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Peer-reviewedCC BYJournal of Infection

Antimicrobial resistance trends and lineage distribution among invasive pneumococcal disease isolates pre- and post-pneumococcal conjugate vaccine introduction, South Africa

  • Cebile Lekhuleni
  • Kedibone Ndlangisa1
  • Linda de Gouveia2
  • Sopio Chochua3
  • Scott Hazelhurst4
  • Benjamin J. Metcalf3
  • Yuan Li3
  • Jackie Kleynhans5
  • Happy Skosana2
  • Arshad Ismail6
  • Sibongile Walaza5
  • Vanessa Quan7
8 more authors
  • Susan Meiring7
  • Paulina A. Hawkins3
  • Lesley McGee3
  • Stephen D. Bentley8
  • Cheryl Cohen5
  • Stephanie W. Lo9
  • Mignon du Plessis1
  • Anne von Gottberg
9 affiliations
  1. 1Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
  2. 2Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
  3. 3Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
  4. 4School of Electrical & Information Engineering, University of the Witwatersrand, South Africa; Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
  5. 5Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa; School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
  6. 6Sequencing Core Facility, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa; Institute for Water and Wastewater Technology, Durban University of Technology, Durban 4000, South Africa
  7. 7Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
  8. 8Parasites and Microbes Programme, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
  9. 9Parasites and Microbes Programme, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK; Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, UK; The Great Ormond Street Institute of Child Health, University College London, London, UK
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Abstract

Objectives: Pneumococcal conjugate vaccines (PCV) have reduced antimicrobial-resistant invasive pneumococcal disease (IPD) globally. We evaluated trends in antimicrobial-resistant IPD and pneumococcal lineages before and after PCV13 introduction in South Africa. Methods: We analysed national, laboratory-based IPD surveillance reported cases (2005–2020) and compared the incidence of resistant-IPD pre- and post-PCV introduction. Antimicrobial susceptibility testing was performed for six antibiotics, and penicillin-multidrug resistance (penicillin-MDR) was defined as penicillin nonsusceptibility plus resistance to ≥2 additional antibiotic classes. Whole-genome sequencing was used to determine serotypes, sequence types, global pneumococcal sequence clusters (GPSC), and antimicrobial resistance (AMR) determinants. Results: Following PCV introduction, overall IPD and AMR IPD incidence declined substantially. Penicillin-cotrimoxazole nonsusceptible and penicillin-MDR IPD incidence decreased from 5.6 to 0.8 per 100,000 population (percentage decrease –86.5%, confidence intervals [CI] –90.5% to –81.4%) and 5.5 to 0.4 (–93.0%, –95.7% to –89.1%), respectively, in children <5 years, with smaller but significant reductions in the ≥5 years old. Despite these declines, residual PCV13 serotypes, particularly 19A and 19F, continued to contribute notably to penicillin-cotrimoxazole nonsusceptible and penicillin-MDR IPD, respectively, after PCV13 introduction. Non-vaccine serotypes (10A, 15A, 15B/C, 16F, 23B, and 35B) increasingly contributed to resistant IPD in the post-PCV13 era through the expansion of both vaccine-type and non-vaccine-type GPSC lineages. Conclusion: PCVs substantially reduced AMR IPD in South Africa, but persistent PCV13 serotypes and expanding resistant non-vaccine-type lineages highlight the potential benefit of higher-valency PCVs, including PCV20.

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Cite

BibTeXRIS
BibTeX
@article{lekhuleni2026antimicrobial,
  title = {{Antimicrobial resistance trends and lineage distribution among invasive pneumococcal disease isolates pre- and post-pneumococcal conjugate vaccine introduction, South Africa}},
  author = {Cebile Lekhuleni and Kedibone Ndlangisa and Linda de Gouveia and Sopio Chochua and Scott Hazelhurst and Benjamin J. Metcalf and Yuan Li and Jackie Kleynhans and Happy Skosana and Arshad Ismail and Sibongile Walaza and Vanessa Quan and Susan Meiring and Paulina A. Hawkins and Lesley McGee and Stephen D. Bentley and Cheryl Cohen and Stephanie W. Lo and Mignon du Plessis and Anne von Gottberg},
  journal = {Journal of Infection},
  year = {2026},
  month = oct,
  doi = {10.1016/j.jinf.2026.106878},
  url = {https://doi.org/10.1016/j.jinf.2026.106878},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - Antimicrobial resistance trends and lineage distribution among invasive pneumococcal disease isolates pre- and post-pneumococcal conjugate vaccine introduction, South Africa
AU  - Cebile Lekhuleni
AU  - Kedibone Ndlangisa
AU  - Linda de Gouveia
AU  - Sopio Chochua
AU  - Scott Hazelhurst
AU  - Benjamin J. Metcalf
AU  - Yuan Li
AU  - Jackie Kleynhans
AU  - Happy Skosana
AU  - Arshad Ismail
AU  - Sibongile Walaza
AU  - Vanessa Quan
AU  - Susan Meiring
AU  - Paulina A. Hawkins
AU  - Lesley McGee
AU  - Stephen D. Bentley
AU  - Cheryl Cohen
AU  - Stephanie W. Lo
AU  - Mignon du Plessis
AU  - Anne von Gottberg
PY  - 2026
DA  - 2026/10/30
JO  - Journal of Infection
DO  - 10.1016/j.jinf.2026.106878
UR  - https://doi.org/10.1016/j.jinf.2026.106878
AB  - Objectives: Pneumococcal conjugate vaccines (PCV) have reduced antimicrobial-resistant invasive pneumococcal disease (IPD) globally. We evaluated trends in antimicrobial-resistant IPD and pneumococcal lineages before and after PCV13 introduction in South Africa. Methods: We analysed national, laboratory-based IPD surveillance reported cases (2005–2020) and compared the incidence of resistant-IPD pre- and post-PCV introduction. Antimicrobial susceptibility testing was performed for six antibiotics, and penicillin-multidrug resistance (penicillin-MDR) was defined as penicillin nonsusceptibility plus resistance to ≥2 additional antibiotic classes. Whole-genome sequencing was used to determine serotypes, sequence types, global pneumococcal sequence clusters (GPSC), and antimicrobial resistance (AMR) determinants. Results: Following PCV introduction, overall IPD and AMR IPD incidence declined substantially. Penicillin-cotrimoxazole nonsusceptible and penicillin-MDR IPD incidence decreased from 5.6 to 0.8 per 100,000 population (percentage decrease –86.5%, confidence intervals [CI] –90.5% to –81.4%) and 5.5 to 0.4 (–93.0%, –95.7% to –89.1%), respectively, in children <5 years, with smaller but significant reductions in the ≥5 years old. Despite these declines, residual PCV13 serotypes, particularly 19A and 19F, continued to contribute notably to penicillin-cotrimoxazole nonsusceptible and penicillin-MDR IPD, respectively, after PCV13 introduction. Non-vaccine serotypes (10A, 15A, 15B/C, 16F, 23B, and 35B) increasingly contributed to resistant IPD in the post-PCV13 era through the expansion of both vaccine-type and non-vaccine-type GPSC lineages. Conclusion: PCVs substantially reduced AMR IPD in South Africa, but persistent PCV13 serotypes and expanding resistant non-vaccine-type lineages highlight the potential benefit of higher-valency PCVs, including PCV20.
SN  - 1532-2742
ER  -