J. D. et al. Influence of environmental dust in transformation capacity of Streptococcus pneumoniae. Genet. Mol. Biol. 44, e20200028 (2020).","journal-title":"Genet. Mol. Biol."},{"key":"2458_CR39","doi-asserted-by":"crossref","unstructured":"Yadav, M. K., Go, Y. Y., Chae, S.-W., Park, M. K. & Song, J.-J. Asian sand dust particles increased pneumococcal biofilm formation in vitro and colonization in human middle ear epithelial cells and rat middle ear mucosa. Front. Genet. 11, 323 (2020).","DOI":"10.3389\/fgene.2020.00323"},{"key":"2458_CR40","doi-asserted-by":"publisher","first-page":"1867","DOI":"10.3201\/eid2707.204403","volume":"27","author":"JD Kellner","year":"2021","unstructured":"Kellner, J. D. et al. Whole-genome analysis of Streptococcus pneumoniae serotype 4 causing outbreak of invasive pneumococcal disease, Alberta, Canada. Emerg. Infect. Dis. 27, 1867\u20131875 (2021).","journal-title":"Emerg. Infect. Dis."},{"key":"2458_CR41","doi-asserted-by":"publisher","first-page":"108216","DOI":"10.1016\/j.ijid.2025.108216","volume":"163","author":"L Cuypers","year":"2026","unstructured":"Cuypers, L. et al. Rapid increase in serotype 4 invasive pneumococcal disease among vulnerable young male adults in Belgium (2020\u20132024). Int. J. Infect. Dis. 163, 108216 (2026).","journal-title":"Int. J. Infect. Dis."},{"key":"2458_CR42","doi-asserted-by":"publisher","first-page":"663","DOI":"10.1111\/j.1365-2958.2009.06796.x","volume":"73","author":"P Shivshankar","year":"2009","unstructured":"Shivshankar, P., Sanchez, C., Rose, L. F. & Orihuela, C. J. The Streptococcus pneumoniae adhesin PsrP binds to Keratin 10 on lung cells. Mol. Microbiol. 73, 663\u2013679 (2009).","journal-title":"Mol. Microbiol."},{"key":"2458_CR43","doi-asserted-by":"publisher","first-page":"e26255","DOI":"10.7554\/eLife.26255","volume":"6","author":"JA Lees","year":"2017","unstructured":"Lees, J. A. et al. Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration. eLife 6, e26255 (2017).","journal-title":"eLife"},{"key":"2458_CR44","doi-asserted-by":"publisher","first-page":"174611","DOI":"10.1016\/j.scitotenv.2024.174611","volume":"948","author":"H Bhattarai","year":"2024","unstructured":"Bhattarai, H., Tai, A. P. K., Val Martin, M. & Yung, D. H. Y. Responses of fine particulate matter (PM2.5) air quality to future climate, land use, and emission changes: insights from modeling across shared socioeconomic pathways. Sci. Total Environ. 948, 174611 (2024).","journal-title":"Sci. Total Environ."},{"key":"2458_CR45","doi-asserted-by":"publisher","first-page":"102459","DOI":"10.1016\/j.apr.2025.102459","volume":"16","author":"M Benyon","year":"2025","unstructured":"Benyon, M. et al. Household PM2.5 in a South African urban and rural setting: a comparative analysis using low-cost sensors. Atmos. Pollut. Res. 16, 102459 (2025).","journal-title":"Atmos. Pollut. Res."},{"key":"2458_CR46","doi-asserted-by":"publisher","DOI":"10.1186\/1752-1505-4-3","volume":"4","author":"A Bellos","year":"2010","unstructured":"Bellos, A. et al. The burden of acute respiratory infections in crisis-affected populations: a systematic review. Confl. Health 4, 3 (2010).","journal-title":"Confl. Health"},{"key":"2458_CR47","first-page":"000746","volume":"8","author":"KM Ndlangisa","year":"2022","unstructured":"Ndlangisa, K. M. et al. A Streptococcus pneumoniae lineage usually associated with pneumococcal conjugate vaccine (PCV) serotypes is the most common cause of serotype 35B invasive disease in South Africa, following routine use of PCV. Microb. Genom. 8, 000746 (2022).","journal-title":"Microb. Genom."},{"key":"2458_CR48","first-page":"e000186","volume":"4","author":"L Epping","year":"2018","unstructured":"Epping, L. et al. SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data. Microb. Genom. 4, e000186 (2018).","journal-title":"Microb. Genom."},{"key":"2458_CR49","doi-asserted-by":"publisher","first-page":"1596","DOI":"10.1086\/598975","volume":"48","author":"MP Weinstein","year":"2009","unstructured":"Weinstein, M. P., Klugman, K. P. & Jones, R. N. Rationale for revised penicillin susceptibility breakpoints versus Streptococcus pneumoniae: coping with antimicrobial susceptibility in an era of resistance. Clin. Infect. Dis. 48, 1596\u20131600 (2009).","journal-title":"Clin. Infect. Dis."},{"key":"2458_CR50","unstructured":"GPS Consortium. Global Pneumococcal Sequencing collection. Microb. Genom. https:\/\/www.microbiologyresearch.org\/content\/global-pneumococcal-sequencing-collection (2022)."},{"key":"2458_CR51","doi-asserted-by":"publisher","unstructured":"Lekhuleni, C. N. et al. Impact of pneumococcal conjugate vaccines on invasive pneumococcal disease-causing lineages in South African Children, 2005\u201320: a National Genomic Epidemiology Study. SSRN https:\/\/doi.org\/10.2139\/ssrn.4652526 (2023).","DOI":"10.2139\/ssrn.4652526"},{"key":"2458_CR52","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1089\/cmb.2012.0021","volume":"19","author":"A Bankevich","year":"2012","unstructured":"Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455\u2013477 (2012).","journal-title":"J. Comput. Biol."},{"key":"2458_CR53","doi-asserted-by":"crossref","unstructured":"Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068\u20132069 https:\/\/academic.oup.com\/bioinformatics\/article\/30\/14\/2068\/2390517 (2014).","DOI":"10.1093\/bioinformatics\/btu153"},{"key":"2458_CR54","doi-asserted-by":"crossref","unstructured":"Tatem, A. WorldPop, open data for spatial demography. Sci. Data 4, 170004 https:\/\/www.nature.com\/articles\/sdata20174 (2017).","DOI":"10.1038\/sdata.2017.4"},{"key":"2458_CR55","unstructured":"Statistics South Africa https:\/\/www.statssa.gov.za\/?PPN=P0302&SCH=74263&page_id=1854 (Republic of South Africa, 2023)."},{"key":"2458_CR56","unstructured":"WHO\/UNICEF Estimates of National Immunization Coverage https:\/\/www.who.int\/teams\/immunization-vaccines-and-biologicals\/immunization-analysis-and-insights\/global-monitoring\/immunization-coverage\/who-unicef-estimates-of-national-immunization-coverage (WHO, 2026)."},{"key":"2458_CR57","unstructured":"Koppen, W. & Geiger, R. Das geographische system der klimate. In Handbuch der Klimatologie (eds Koppen, W. & Geiger, R.) Bd. 1, T. C. 5\u201344 https:\/\/d-nb.info\/362276706\/04 (Verlag Gebr\u00fcder Borntrager, 1936)."},{"key":"2458_CR58","doi-asserted-by":"publisher","first-page":"4349","DOI":"10.5194\/essd-13-4349-2021","volume":"13","author":"J Mu\u00f1oz-Sabater","year":"2021","unstructured":"Mu\u00f1oz-Sabater, J. et al. ERA5-Land: a state-of-the-art global reanalysis dataset for land applications. Earth Syst. Sci. Data 13, 4349\u20134383 (2021).","journal-title":"Earth Syst. Sci. Data"},{"key":"2458_CR59","unstructured":"Beguer\u00eda, S. & Vicente-Serrano, S. M. SPEI: calculation of the standardized precipitation\u2013evapotranspiration index. R package version 1.8.1 (2023)."},{"key":"2458_CR60","unstructured":"BSC-CNS et al. ClimProjDiags: set of tools to compute various climate indices. R package version 0.3.6 (2026)."},{"key":"2458_CR61","unstructured":"Perez-Zanon, N. et al. CSIndicators: climate services\u2019 indicators based on sub-seasonal to decadal predictions. R package version 1.2.0 (2026)."},{"key":"2458_CR62","unstructured":"Perez-Zanon, N. et al. CSTools: assessing skill of climate forecasts on seasonal-to-decadal timescales. R package version 5.3.2 (2026)."},{"key":"2458_CR63","doi-asserted-by":"crossref","unstructured":"Gelaro, R. et al. The modern-era retrospective analysis for research and applications, version 2 (MERRA-2). J. Climate 30, 5419\u20135454 https:\/\/journals.ametsoc.org\/view\/journals\/clim\/30\/14\/jcli-d-16-0758.1.xml (2017).","DOI":"10.1175\/JCLI-D-16-0758.1"},{"key":"2458_CR64","unstructured":"CAMS Air Quality Data \u2013 Quality Assured https:\/\/atmosphere.copernicus.eu\/cams-air-quality-data-quality-assured (Copernicus, 2025)."},{"key":"2458_CR65","unstructured":"SAAQIS https:\/\/saaqis.environment.gov.za\/ (Republic of South Africa, 2025)."},{"key":"2458_CR66","unstructured":"MERRA-2 https:\/\/gmao.gsfc.nasa.gov\/reanalysis\/MERRA-2\/ (GMAO, 2025)."},{"key":"2458_CR67","doi-asserted-by":"publisher","unstructured":"Gupta, P. MERRA2_CNN_HAQAST bias corrected global hourly surface total PM2.5 mass concentration, V1 https:\/\/doi.org\/10.5067\/OCKK5HCFW5N3 (NASA Goddard Earth Sciences Data and Information Services Center, 2023).","DOI":"10.5067\/OCKK5HCFW5N3"},{"key":"2458_CR68","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-43862-3","volume":"14","author":"J Wei","year":"2023","unstructured":"Wei, J. et al. First close insight into global daily gapless 1 km PM2.5 pollution, variability, and health impact. Nat. Commun. 14, 8349 (2023).","journal-title":"Nat. Commun."},{"key":"2458_CR69","doi-asserted-by":"publisher","first-page":"33","DOI":"10.17159\/2410-972X\/2017\/v27n1a8","volume":"27","author":"RM Garland","year":"2017","unstructured":"Garland, R. M., Naidoo, M., Sibiya, B. & Oosthuizen, R. Air quality indicators from the Environmental Performance Index: potential use and limitations in South Africa. Clean Air J. 27, 33\u201333 (2017).","journal-title":"Clean Air J."},{"key":"2458_CR70","doi-asserted-by":"crossref","unstructured":"Garland, R., Wernecke, B., Feig, G. & Langerman, K. The new WHO Global Air Quality Guidelines: what do they mean for South Africa? Clean Air J. 31, 1\u20132 (2021).","DOI":"10.17159\/caj\/2020\/31\/2.12915"},{"key":"2458_CR71","doi-asserted-by":"publisher","first-page":"1811","DOI":"10.1016\/S0140-6736(25)01917-8","volume":"406","author":"M Naghavi","year":"2025","unstructured":"Naghavi, M. et al. Global burden of 292 causes of death in 204 countries and territories and 660 subnational locations, 1990\u20132023: a systematic analysis for the Global Burden of Disease Study 2023. Lancet 406, 1811\u20131872 (2025).","journal-title":"Lancet"},{"key":"2458_CR72","unstructured":"Manubens, N. et al. startR: automatically retrieve multidimensional distributed data sets. R package version 3.0.0 (2025)."},{"key":"2458_CR73","unstructured":"R Core Team. R A Language and Environment for Statistical Computing https:\/\/www.scirp.org\/reference\/referencespapers?referenceid=3131254 (R Foundation for Statistical Computing, 2021)."},{"key":"2458_CR74","doi-asserted-by":"crossref","unstructured":"Rue, H., Martino, S. & Chopin, N. Approximate Bayesian inference for latent Gaussian models by using integrated nested Laplace approximations. J. R. Stat. Soc. B 71, 319\u2013392 https:\/\/rss.onlinelibrary.wiley.com\/doi\/10.1111\/j.1467-9868.2008.00700.x (2009).","DOI":"10.1111\/j.1467-9868.2008.00700.x"},{"key":"2458_CR75","doi-asserted-by":"publisher","first-page":"1","DOI":"10.18637\/jss.v043.i08","volume":"43","author":"A Gasparrini","year":"2011","unstructured":"Gasparrini, A. Distributed lag linear and non-linear models in R: the package dlnm. J. Stat. Softw. 43, 1\u201320 (2011).","journal-title":"J. Stat. Softw."},{"key":"2458_CR76","unstructured":"Wickham, H., Francois, R., Henry, L., Muller, K. & Vaughan, D. A grammar of data manipulation. R package version 1.2.1 (2026)."},{"key":"2458_CR77","doi-asserted-by":"publisher","unstructured":"Pebesma, E. & Bivand, R. Spatial Data Science: With Applications in R https:\/\/doi.org\/10.1201\/9780429459016 (Chapman and Hall\/CRC, 2023).","DOI":"10.1201\/9780429459016"},{"key":"2458_CR78","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/BF00116466","volume":"43","author":"J Besag","year":"1991","unstructured":"Besag, J., York, J. & Molli\u00e9, A. Bayesian image restoration, with two applications in spatial statistics. Ann. Inst. Stat. Math. 43, 1\u201320 (1991).","journal-title":"Ann. Inst. Stat. Math."},{"key":"2458_CR79","doi-asserted-by":"publisher","first-page":"1586","DOI":"10.1093\/cid\/ciw139","volume":"62","author":"M-R B-Lajoie","year":"2016","unstructured":"B-Lajoie, M.-R. et al. Incidence and prevalence of opportunistic and other infections and the impact of antiretroviral therapy among HIV-infected children in low- and middle-income countries: a systematic review and meta-analysis. Clin. Infect. Dis. 62, 1586\u20131594 (2016).","journal-title":"Clin. Infect. Dis."},{"key":"2458_CR80","doi-asserted-by":"publisher","first-page":"1595","DOI":"10.1093\/cid\/ciw125","volume":"62","author":"A Low","year":"2016","unstructured":"Low, A. et al. Incidence of opportunistic infections and the impact of antiretroviral therapy among HIV-infected adults in low- and middle-income countries: a systematic review and meta-analysis. Clin. Infect. Dis. 62, 1595\u20131603 (2016).","journal-title":"Clin. Infect. Dis."},{"key":"2458_CR81","doi-asserted-by":"publisher","first-page":"e360","DOI":"10.1016\/S2589-7500(21)00077-7","volume":"3","author":"AB Brueggemann","year":"2021","unstructured":"Brueggemann, A. B. et al. Changes in the incidence of invasive disease due to Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis during the COVID-19 pandemic in 26 countries and territories in the Invasive Respiratory Infection Surveillance Initiative: a prospective analysis of surveillance data. Lancet Digit. Health 3, e360\u2013e370 (2021).","journal-title":"Lancet Digit. Health"},{"key":"2458_CR82","doi-asserted-by":"publisher","first-page":"1837","DOI":"10.1097\/QAD.0000000000000755","volume":"29","author":"E Heinsbroek","year":"2015","unstructured":"Heinsbroek, E. et al. Persisting high prevalence of pneumococcal carriage among HIV-infected adults receiving antiretroviral therapy in Malawi: a cohort study. AIDS 29, 1837\u20131844 (2015).","journal-title":"AIDS"},{"key":"2458_CR83","doi-asserted-by":"publisher","first-page":"546","DOI":"10.1016\/S1473-3099(23)00706-5","volume":"24","author":"M Bertran","year":"2024","unstructured":"Bertran, M. et al. Invasive pneumococcal disease 3 years after introduction of a reduced 1 + 1 infant 13-valent pneumococcal conjugate vaccine immunisation schedule in England: a prospective national observational surveillance study. Lancet Infect. Dis. 24, 546\u2013556 (2024).","journal-title":"Lancet Infect. Dis."},{"key":"2458_CR84","doi-asserted-by":"publisher","first-page":"378","DOI":"10.1080\/23744235.2025.2464857","volume":"57","author":"A Akingbola","year":"2025","unstructured":"Akingbola, A., Adegbesan, A., Mariaria, P., Isaiah, O. & Adeyemi, E. A pause that hurts: the global impact of halting PEPFAR funding for HIV\/AIDS programs. Infect. Dis. 57, 378\u2013384 (2025).","journal-title":"Infect. Dis."},{"key":"2458_CR85","doi-asserted-by":"publisher","first-page":"424","DOI":"10.1186\/s12931-024-03054-z","volume":"25","author":"J Seok","year":"2024","unstructured":"Seok, J., Lee, B. Y. & Yoon, H.-Y. Association between humidity and respiratory health: the 2016\u20132018 Korea National Health and Nutrition Examination Survey. Respir. Res. 25, 424 (2024).","journal-title":"Respir. Res."},{"key":"2458_CR86","doi-asserted-by":"publisher","first-page":"11010","DOI":"10.7189\/jogh.12.11010","volume":"12","author":"Z Wu","year":"2022","unstructured":"Wu, Z. et al. The lag-effects of meteorological factors and air pollutants on child respiratory diseases in Fuzhou, China. J. Glob. Health 12, 11010 (2022).","journal-title":"J. Glob. Health"},{"key":"2458_CR87","doi-asserted-by":"publisher","first-page":"2224","DOI":"10.1002\/sim.3940","volume":"29","author":"A Gasparrini","year":"2010","unstructured":"Gasparrini, A., Armstrong, B. & Kenward, M. G. Distributed lag non-linear models. Stat. Med. 29, 2224\u20132234 (2010).","journal-title":"Stat. Med."},{"key":"2458_CR88","doi-asserted-by":"publisher","first-page":"938","DOI":"10.1111\/biom.12645","volume":"73","author":"A Gasparrini","year":"2017","unstructured":"Gasparrini, A., Scheipl, F., Armstrong, B. & Kenward, M. G. A penalized framework for distributed lag non-linear models. Biometrics 73, 938\u2013948 (2017).","journal-title":"Biometrics"},{"key":"2458_CR89","doi-asserted-by":"publisher","first-page":"e209","DOI":"10.1016\/S2542-5196(20)30292-8","volume":"5","author":"R Lowe","year":"2021","unstructured":"Lowe, R. et al. Combined effects of hydrometeorological hazards and urbanisation on dengue risk in Brazil: a spatiotemporal modelling study. Lancet Planet. Health 5, e209\u2013e219 (2021).","journal-title":"Lancet Planet. Health"},{"key":"2458_CR90","first-page":"3571","volume":"11","author":"S Watanabe","year":"2010","unstructured":"Watanabe, S. Asymptotic equivalence of Bayes cross validation and widely applicable information criterion in singular learning theory. J. Mach. Learn. Res. 11, 3571\u20133594 (2010).","journal-title":"J. Mach. Learn. Res."},{"key":"2458_CR91","doi-asserted-by":"crossref","unstructured":"Menard, S. Coefficients of determination for multiple logistic regression analysis. Am. Stat. 54, 17\u201324 (2000).","DOI":"10.1080\/00031305.2000.10474502"},{"key":"2458_CR92","doi-asserted-by":"crossref","unstructured":"Cox, D. R. & Snell, E. J. The Analysis of Binary Data 2nd edn (Chapman and Hall, 1989).","DOI":"10.2307\/2531476"},{"key":"2458_CR93","doi-asserted-by":"publisher","unstructured":"Belman, S. Pneumococcal population structure influences the effects of air pollution on invasive disease risk in South Africa [Dataset]. Zenodo https:\/\/doi.org\/10.5281\/zenodo.17877255 (2025).","DOI":"10.5281\/zenodo.17877255"},{"key":"2458_CR94","doi-asserted-by":"crossref","unstructured":"Belman, S. Pneumococcal population structure influences the effects of air pollution on invasive disease risk in South Africa. GitHub https:\/\/github.com\/sophbel\/env_sa_manuscript (2026).","DOI":"10.1038\/s41564-026-02458-5"}],"container-title":["Nature Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41564-026-02458-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41564-026-02458-5","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41564-026-02458-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,28]],"date-time":"2026-10-28T23:02:26Z","timestamp":1793228546000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41564-026-02458-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,14]]},"references-count":94,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2026,10]]}},"alternative-id":["2458"],"URL":"https:\/\/doi.org\/10.1038\/s41564-026-02458-5","relation":{},"ISSN":["2058-5276"],"issn-type":[{"value":"2058-5276","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,14]]},"assertion":[{"value":"17 December 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 July 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 September 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors report no conflicts of interest.","order":1,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Ethics"}}]}}