Tracking the evolution of emerging serotypes and antibiotic resistance patterns in Streptococcus pneumoniae among Indian adults using high-throughput genome sequencing

Streptococcus pneumoniae is a major cause of respiratory infections, particularly affecting children and the elderly. However, data on pneumococcal disease among Indian adults remain limited. This study investigated the epidemiology of S. pneumoniae from invasive and non-invasive sources in Indian adults using whole-genome sequencing (WGS). A prospective study was undertaken in five hospitals of India between 2022 and 2023, including 254 S. pneumoniae isolates, 126 from invasive and 128 from non-invasive specimens. WGS was performed using the Illumina platform to determine serotypes, multi locus sequence types (STs), lineages, antimicrobial resistance (AMR), and virulence profiles. Antimicrobial susceptibility was assessed using the Vitek-2 system. A total of 37 serotypes, 53 Global Pneumococcal Sequence Clusters (GPSCs), and 128 STs (including 39 novel STs) were identified. Predominant serotypes included 19 F, 19 A, and 9 V, with GPSC1, GPSC10, and GPSC6 being the most common lineages. Vaccine coverage was estimated at 64% for PCV13 and 72% for PPSV23. Multidrug resistance (MDR) was observed in 70% of isolates, mainly among GPSC1, 10, and 6. Virulence genes were widely distributed, and pilus genes were more common in non-invasive isolates. Phylogenetic analysis showed GPSC1, 10, and 6 as dominant in both invasive and non-invasive sources. The high prevalence of non-vaccine lineages, elevated MDR, and large number of novel STs reflect ongoing pneumococcal evolution in India, likely driven by recombination and capsular switching. These dynamics may reduce vaccine effectiveness. Continuous genomic surveillance is crucial to inform vaccine strategies and control pneumococcal disease in Indian adults.