Genomic surveillance of Streptococcus pneumoniae in India: vaccine-driven serotype shifts, antimicrobial resistance, and emerging clonal lineages.

AIMS: Streptococcus pneumoniae remains a leading cause of invasive disease in India despite pneumococcal conjugate vaccine (PCV) introduction. This study aimed analyzed 617 Indian pneumococcal isolates data from the global pneumococcal sequencing (GPS) database to evaluate long-term trends in serotype distribution, antimicrobial resistance (AMR), and clonal expansion of S. pneumoniae in India to update public health strategies.

METHODS AND

RESULTS

This retrospective genomic epidemiology study analyzed 617 S. pneumoniae isolates (1999-2023) from the GPS project. Isolates were classified by source, age, vaccine period, and serotype. Post-PCV13 (after 2017), vaccine-type serotypes declined (65%→32%), while non-vaccine types increased, notably 35B and 24F. Resistance rose sharply, with cefotaxime (12%→63%), erythromycin (∼30%→83%), and meropenem (5%→25%) showing major increases, particularly among children ≤5 years. Among 127 invasive pneumococcal isolates from children ≤5 years, 31.4% showed discordance between phenotypic and whole-genome sequencing (WGS) serotyping, indicating that older phenotypic methods likely overestimated PCV coverage by ∼10%-12%. Multilocus sequence typing (MLST) identified 73 sequence types, including 31 novel Indian lineages. High-risk clones such as ST320 (19A), ST271 (19F), ST12470 (24F), and ST7551 (35B) drove multidrug resistance (MDR) and serotype replacement following PCV13 introduction in India.

CONCLUSIONS

India's pneumococcal population is undergoing vaccine-driven serotype replacement with concurrent expansion of MDR NVTs. Moreover, 31.4% discordance between phenotypic and WGS serotyping indicates that older phenotypic methods likely overestimated PCV coverage by ∼10%-12%, underscoring the need for genomics-first surveillance, incorporation of WGS into national monitoring, and evaluation of higher-valency or protein-based vaccines to ensure long-term disease control.