Early signals of vaccine driven perturbation seen in pneumococcal carriage population genomic data.

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Chaguza, Chrispin ORCID: 0000-0002-2108-1757, Heinsbroek, Ellen, Gladstone, Rebecca A, Tafatatha, Terence, Alaerts, Maaike, Peno, Chikondi, Cornick, Jennifer E, Musicha, Patrick, Bar-Zeev, Naor, Kamng'ona, Arox et al (show 8 more authors) (2020) Early signals of vaccine driven perturbation seen in pneumococcal carriage population genomic data. Clinical infectious diseases: an official publication of the Infectious Diseases Society of America, 70 (7). 1294 - 1303.

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Abstract

BACKGROUND: Pneumococcal conjugate vaccines (PCV) 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 of 660 pneumococcal isolates collected through surveys from healthy carriers two years from PCV14 introduction and one-year post-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 the under-fives, frequency and diversity of vaccine serotypes (VT) decreased significantly post-PCV but no significant changes occurred in over-fives. Clearance of VT serotypes was consistent across different genetic backgrounds (lineages). There was an increase of non-vaccine serotypes (NVT) namely 7C, 15B/C, 23A in under-fives but 28F increased in both age groups. While carriage rates have been recently shown to remain stable post-PCV due replacement serotypes, there was no change in diversity of NVTs. Additionally, frequency of intermediate-penicillin-resistant lineages decreased post-PCV. While frequency of ABR genes remained stable, other accessory genes especially those associated with MGEs 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 under-fives. Continued surveillance with WGS remains crucial to fully understand dynamics of the residual VTs and replacement NVT serotypes post-PCV.

Item Type:	Article
Uncontrolled Keywords:	pneumococcus, Carriage, Genomics, Serotypes
Depositing User:	Symplectic Admin
Date Deposited:	21 May 2019 11:53
Last Modified:	19 Jan 2023 00:44
DOI:	10.1093/cid/ciz404
Open Access URL:	https://academic.oup.com/cid/advance-article/doi/1...
Related URLs:	Publisher
URI:	https://livrepository.liverpool.ac.uk/id/eprint/3042010