Publication: Early signals of vaccine-driven perturbation seen in pneumococcal carriage population genomic data
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Issued Date
2020-03-17
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15376591
10584838
10584838
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2-s2.0-85082096197
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Mahidol University
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SCOPUS
Bibliographic Citation
Clinical Infectious Diseases. Vol.70, No.7 (2020), 1294-1303
Suggested Citation
Chrispin Chaguza, Ellen Heinsbroek, Rebecca A. Gladstone, Terence Tafatatha, Maaike Alaerts, Chikondi Peno, Jennifer E. Cornick, Patrick Musicha, Naor Bar-Zeev, Arox Kamng'Ona, Aras Kadioglu, Lesley McGee, William P. Hanage, Robert F. Breiman, Robert S. Heyderman, Neil French, Dean B. Everett, Stephen D. Bentley Early signals of vaccine-driven perturbation seen in pneumococcal carriage population genomic data. Clinical Infectious Diseases. Vol.70, No.7 (2020), 1294-1303. doi:10.1093/cid/ciz404 Retrieved from: https://repository.li.mahidol.ac.th/handle/123456789/54618
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Title
Early signals of vaccine-driven perturbation seen in pneumococcal carriage population genomic data
Author(s)
Other Contributor(s)
Public Health England
Malawi Epidemiology and Intervention Research Unit
Malawi-Liverpool-Wellcome Trust Clinical Research Programme
University of Malawi College of Medicine
Harvard T.H. Chan School of Public Health
University of Cambridge
University of Edinburgh
Rollins School of Public Health
UCL
University of Liverpool
Universiteit Antwerpen
Mahidol University
National Center for Immunization and Respiratory Diseases
Nuffield Department of Clinical Medicine
Johns Hopkins Bloomberg School of Public Health
Wellcome Sanger Institute
Malawi Epidemiology and Intervention Research Unit
Malawi-Liverpool-Wellcome Trust Clinical Research Programme
University of Malawi College of Medicine
Harvard T.H. Chan School of Public Health
University of Cambridge
University of Edinburgh
Rollins School of Public Health
UCL
University of Liverpool
Universiteit Antwerpen
Mahidol University
National Center for Immunization and Respiratory Diseases
Nuffield Department of Clinical Medicine
Johns Hopkins Bloomberg School of Public Health
Wellcome Sanger Institute
Abstract
© 2019 The Author(s). Published by Oxford University Press for the Infectious Diseases Society of America. Background: Pneumococcal conjugate vaccines (PCVs) have reduced pneumococcal diseases globally. Pneumococcal genomic surveys elucidate PCV effects on population structure but are rarely conducted in low-income settings despite the high disease burden. Methods: We undertook whole-genome sequencing (WGS) of 660 pneumococcal isolates collected through surveys from healthy carriers 2 years from 13-valent PCV (PCV13) introduction and 1 year after rollout in northern Malawi. We investigated changes in population structure, within-lineage serotype dynamics, serotype diversity, and frequency of antibiotic resistance (ABR) and accessory genes. Results: In children <5 years of age, frequency and diversity of vaccine serotypes (VTs) decreased significantly post-PCV, but no significant changes occurred in persons ≥5 years of age. Clearance of VT serotypes was consistent across different genetic backgrounds (lineages). There was an increase of nonvaccine serotypes (NVTs) - namely 7C, 15B/C, and 23A - in children <5 years of age, but 28F increased in both age groups. While carriage rates have been recently shown to remain stable post-PCV due to replacement serotypes, there was no change in diversity of NVTs. Additionally, frequency of intermediate-penicillin-resistant lineages decreased post-PCV. Although frequency of ABR genes remained stable, other accessory genes, especially those associated with mobile genetic element and bacteriocins, showed changes in frequency post-PCV. Conclusions: We demonstrate evidence of significant population restructuring post-PCV driven by decreasing frequency of vaccine serotypes and increasing frequency of few NVTs mainly in children under 5. Continued surveillance with WGS remains crucial to fully understand dynamics of the residual VTs and replacement NVT serotypes post-PCV.