{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,30]],"date-time":"2026-10-30T14:49:05Z","timestamp":1793371745369,"version":"4.5.0"},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2025,10,29]],"date-time":"2025-10-29T00:00:00Z","timestamp":1761696000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001411","name":"ICMR","doi-asserted-by":"publisher","award":["IIRPSG-2024-01-01597"],"award-info":[{"award-number":["IIRPSG-2024-01-01597"]}],"id":[{"id":"10.13039\/501100001411","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Sathyabama Institute of Science and Technology"},{"name":"Central Leprosy Teaching and Research Institute"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,11,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Aims<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods and Results<\/jats:title>\n                    <jats:p>This retrospective genomic epidemiology study analyzed 617 S. pneumoniae isolates (1999\u20132023) from the GPS project. Isolates were classified by source, age, vaccine period, and serotype. Post-PCV13 (after 2017), vaccine-type serotypes declined (65%\u219232%), while non-vaccine types increased, notably 35B and 24F. Resistance rose sharply, with cefotaxime (12%\u219263%), erythromycin (\u223c30%\u219283%), and meropenem (5%\u219225%) showing major increases, particularly among children\u00a0\u22645 years. Among 127 invasive pneumococcal isolates from children\u00a0\u22645 years, 31.4% showed discordance between phenotypic and whole-genome sequencing (WGS) serotyping, indicating that older phenotypic methods likely overestimated PCV coverage by \u223c10%\u201312%. 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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>India\u2019s 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 \u223c10%\u201312%, 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.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/jambio\/lxaf268","type":"journal-article","created":{"date-parts":[[2025,10,28]],"date-time":"2025-10-28T12:44:38Z","timestamp":1761655478000},"source":"Crossref","is-referenced-by-count":1,"title":["Genomic surveillance of\n                    <i>Streptococcus pneumoniae<\/i>\n                    in India: vaccine-driven serotype shifts, antimicrobial resistance, and emerging clonal lineages"],"prefix":"10.1093","volume":"136","author":[{"given":"Sangeetha","family":"Gopalakrishnan","sequence":"first","affiliation":[{"name":"School of Allied Health Sciences, Sathyabama Institute of Science and Technology Department of Medical Laboratory Technology, , Jeppiaar Nagar, Chennai, Tamil Nadu 600119, Chennai ,","place":["India"]},{"name":"Division of Laboratories, Biochemistry & Hematology Section, Central Leprosy Teaching and Research Institute , Chengalpattu 603001 ,","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Premkumar","family":"Jayapal","sequence":"additional","affiliation":[{"name":"School of Allied Health Sciences, Sathyabama Institute of Science and Technology Department of Medical Laboratory Technology, , Jeppiaar Nagar, Chennai, Tamil Nadu 600119, Chennai ,","place":["India"]},{"name":"School of Bio & Chemical Engineering, Sathyabama Institute of Science and Technology Department of Biomedical Engineering, , Chennai , Tamil Nadu 600119,","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James","family":"John","sequence":"additional","affiliation":[{"name":"School of Allied Health Sciences, Sathyabama Institute of Science and Technology Department of Medical Laboratory Technology, , Jeppiaar Nagar, Chennai, Tamil Nadu 600119, Chennai ,","place":["India"]},{"name":"School of Bio & Chemical Engineering, Sathyabama Institute of Science and Technology Department of Biomedical Engineering, , Chennai, Tamil Nadu 600119 ,","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,10,29]]},"reference":[{"key":"2025111802463623900_bib1","doi-asserted-by":"publisher","first-page":"103","DOI":"10.33073\/pjm-2023-023","article-title":"The molecular approaches and challenges of Streptococcus pneumoniae serotyping for epidemiological surveillance in the vaccine era","volume":"72","author":"Abdul\u00a0Rahman","year":"2023","journal-title":"Pol J Microbiol"},{"key":"2025111802463623900_bib2","doi-asserted-by":"publisher","first-page":"255","DOI":"10.4103\/jlp.jlp_173_21","article-title":"Serotype 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