{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T06:17:57Z","timestamp":1772173077783,"version":"3.50.1"},"reference-count":61,"publisher":"Public Library of Science (PLoS)","issue":"12","license":[{"start":{"date-parts":[[2021,12,23]],"date-time":"2021-12-23T00:00:00Z","timestamp":1640217600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"}],"funder":[{"name":"US Centres for Disease Control and Prevention","award":["1U01IP001048"],"award-info":[{"award-number":["1U01IP001048"]}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1164778"],"award-info":[{"award-number":["OPP1164778"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000272","name":"National Institute of Health Research","doi-asserted-by":"crossref","award":["16\/136\/46"],"award-info":[{"award-number":["16\/136\/46"]}],"id":[{"id":"10.13039\/501100000272","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000272","name":"National Institute for Health Research","doi-asserted-by":"crossref","award":["16\/136\/46"],"award-info":[{"award-number":["16\/136\/46"]}],"id":[{"id":"10.13039\/501100000272","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1139859"],"award-info":[{"award-number":["OPP1139859"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["208812\/Z\/17\/Z"],"award-info":[{"award-number":["208812\/Z\/17\/Z"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100014588","name":"Sanofi Pasteur","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100014588","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100014588","name":"Sanofi Pasteur","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100014588","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>Human immunodeficiency virus (HIV) infected adults are at a higher risk of pneumococcal colonisation and disease, even while receiving antiretroviral therapy (ART). To help evaluate potential indirect effects of vaccination of HIV-infected adults, we assessed whether HIV-infected adults disproportionately contribute to household transmission of pneumococci. We constructed a hidden Markov model to capture the dynamics of pneumococcal carriage acquisition and clearance observed during a longitudinal household-based nasopharyngeal swabbing study, while accounting for sample misclassifications. Households were followed-up twice weekly for approximately 10 months each year during a three-year study period for nasopharyngeal carriage detection via real-time PCR. We estimated the effect of participant\u2019s age, HIV status, presence of a HIV-infected adult within the household and other covariates on pneumococcal acquisition and clearance probabilities. Of 1,684 individuals enrolled, 279 (16.6%) were younger children (&lt;5 years-old) of whom 4 (1.5%) were HIV-infected and 726 (43.1%) were adults (\u226518 years-old) of whom 214 (30.4%) were HIV-infected, most (173, 81.2%) with high CD4+ count. The observed range of pneumococcal carriage prevalence across visits was substantially higher in younger children (56.9\u201380.5%) than older children (5\u201317 years-old) (31.7\u201350.0%) or adults (11.5\u201323.5%). We estimate that 14.4% (95% Confidence Interval [CI]: 13.7\u201315.0) of pneumococcal-negative swabs were false negatives. Daily carriage acquisition probabilities among HIV-uninfected younger children were similar in households with and without HIV-infected adults (hazard ratio: 0.95, 95%CI: 0.91\u20131.01). Longer average carriage duration (11.4 days, 95%CI: 10.2\u201312.8 vs 6.0 days, 95%CI: 5.6\u20136.3) and higher median carriage density (622 genome equivalents per millilitre, 95%CI: 507\u2013714 vs 389, 95%CI: 311.1\u2013435.5) were estimated in HIV-infected vs HIV-uninfected adults. The use of ART and antibiotics substantially reduced carriage duration in all age groups, and acquisition rates increased with household size. Although South African HIV-infected adults on ART have longer carriage duration and density than their HIV-uninfected counterparts, they show similar patterns of pneumococcal acquisition and onward transmission.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1009680","type":"journal-article","created":{"date-parts":[[2021,12,23]],"date-time":"2021-12-23T13:24:08Z","timestamp":1640265848000},"page":"e1009680","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":17,"title":["Estimating the contribution of HIV-infected adults to household pneumococcal transmission in South Africa, 2016\u20132018: A hidden Markov modelling study"],"prefix":"10.1371","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4845-7862","authenticated-orcid":true,"given":"Deus","family":"Thindwa","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9526-0133","authenticated-orcid":true,"given":"Nicole","family":"Wolter","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Amy","family":"Pinsent","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2717-5540","authenticated-orcid":true,"given":"Maimuna","family":"Carrim","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3010-1158","authenticated-orcid":true,"given":"John","family":"Ojal","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4395-347X","authenticated-orcid":true,"given":"Stefano","family":"Tempia","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8040-1717","authenticated-orcid":true,"given":"Jocelyn","family":"Moyes","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6363-4033","authenticated-orcid":true,"given":"Meredith","family":"McMorrow","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7081-6273","authenticated-orcid":true,"given":"Jackie","family":"Kleynhans","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0243-7455","authenticated-orcid":true,"given":"Anne von","family":"Gottberg","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4814-8293","authenticated-orcid":true,"given":"Neil","family":"French","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"name":"PHIRST group","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cheryl","family":"Cohen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5808-2606","authenticated-orcid":true,"given":"Stefan","family":"Flasche","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2021,12,23]]},"reference":[{"key":"pcbi.1009680.ref001","doi-asserted-by":"crossref","first-page":"893","DOI":"10.1016\/S0140-6736(09)61204-6","article-title":"Burden of disease caused by Streptococcus pneumoniae in children younger than 5 years: global estimates","volume":"374","author":"KL O\u2019Brien","year":"2009","journal-title":"The Lancet"},{"key":"pcbi.1009680.ref002","doi-asserted-by":"crossref","first-page":"e744","DOI":"10.1016\/S2214-109X(18)30247-X","article-title":"Burden of Streptococcus pneumoniae and Haemophilus influenzae type b disease in children in the era of conjugate vaccines: global, regional, and national estimates for 2000\u201315","volume":"6","author":"B Wahl","year":"2018","journal-title":"The Lancet Global Health"},{"key":"pcbi.1009680.ref003","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1016\/j.tmaid.2018.05.016","article-title":"Incidence of invasive pneumococcal disease in immunocompromised patients: A systematic review and meta-analysis.","volume":"24","author":"M van Aalst","year":"2018","journal-title":"Travel Medicine and Infectious Disease"},{"key":"pcbi.1009680.ref004","doi-asserted-by":"crossref","first-page":"2390","DOI":"10.1017\/S0950268817001194","article-title":"The epidemiology of invasive pneumococcal disease in older adults in the post-PCV era. 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