Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2025 Sep 29;25(1):1181.
doi: 10.1186/s12879-025-11587-x.

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

Geetha Nagaraj  1 , Varun Shamanna  2   3 , Harshitha Gangaiah Krishnappa  2 , Vandana Govindan  2 , Mettingal Ramakrishnan Shincy  2 , Ravikumar Kadahalli Lingegowda  2
Affiliations

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

Geetha Nagaraj et al. BMC Infect Dis. .

Abstract

Background: 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).

Methods: 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.

Results: 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.

Conclusion: 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.

Supplementary Information: The online version contains supplementary material available at 10.1186/s12879-025-11587-x.

Keywords: S. pneumoniae; AMR; GPSC; India; Serotypes; WGS.

PubMed Disclaimer

Conflict of interest statement

Declarations. Ethics approval and consent to participate: The Study was approved by Kempegowda Institute of Medical Sciences independent ethics committee (Approval ID: KIMS/IEC/S06/2022 dated 22-July-2022). The study was conducted according to the guidelines and recommendations of Good Clinical Practice and the Declaration of Helsinki. Written informed consent was obtained from each participant or legal guardian as applicable. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Distribution of serotypes among invasive and non-invasive specimens. The bars are stratified by the number of samples in each serotype belonging to invasive and non-invasive specimens. The serotypes are divided based on their presence in either PCV13 or PPSV23 vaccine and Non-PPSV23 serotypes. The bars are stacked to total number of isolates. Blue bars – Non-Invasive, Red bars – Invasive
Fig. 2
Fig. 2
Sequence type distribution of S.pneumoniae isolates. The bars are stratified by the number of samples in each sequence type and their association with serotype. The bars are stacked to total number of isolates
Fig. 3
Fig. 3
Distribution of antibiotic susceptibility among clinical isolates of Streptococcus pneumoniae. Categorized into susceptible (S, blue), intermediate (I, yellow), and resistant (R, red). The bar graph shows the number of isolates for each susceptibility category across the different antibiotics tested
Fig. 4
Fig. 4
Phylogenetic tree illustrating the distribution of Streptococcus pneumoniae serotypes and global pneumococcal sequence clusters (GPSCs) based on genome-wide analysis. The tree illustrates the genetic diversity of 234 isolates, annotated with Global Pneumococcal Sequence Clusters (GPSCs) and corresponding serotypes. Major GPSCs are shaded and labeled with node colors indicating GPSC assignments as per the legend. Clusters containing vaccine (PPSV23/PCV13) and non-vaccine serotypes are observed, with evidence of clonal expansion and serotype switching within dominant GPSCs. The scale bar represents the number of substitutions per site
See this image and copyright information in PMC

References

    1. Weiser JN, Ferreira DM, Paton JC. Streptococcus pneumoniae: transmission, colonization and invasion. Nat Rev Microbiol. 2018;16(6):355–67. 10.1038/s41579-018-0001-8. PMID: 29599457; PMCID: PMC5949087. - PMC - PubMed
    1. Centers for Disease Control Prevention. Pneumococcal Disease: Causes and How It Spreads. (2024). Available from: https://www.cdc.gov/pneumococcal/causes/index.html#cdc_causes_risk-risk-.... [Accessed on 12th July 2024].
    1. Torres A, Blasi F, Dartois N, Akova M. Which individuals are at increased risk of Pneumococcal disease and why? Impact of COPD, asthma, smoking, diabetes, and/or chronic heart disease on community-acquired pneumonia and invasive Pneumococcal disease. Thorax. 2015;70(10):984–9. 10.1136/thoraxjnl-2015-206780. Epub 2015 Jul 28. PMID: 26219979; PMCID: PMC4602259. - PMC - PubMed
    1. Wahl B, O’Brien KL, Greenbaum A, Majumder A, Liu L, Chu Y, et al. Burden of Streptococcus pneumoniae and Haemophilus influenzae type b disease in children in the era of conjugate vaccines: global, regional, and National estimates for 2000-15. Lancet Glob Health. 2018;6(7):e744–57. (18)30247-X. PMID: 29903376; PMCID: PMC6005122. - PMC - PubMed
    1. O’Brien KL, Wolfson LJ, Watt JP, Henkle E, Deloria-Knoll M, McCall N, Lee E, Mulholland K, Levine OS, Cherian T, Hib and Pneumococcal Global Burden of Disease Study Team. Burden of disease caused by Streptococcus pneumoniae in children younger than 5 years: global estimates. Lancet. 2009;374(9693):893–902. 10.1016/S0140-6736(09)61204-6. PMID: 19748398. - PubMed

LinkOut - more resources