{
  "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.",
  "abstract_shown": true,
  "affiliations": [
    "Centre 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",
    "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa",
    "Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA",
    "School 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",
    "Centre 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",
    "Sequencing 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",
    "Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa",
    "Parasites and Microbes Programme, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK",
    "Parasites 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"
  ],
  "article_type": null,
  "arxiv": null,
  "author_total": 20,
  "authors": [
    {
      "name": "Cebile Lekhuleni"
    },
    {
      "affs": [
        0
      ],
      "name": "Kedibone Ndlangisa"
    },
    {
      "affs": [
        1
      ],
      "name": "Linda de Gouveia"
    },
    {
      "affs": [
        2
      ],
      "name": "Sopio Chochua"
    },
    {
      "affs": [
        3
      ],
      "name": "Scott Hazelhurst"
    },
    {
      "affs": [
        2
      ],
      "name": "Benjamin J. Metcalf"
    },
    {
      "affs": [
        2
      ],
      "name": "Yuan Li"
    },
    {
      "affs": [
        4
      ],
      "name": "Jackie Kleynhans"
    },
    {
      "affs": [
        1
      ],
      "name": "Happy Skosana"
    },
    {
      "affs": [
        5
      ],
      "name": "Arshad Ismail"
    },
    {
      "affs": [
        4
      ],
      "name": "Sibongile Walaza"
    },
    {
      "affs": [
        6
      ],
      "name": "Vanessa Quan"
    },
    {
      "affs": [
        6
      ],
      "name": "Susan Meiring"
    },
    {
      "affs": [
        2
      ],
      "name": "Paulina A. Hawkins"
    },
    {
      "affs": [
        2
      ],
      "name": "Lesley McGee"
    },
    {
      "affs": [
        7
      ],
      "name": "Stephen D. Bentley"
    },
    {
      "affs": [
        4
      ],
      "name": "Cheryl Cohen"
    },
    {
      "affs": [
        8
      ],
      "name": "Stephanie W. Lo"
    },
    {
      "affs": [
        0
      ],
      "name": "Mignon du Plessis"
    },
    {
      "name": "Anne von Gottberg"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/07wscrs0b182h.bib",
  "cited_by": 0,
  "doi": "10.1016/j.jinf.2026.106878",
  "fulltext_url": "http://www.sciencedirect.com/science/article/pii/S0163445326002045",
  "id": "07wscrs0b182h",
  "issns": [
    "1532-2742"
  ],
  "landing_url": "https://doi.org/10.1016/j.jinf.2026.106878",
  "language": "en",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "journal",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "lcc",
      "RA1-1270"
    ],
    [
      "lcc",
      "RC109-216"
    ],
    [
      "openalex",
      "2713|Pneumonia and Respiratory Infections"
    ]
  ],
  "openalex": "W7222085724",
  "pdf_url": "https://www.journalofinfection.com/article/S0163-4453(26)00204-5/pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-30",
  "publisher": "Elsevier",
  "ris": "https://research.draconitic.com/paper/07wscrs0b182h.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T13:44:35Z",
      "native_id": "b6233e7f761e4e4aad29af199bbbcbcf",
      "source": "doaj",
      "url": "https://doi.org/10.1016/j.jinf.2026.106878"
    }
  ],
  "subjects": [
    {
      "field": "medicine",
      "origin": "openalex:2713|Pneumonia and Respiratory Infections",
      "subfield": "epidemiology-public-health"
    }
  ],
  "title": "Antimicrobial resistance trends and lineage distribution among invasive pneumococcal disease isolates pre- and post-pneumococcal conjugate vaccine introduction, South Africa",
  "title_text": "Antimicrobial resistance trends and lineage distribution among invasive pneumococcal disease isolates pre- and post-pneumococcal conjugate vaccine introduction, South Africa",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T13:44:35Z",
  "url": "https://research.draconitic.com/paper/07wscrs0b182h",
  "venue": "Journal of Infection",
  "versions": []
}