{"doi":"10.1371/journal.pone.0302400","title":"Serotype epidemiology and antibiotic resistance of pneumococcal isolates colonizing infants in Botswana (2016–2019)","abstract":"BACKGROUND: In 2012, Botswana introduced 13-valent pneumococcal conjugate vaccine (PCV-13) to its childhood immunization program in a 3+0 schedule, achieving coverage rates of above 90% by 2014. In other settings, PCV introduction has been followed by an increase in carriage or disease caused by non-vaccine serotypes, including some serotypes with a high prevalence of antibiotic resistance. METHODS: We characterized the serotype epidemiology and antibiotic resistance of pneumococcal isolates cultured from nasopharyngeal samples collected from infants (≤12 months) in southeastern Botswana between 2016 and 2019. Capsular serotyping was performed using the Quellung reaction. E-tests were used to determine minimum inhibitory concentrations for common antibiotics. RESULTS: We cultured 264 pneumococcal isolates from samples collected from 150 infants. At the time of sample collection, 81% of infants had received at least one dose of PCV-13 and 53% had completed the three-dose series. PCV-13 serotypes accounted for 27% of isolates, with the most prevalent vaccine serotypes being 19F (n = 20, 8%), 19A (n = 16, 6%), and 6A (n = 10, 4%). The most frequently identified non-vaccine serotypes were 23B (n = 29, 11%), 21 (n = 12, 5%), and 16F (n = 11, 4%). Only three (1%) pneumococcal isolates were resistant to amoxicillin; however, we observed an increasing prevalence of penicillin resistance using the meningitis breakpoint (2016: 41%, 2019: 71%; Cochran-Armitage test for trend, p = 0.0003) and non-susceptibility to trimethoprim-sulfamethoxazole (2016: 55%, 2019: 79%; p = 0.04). Three (1%) isolates were multi-drug resistant. CONCLUSIONS: PCV-13 serotypes accounted for a substantial proportion of isolates colonizing infants in Botswana during a four-year period starting four years after vaccine introduction. A low prevalence of amoxicillin resistance supports its continued use as the first-line agent for non-meningeal pneumococcal infections. The observed increase in penicillin resistance at the meningitis breakpoint and the low prevalence of resistance to ceftriaxone supports use of third-generation cephalosporins for empirical treatment of suspected bacterial meningitis.","journal":"PLoS ONE","year":2024,"id":464092,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":5,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9647,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":936744,"name":"Yazdani B. Shaik-Dasthagirisaheb","orcid":null,"position":1,"is_corresponding":false},{"id":1295133,"name":"Loc Truong","orcid":null,"position":2,"is_corresponding":false},{"id":420333,"name":"Sefelani Boiditswe","orcid":"0000-0003-0382-4243","position":3,"is_corresponding":false},{"id":420332,"name":"Sweta Patel","orcid":"0000-0001-7867-7706","position":4,"is_corresponding":false},{"id":1294732,"name":"Jodi Gilchrist","orcid":"0000-0002-2965-9007","position":5,"is_corresponding":false},{"id":1294733,"name":"Julia Maciejewski","orcid":"0009-0006-2838-081X","position":6,"is_corresponding":false},{"id":1295134,"name":"Kathy Luinstra","orcid":null,"position":7,"is_corresponding":false},{"id":671394,"name":"Marek Smieja","orcid":"0000-0003-1655-3761","position":8,"is_corresponding":false},{"id":416596,"name":"Andrew P. Steenhoff","orcid":"0000-0001-9002-8207","position":9,"is_corresponding":false},{"id":325730,"name":"Coleen K. Cunningham","orcid":"0000-0002-7725-3052","position":10,"is_corresponding":false},{"id":936282,"name":"Stephen I. Pelton","orcid":"0000-0003-4862-5344","position":11,"is_corresponding":false},{"id":322359,"name":"Matthew S. Kelly","orcid":"0000-0001-8819-2315","position":12,"is_corresponding":false},{"id":325723,"name":"Jillian H. Hurst","orcid":"0000-0001-5079-9920","position":0,"is_corresponding":true}],"reference_count":52,"raw_metadata":null,"created_at":"2026-07-19T02:04:37.468651Z","pmid":"38787847","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}