{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,2]],"date-time":"2026-08-02T23:31:12Z","timestamp":1785713472294,"version":"3.56.0"},"reference-count":40,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2026,1,8]],"date-time":"2026-01-08T00:00:00Z","timestamp":1767830400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["22K15924"],"award-info":[{"award-number":["22K15924"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009619","name":"Japan Agency for Medical Research and Development","doi-asserted-by":"crossref","award":["JP223fa627004"],"award-info":[{"award-number":["JP223fa627004"]}],"id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Vaccines"],"abstract":"<jats:p>Background:\u00a0Streptococcus pneumoniae is a leading cause of child mortality in Nepal despite the introduction of the 10-valent pneumococcal conjugate vaccine (PCV10). Vaccine effectiveness is threatened by the emergence of non-vaccine serotypes (NVTs) and the multiple serotypes carriage which often fail to be detected by traditional methods. We aimed to study changes in serotype distribution before and after PCV10 immunization among infants, including serotype dominance in Nepalese infants in the post-vaccine era. Methods: We enrolled infants in a longitudinal cohort study (2020\u20132022) conducted in Bhaktapur, Nepal. Nasopharyngeal swabs were collected before PCV10 dose 1 (6 weeks) and at 9 and 12 months post-immunization. We used a sensitive nanofluidic qPCR platform to detect multiple serotypes and establish their hierarchy by quantifying the bacterial load of each strain. Inverse Probability Weighting (IPW) adjusted risk factor analysis was used to account for loss to follow-up. Results: PCV10 successfully reduced vaccine-type (VT) carriage, declining sharply from 32.8% at 6 weeks to 4.8% at 12 months. VTs were pushed from being the dominant strain to occupying subdominant roles in co-colonization. Conversely, NVTs rapidly filled the vacated niche, showing a significant increase in their dominant status (p &lt; 0.001). The most common replacing NVTs that rose to dominance were 35B, 19A, 6C\/6D, and 15B\/15C. Significant risk factors for carriage included older infancy (aOR 3.4, 95%CI: 2.6\u20134.5 at 9 months), a household kitchen in the living area (aOR 1.4, 95%CI: 1.0\u20131.9), and winter (aOR 1.7, 95%CI: 1.5\u20132.7) and pre-monsoon seasons (aOR 2.0, 95%CI: 1.5\u20132.8). Conclusions: While PCV10 reduced overall VT circulation, the persistence of VTs in subdominant niches creates a continuous reservoir for potential re-emergence and antibiotic resistance. This clear hierarchical shift in dominance towards NVTs underscores the urgent need for a public health strategy that includes the adoption of a higher-valent PCV to provide broader protection, and interventions targeting environmental risk factors are essential to sustain long-term reductions in pneumococcal colonization.<\/jats:p>","DOI":"10.3390\/vaccines14010073","type":"journal-article","created":{"date-parts":[[2026,1,8]],"date-time":"2026-01-08T14:32:38Z","timestamp":1767882758000},"page":"73","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Non-Vaccine Serotype Replacement and Subdominant Persistence of Vaccine Types in Nepalese Infants Following PCV10 Introduction"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1554-9894","authenticated-orcid":false,"given":"Fleurette Mbuyakala","family":"Domai","sequence":"first","affiliation":[{"name":"Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan"},{"name":"Program for Nurturing Global Leaders in Tropical and Emerging Communicable Diseases, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8523, Japan"},{"name":"National Dracunculosis Eradication Program, Kinshasa 01204, Democratic Republic of the Congo"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dhruba","family":"Shrestha","sequence":"additional","affiliation":[{"name":"Siddhi Memorial Hospital (For Women and Children), Bhaktapur 44800, Nepal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Raj Kumar","family":"Shrestha","sequence":"additional","affiliation":[{"name":"Siddhi Memorial Hospital (For Women and Children), Bhaktapur 44800, Nepal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Monika","family":"Thimi","sequence":"additional","affiliation":[{"name":"Siddhi Memorial Hospital (For Women and Children), Bhaktapur 44800, Nepal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Desmond Opoku","family":"Ntiamoah","sequence":"additional","affiliation":[{"name":"School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki 852-8523, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yumiko","family":"Hayashi","sequence":"additional","affiliation":[{"name":"School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki 852-8523, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9238-3202","authenticated-orcid":false,"given":"Chris","family":"Smith","sequence":"additional","affiliation":[{"name":"School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki 852-8523, Japan"},{"name":"Department of Clinical Research, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6592-8035","authenticated-orcid":false,"given":"Yoshinao","family":"Kubo","sequence":"additional","affiliation":[{"name":"Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0997-0850","authenticated-orcid":false,"given":"Shunmay","family":"Yeung","sequence":"additional","affiliation":[{"name":"School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki 852-8523, Japan"},{"name":"Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Motoi","family":"Suzuki","sequence":"additional","affiliation":[{"name":"Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Konosuke","family":"Morimoto","sequence":"additional","affiliation":[{"name":"Department of Respiratory Infections, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Koya","family":"Ariyoshi","sequence":"additional","affiliation":[{"name":"Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan"},{"name":"School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki 852-8523, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5279-2044","authenticated-orcid":false,"given":"Bhim Gopal","family":"Dhoubhadel","sequence":"additional","affiliation":[{"name":"Siddhi Memorial Hospital (For Women and Children), Bhaktapur 44800, Nepal"},{"name":"Department of Respiratory Infections, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,1,8]]},"reference":[{"key":"ref_1","unstructured":"(2025, April 14). 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