. 2023 Feb 8;76(3):e710-e717.

doi: 10.1093/cid/ciac499.

Unmasking Pneumococcal Carriage in a High Human Immunodeficiency Virus (HIV) Prevalence Population in two Community Cohorts in South Africa, 2016-2018: The PHIRST Study

Maimuna Carrim^{1

2}, Stefano Tempia^{1

3

4

5

6}, Deus Thindwa^{7

8}, Neil A Martinson^{9

10

11}, Kathleen Kahn¹², Stefan Flasche⁷, Orienka Hellferscee², Florette K Treurnicht^{2

13}, Meredith L McMorrow^{4

5}, Jocelyn Moyes^{1

3}, Thulisa Mkhencele¹, Azwifarwi Mathunjwa¹, Jackie Kleynhans^{1

3}, Limakatso Lebina^{9

14}, Katlego Mothlaoleng^{1

9}, Floidy Wafawanaka¹⁰, Francesc Xavier Gómez-Olivé¹⁰, Cheryl Cohen^{1

3}, Anne von Gottberg^{1

2}, Nicole Wolter^{1

2}; PHIRST group

Affiliations

¹ Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.
² School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
³ School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
⁴ Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
⁵ Influenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa.
⁶ MassGenics, Duluth, Georgia, USA.
⁷ Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom.
⁸ Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi.
⁹ Perinatal HIV Research Unit, MRC Soweto Matlosana Collaborating Centre for HIV/AIDS and TB, University of the Witwatersrand, Johannesburg, South Africa.
¹⁰ DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, University of the Witwatersrand, Johannesburg, South Africa.
¹¹ Johns Hopkins University Center for TB Research, Baltimore, Maryland, USA.
¹² MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa.
¹³ Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa.
¹⁴ Africa Health Research Institute, KwaZulu-Natal, South Africa.

PMID: 35717655
PMCID: PMC10169447
DOI: 10.1093/cid/ciac499

Unmasking Pneumococcal Carriage in a High Human Immunodeficiency Virus (HIV) Prevalence Population in two Community Cohorts in South Africa, 2016-2018: The PHIRST Study

Maimuna Carrim et al. Clin Infect Dis. 2023.

. 2023 Feb 8;76(3):e710-e717.

doi: 10.1093/cid/ciac499.

Authors

Affiliations

¹ Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.
² School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
³ School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
⁴ Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
⁵ Influenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa.
⁶ MassGenics, Duluth, Georgia, USA.
⁷ Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom.
⁸ Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi.
⁹ Perinatal HIV Research Unit, MRC Soweto Matlosana Collaborating Centre for HIV/AIDS and TB, University of the Witwatersrand, Johannesburg, South Africa.
¹⁰ DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, University of the Witwatersrand, Johannesburg, South Africa.
¹¹ Johns Hopkins University Center for TB Research, Baltimore, Maryland, USA.
¹² MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa.
¹³ Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa.
¹⁴ Africa Health Research Institute, KwaZulu-Natal, South Africa.

PMID: 35717655
PMCID: PMC10169447
DOI: 10.1093/cid/ciac499

Abstract

Background: Longitudinal pneumococcus colonization data in high human immunodeficiency virus (HIV) prevalence settings following pneumococcal conjugate vaccine introduction are limited.

Methods: In 327 randomly selected households, 1684 individuals were enrolled and followed-up for 6 to 10 months during 2016 through 2018 from 2 communities. Nasopharyngeal swabs were collected twice weekly and tested for pneumococcus using quantitative lytA real-time polymerase chain reaction. A Markov model was fitted to the data to define the start and end of an episode of colonization. We assessed factors associated with colonization using logistic regression.

Results: During the study period, 98% (1655/1684) of participants were colonized with pneumococcus at least once. Younger age (<5 years: adjusted odds ratio [aOR], 14.1; 95% confidence [CI], 1.8-111.3, and 5-24 years: aOR, 4.8, 95% CI, 1.9-11.9, compared with 25-44 years) and HIV infection (aOR, 10.1; 95% CI, 1.3-77.1) were associated with increased odds of colonization. Children aged <5 years had fewer colonization episodes (median, 9) than individuals ≥5 years (median, 18; P < .001) but had a longer episode duration (<5 years: 35.5 days; interquartile range, 17-88) vs. ≥5 years: 5.5 days (4-12). High pneumococcal loads were associated with age (<1 year: aOR 25.4; 95% CI, 7.4-87.6; 1-4 years: aOR 13.5, 95% CI 8.3-22.9; 5-14 years: aOR 3.1, 95% CI, 2.1-4.4 vs. 45-65 year old patients) and HIV infection (aOR 1.7; 95% CI 1.2-2.4).

Conclusions: We observed high levels of pneumococcus colonization across all age groups. Children and people with HIV were more likely to be colonized and had higher pneumococcal loads. Carriage duration decreased with age highlighting that children remain important in pneumococcal transmission.

Keywords: Streptococcus pneumoniae; South Africa; carriage; community cohort; pneumococcus colonization.

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Conflict of interest statement

Potential conflicts of interest. M. C. has received the Robert Austrian Award sponsored by Pfizer as well as received funding as part of the South Africa-Pittsburgh Public Health Genomic Epidemiology (SAPPHGenE) training program and reports support for attending meetings and/or travel paid to the institution from Bill and Melinda Gates Foundation. D. T. received funding from the UK National Institute of Health Research Mucosal Pathogen Research 336 Unit (NIHR-MPRU) at University College London. C. C. has received grant support from Sanofi Pasteur, Advanced Vaccine Initiative, CDC, Wellcome Trust, PATH, Bill and Melinda Gates Foundation, and South African Medical Research Council (SA-MRC). A. v. G. has received grant support from Sanofi Pasteur, Pfizer related to pneumococcal vaccine, CDC, and the Bill and Melinda Gates Foundation and reports being chairperson at their local NiTAG. N. W. report grants from Sanofi Pasteur and the Bill and Melinda Gates Foundation paid to the institution. All other authors report no potential conflicts. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed.

Figures

**Figure 1.**
Distribution of the percentage of individuals that carried the pneumococcus at least once during the study period by number of pneumococcal colonization episodes and age group, PHIRST study, South Africa, 2016–2018 (N = 1585).

**Figure 2.**
Median pneumococcal carriage duration by age group, with error bars indicating interquartile range, PHIRST study, South Africa, 2016–2018 (N = 1585).

**Figure 3.**
Median pneumococcal colonization density with interquartile range by age group, PHIRST study, South Africa, 2016–2018 (N = 1585).

See this image and copyright information in PMC

References

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Unmasking Pneumococcal Carriage in a High Human Immunodeficiency Virus (HIV) Prevalence Population in two Community Cohorts in South Africa, 2016-2018: The PHIRST Study

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Unmasking Pneumococcal Carriage in a High Human Immunodeficiency Virus (HIV) Prevalence Population in two Community Cohorts in South Africa, 2016-2018: The PHIRST Study

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Abstract

Conflict of interest statement

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