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.
There is a more recent version of this item available. |
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 |
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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: | |
URI: | https://livrepository.liverpool.ac.uk/id/eprint/3042010 |
Available Versions of this Item
- Early signals of vaccine driven perturbation seen in pneumococcal carriage population genomic data. (deposited 21 May 2019 11:53) [Currently Displayed]