Genomic Characterization and Predictors of Mortality in Invasive Streptococcus pneumoniae Disease in Oman: A Four-Year National Genomic Study.

Authors

Amina Al-Jardani, Najma Al-Kharusi, Mohamed Al-Bulushi, Adil Al-Wahaibi, Neima Al-Shekaili, Suad Al-Fahdi, Rajesh Kumar, Seif Al-Abri, Azza Al-Rashdi

Published in

Vaccines. Volume 14. Issue 6. May 31, 2026. Epub May 31, 2026.

Abstract

Background/Objectives: Following the introduction of the 13-valent pneumococcal conjugate vaccine (PCV13) in Oman, this study aimed to characterize the genomic epidemiology, serotype distribution, and antimicrobial resistance (AMR) of Streptococcus pneumoniae causing invasive pneumococcal disease (IPD). Methods: All IPD isolates collected through national laboratory-based surveillance between 2018 and 2021 were analyzed using Whole-Genome Sequencing (WGS). Bioinformatics tools determined serotypes, multilocus sequence types (MLSTs), and Global Pneumococcal Sequence Clusters (GPSCs). Clinical correlates and predictors of mortality were assessed via multivariate logistic regression. Results: A total of 129 IPD isolates were included. Serotype 3 (11.6%) was the most prevalent, followed by 23B and 9N (10.8% each), and 8 (8.5%). PCV13 serotypes accounted for only 26.4% of isolates, while PCV20 coverage reached 59.7%. Significant clonal diversity was observed, with GPSC12 (Serotype 3) and GPSC699 (Serotype 9N/13) being prominent lineages. Multidrug resistance (MDR) was identified in 36.4% of isolates, primarily driven by GPSC6 and GPSC699. The case fatality rate was 23.0%. Advanced age (≥65 years) and clinical presentation with bacteremia were significant independent predictors of death, whereas bacterial genotype and AMR status were not. Conclusions: The findings demonstrate significant serotype replacement in Oman after the introduction of PCV13. The high prevalence of non-vaccine serotypes and emerging MDR clones justifies the transition to higher-valency vaccines like PCV20. Sustained genomic surveillance remains essential to monitor the evolving landscape of invasive pneumococcal lineages.

PMID:
42347617
Bibliographic data and abstract were imported from PubMed on 25 Jun 2026.

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