{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,22]],"date-time":"2026-10-22T21:45:04Z","timestamp":1792705504323,"version":"4.5.0"},"reference-count":60,"publisher":"Microbiology Society","issue":"2","license":[{"start":{"date-parts":[[2024,2,5]],"date-time":"2024-02-05T00:00:00Z","timestamp":1707091200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100004319","name":"Pfizer","doi-asserted-by":"crossref","award":["57039923"],"award-info":[{"award-number":["57039923"]}],"id":[{"id":"10.13039\/100004319","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,2,5]]},"abstract":"<jats:p>\n                    <jats:italic>Streptococcus pneumoniae<\/jats:italic>\n                    is a major cause of invasive disease of young children in low- and middle-income countries. In southern India, pneumococcal conjugate vaccines (PCVs) that can prevent invasive pneumococcal disease began to be used more frequently after 2015. To characterize pneumococcal evolution during the early time period of PCV uptake in southern India, genomes were sequenced and selected characteristics were determined for 402 invasive isolates collected from children &lt;5\u2009years of age during routine surveillance from 1991 to 2020. Overall, the prevalence and diversity of vaccine type (VT) and non-vaccine type (NVT) isolates did not significantly change post-uptake of PCV. Individually, serotype 1 and global pneumococcal sequence cluster (GPSC or strain lineage) 2 significantly decreased, whereas serotypes 6B, 9V and 19A and GPSCs 1, 6, 10 and 23 significantly increased in proportion post-uptake of PCV. Resistance determinants to penicillin, erythromycin, co-trimoxazole, fluoroquinolones and tetracycline, and multidrug resistance significantly increased in proportion post-uptake of PCV and especially among VT isolates. Co-trimoxazole resistance determinants were common pre- and post-uptake of PCV (85 and 93\u200a%, respectively) and experienced the highest rates of recombination in the genome. Accessory gene frequencies were seen to be changing by small amounts across the frequency spectrum specifically among VT isolates, with the largest changes linked to antimicrobial resistance determinants. In summary, these results indicate that as of 2020 this pneumococcal population was not yet approaching a PCV-induced equilibrium and they highlight changes related to antimicrobial resistance. Augmenting PCV coverage and prudent use of antimicrobials are needed to counter invasive pneumococcal disease in this region.\n                  <\/jats:p>","DOI":"10.1099\/mgen.0.001191","type":"journal-article","created":{"date-parts":[[2024,2,5]],"date-time":"2024-02-05T10:17:14Z","timestamp":1707128234000},"source":"Crossref","is-referenced-by-count":9,"title":["Pneumococcal population genomics changes during the early time period of conjugate vaccine uptake in southern India"],"prefix":"10.1099","volume":"10","author":[{"given":"Iftekhar M.","family":"Rafiqullah","sequence":"first","affiliation":[{"name":"Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rosemol","family":"Varghese","sequence":"additional","affiliation":[{"name":"Department of Clinical Microbiology, Christian Medical College and Hospital, Vellore, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"K. Taylor","family":"Hellmann","sequence":"additional","affiliation":[{"name":"Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aravind","family":"Velmurugan","sequence":"additional","affiliation":[{"name":"Department of Clinical Microbiology, Christian Medical College and Hospital, Vellore, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ayyanraj","family":"Neeravi","sequence":"additional","affiliation":[{"name":"Department of Clinical Microbiology, Christian Medical College and Hospital, Vellore, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jones Lionel","family":"Kumar Daniel","sequence":"additional","affiliation":[{"name":"Department of Clinical Microbiology, Christian Medical College and Hospital, Vellore, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jorge E.","family":"Vidal","sequence":"additional","affiliation":[{"name":"Center for Immunology and Microbial Research, University of Mississippi Medical Center, Jackson, MS, USA"},{"name":"Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rajeev Z.","family":"Kompithra","sequence":"additional","affiliation":[{"name":"Department of Child Health, Christian Medical College and Hospital, Vellore, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Valsan P.","family":"Verghese","sequence":"additional","affiliation":[{"name":"Department of Child Health, Christian Medical College and Hospital, Vellore, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Balaji","family":"Veeraraghavan","sequence":"additional","affiliation":[{"name":"Department of Clinical Microbiology, Christian Medical College and Hospital, Vellore, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"D. Ashley","family":"Robinson","sequence":"additional","affiliation":[{"name":"Center for Immunology and Microbial Research, University of Mississippi Medical Center, Jackson, MS, USA"},{"name":"Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"345","reference":[{"key":"R1","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(17)30396-1"},{"key":"R2","doi-asserted-by":"publisher","DOI":"10.1016\/S2214-109X(18)30247-X"},{"key":"R3","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0129191"},{"key":"R4","volume-title":"National Operational Guidelines for PCV Introduction","year":"2021"},{"key":"R5","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pmed.1001517"},{"key":"R6","doi-asserted-by":"publisher","DOI":"10.1086\/648593"},{"key":"R7","doi-asserted-by":"publisher","DOI":"10.1086\/521626"},{"key":"R8","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pmed.1001017"},{"key":"R9","doi-asserted-by":"publisher","DOI":"10.1086\/521833"},{"key":"R10","doi-asserted-by":"publisher","DOI":"10.3201\/eid2306.170071"},{"key":"R11","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(19)30297-X"},{"key":"R12","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa051642"},{"key":"R13","doi-asserted-by":"publisher","DOI":"10.1086\/650496"},{"key":"R14","doi-asserted-by":"publisher","DOI":"10.1038\/s41559-017-0337-x"},{"key":"R15","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1006966"},{"key":"R16","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1005034"},{"key":"R17","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-08990-z"},{"key":"R18","doi-asserted-by":"publisher","DOI":"10.3855\/jidc.12166"},{"key":"R19","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-17327-w"},{"key":"R20","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-020-75988-5"},{"key":"R21","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000645"},{"key":"R22","doi-asserted-by":"publisher","DOI":"10.1097\/INF.0b013e318199f2a1"},{"key":"R23","article-title":"SourceForge [Internet]","year":"2022"},{"key":"R24","doi-asserted-by":"publisher","DOI":"10.1002\/cpbi.102"},{"key":"R25","doi-asserted-by":"publisher","DOI":"10.1101\/gr.186072.114"},{"key":"R26","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000186"},{"key":"R27","doi-asserted-by":"publisher","DOI":"10.1101\/gr.241455.118"},{"key":"R28","article-title":"tseemann\/mlst [Internet]","author":"Seemann","year":"2021"},{"key":"R29","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-017-4017-7"},{"key":"R30","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp324"},{"key":"R31","doi-asserted-by":"publisher","DOI":"10.1002\/0471250953.bi1110s43"},{"key":"R32","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.02016-17"},{"key":"R33","doi-asserted-by":"publisher","DOI":"10.1093\/sysbio\/syq010"},{"key":"R34","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evu263"},{"key":"R35","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1004041"},{"key":"R36","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq033"},{"key":"R37","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu153"},{"key":"R38","article-title":"Prodigal [Internet]","author":"Hyatt","year":"2023"},{"key":"R39","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv421"},{"key":"R40","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.39.11.4190-4192.2001"},{"key":"R41","article-title":"R: The R Project for Statistical Computing [Internet]"},{"key":"R42","doi-asserted-by":"publisher","DOI":"10.1111\/j.1755-0998.2012.03174.x"},{"key":"R43","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-294x.2008.03887.x"},{"key":"R44","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkt384"},{"key":"R45","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2958.2011.07722.x"},{"key":"R46","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.3000878"},{"key":"R47","article-title":"India | ViewHub [Internet]"},{"key":"R48","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-38277-z"},{"key":"R49","doi-asserted-by":"publisher","DOI":"10.4103\/ijmm.IJMM_19_348"},{"key":"R50","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(18)30660-1"},{"key":"R51","doi-asserted-by":"publisher","DOI":"10.1542\/peds.2008-3099"},{"key":"R52","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000746"},{"key":"R53","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pmed.1000081"},{"key":"R54","doi-asserted-by":"publisher","DOI":"10.1016\/j.tim.2022.06.001"},{"key":"R55","doi-asserted-by":"publisher","DOI":"10.1016\/S2666-5247(22)00066-0"},{"key":"R56","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijid.2018.12.017"},{"key":"R57","doi-asserted-by":"publisher","DOI":"10.1038\/ng.2895"},{"key":"R58","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evu120"},{"key":"R59","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.aaz6137"},{"key":"R60","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.45.3.805-809.2001"}],"container-title":["Microbial Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.001191?crawler=true&mimetype=application\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,5]],"date-time":"2024-02-05T10:17:18Z","timestamp":1707128238000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.001191"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,2,5]]},"references-count":60,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2024,2,5]]}},"URL":"https:\/\/doi.org\/10.1099\/mgen.0.001191","relation":{},"ISSN":["2057-5858"],"issn-type":[{"value":"2057-5858","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,2,5]]}}}