Strain features of pneumococcal isolates in the pre- and post-PCV10 era in Pakistan

Nida Javaid, Stephanie W Lo, Muhammad Imran Nisar, Asma Basharat, Hadiqa Jaleel, Karam Rasool, Qamar Sultana, Furqan Kabir, Aneeta Hotwani, Robert F Breiman, Stephen D Bentley, Sadia Shakoor, Shaper Mirza

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Abstract

Pakistan is amongst the four countries with the highest number of pneumococcal deaths. While the PCV10 vaccine was introduced in Pakistan in October 2012, data regarding the impact of the vaccine on the population dynamics of Streptococcus pneumoniae in Pakistan remain obscure. Using whole genome sequencing of 190 isolates (nasopharyngeal carriage=75, disease=113, unknown sites=2) collected between 2002 and 2020, this study presents characteristics of pneumococcal strains in Pakistan in the pre- and post-vaccine era. The isolates were characterized on the basis of serotype distribution, genetic lineages (or Global Pneumococcal Sequence Cluster, GPSC) and antibiotic resistance. A high level of diversity in serotype and genetic lineages of pneumococci was observed in Pakistan. Among 190 isolates, we identified 54 serotypes, 67 GPSCs and 116 sequence types (STs) including 23 new STs. The most prevalent GPSCs and their associated serotypes in nasopharyngeal carriage were GPSC54 (expressing serotype 9V), GPSC5 (15A and 7B, and serogroup 24), GPSC25 (15B/15C), GPSC67 (18C) and GPSC376 (6A and 6D). Similarly, among 113 disease-causing isolates, the most prevalent GPSC/serotype combinations were GPSC2 (serotype 1), GPSC10 (serotypes 14, 10A, 19A and 19F), GPSC43 (serotypes 13, 11A, 23B, 35A and 9V), GPSC67 (serotypes 18A and 18C) and GPSC642 (serotype 11A). Of the 190 isolates, the highest levels of resistance were observed against penicillin (58.9 %, n=122), erythromycin (29.5 %, n=56), clindamycin (13.2 %, n=25), co-trimoxazole (94.2 %, n=179) and tetracycline/doxycycline (53.2 %, n=101). A higher proportion of disease-causing isolates were multidrug resistant as compared to carriage isolates (54 % vs 25 %). Our data suggest limited coverage of PCV10 in nasopharyngeal (21.6 %, 16/74) as well as disease-causing (38.1 %, 16/42) isolates among children ≤5 years old; however, higher valent vaccine PCV13 would increase the coverage rates to 33.8 % in nasopharyngeal and 54.8 % in disease-causing isolates, whereas PCV24/25 would offer the highest coverage rates. Owing to the diversity of serotypes observed during the post-vaccine period, the suggested inclusion of serotype in future vaccine formulations will require investigations with larger data sets with an extended temporal window. This article contains data hosted by Microreact.
Original languageEnglish
JournalMicrobial Genomics
Volume10
Issue number1
DOIs
Publication statusPublished - 25 Jan 2024

Funding

This study was co-funded by the Bill and Melinda Gates Foundation (grant code OPP1034556), the Wellcome Sanger Institute (core Wellcome grants 098051 and 206194), the US Centers for Disease Control and Prevention and Lahore University of Management Sciences Faculty initiative fund FIF 502. The funding sources had no role in isolate selection, analysis or data interpretation. The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the CDC. The corresponding author had full access to the data and is responsible for the final decision to submit for publication.

FundersFunder number
Bill and Melinda Gates FoundationOPP1034556
Wellcome Sanger Institute098051, 206194
Centers for Disease Control and Prevention

    Keywords

    • Child
    • Humans
    • Child, Preschool
    • Pakistan/epidemiology
    • Streptococcus pneumoniae/genetics
    • Pneumococcal Vaccines
    • Anti-Bacterial Agents/pharmacology

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