{"doi":"10.1016/j.jinf.2020.06.013","title":"Viral-bacterial (co-)occurrence in the upper airways and the risk of childhood pneumonia in resource-limited settings","abstract":"OBJECTIVE: To examine the association between bacterial-viral co-occurrence in the nasopharynx and the risk of community acquired pneumonia (CAP) in young children living in resource-limited settings. METHODS: A case-control study was conducted between January and December 2017 in Moshi, Tanzania. Children 2-59 months with CAP and healthy controls were enrolled. RSV and Influenza A/B were detected with a standardized polymerase chain reaction (PCR) method, and a simplified real-time quantitative PCR method, without sample pre-processing, was developed to detect bacterial pathogens in nasopharyngeal samples. RESULTS: A total of 109 CAP patients and 324 healthy controls were enrolled. Co-detection of H. influenzae and S. pneumoniae in nasopharyngeal swabs was linked with higher odds of CAP (aOR=3.2, 95% CI=1.1-9.5). The majority of the H. influenzae isolated in cases and controls (95.8%) were non-typeable. Of the viruses examined, respiratory syncytial virus (RSV) was most common (n = 31, 7.2%) in cases and controls. Children with RSV had 8.4 times higher odds to develop pneumonia than healthy children (aOR=8.4, 95%CI= 3.2 - 22.1). CONCLUSIONS: Co-occurence of H. influenzae and S. pneumoniae in the nasopharynx was strongly associated with CAP. The high prevalence of non-typeable H. influenzae might be a sign of replacement as a consequence of Haemophilus influenzae type b vaccination.","journal":"Journal of Infection","year":2020,"id":76397,"datarank":0.4636563680037475,"base_score":3.091042453358316,"endowment":3.091042453358316,"self_citation_contribution":0.4636563680037475,"citation_network_contribution":0.0,"self_endowment_contribution":0.4636563680037475,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":21,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9214,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":398194,"name":"Linda Minja","orcid":"0000-0002-3627-6733","position":1,"is_corresponding":false},{"id":398195,"name":"Christa E. van der Gaast‐de Jongh","orcid":"0000-0002-3287-6977","position":2,"is_corresponding":false},{"id":231831,"name":"Janette Rahamat‐Langendoen","orcid":"0000-0003-0120-7962","position":3,"is_corresponding":false},{"id":144807,"name":"Jeroen D. Langereis","orcid":"0000-0001-5317-3202","position":4,"is_corresponding":false},{"id":341832,"name":"Blandina T. Mmbaga","orcid":"0000-0002-5550-1916","position":5,"is_corresponding":false},{"id":65572,"name":"Marien I. de Jonge","orcid":"0000-0003-2812-5895","position":6,"is_corresponding":false},{"id":376443,"name":"James S. Ngocho","orcid":"0000-0001-6242-9863","position":0,"is_corresponding":true}],"reference_count":41,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-18T21:47:46.469293Z","pmid":"32533999","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":[]}