{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T12:38:14Z","timestamp":1791549494631,"version":"4.3.4"},"reference-count":17,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2025,4,22]],"date-time":"2025-04-22T00:00:00Z","timestamp":1745280000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pathogens"],"abstract":"<jats:p>Detection of viral RNA in nasopharyngeal (NP) samples by reverse transcription polymerase chain reaction (RT-PCR) is the standard diagnostic test for influenza or respiratory syncytial virus (RSV) in hospitalized patients with community-acquired pneumonia (CAP). This study compared the sensitivity of RT-PCR using NP swab, saliva, and sputum samples for the diagnosis of CAP due to influenza or RSV. A total of 60 patients were evaluated, of which 40 (67%) had influenza CAP, 19 (32%) had RSV CAP, and one patient (1%) had both RSV and influenza CAP. RT-PCR on NP swab, saliva, and sputum samples was performed using the Luminex ARIES platform. In patients with influenza CAP, the sensitivity was 34% for NP swabs, 68% for saliva, and 71% for sputum. In patients with RSV CAP, the sensitivity was 60% for NP swabs, 75% for saliva, and 85% for sputum. RT-PCR of nasopharyngeal swab samples was associated with a significant number of false negative results. A negative NP swab RT-PCR test should not be used to rule out CAP due to influenza or RSV. Saliva and sputum samples should be considered when performing a microbiological work-up in patients with suspected influenza or RSV CAP.<\/jats:p>","DOI":"10.3390\/pathogens14050400","type":"journal-article","created":{"date-parts":[[2025,4,22]],"date-time":"2025-04-22T02:00:53Z","timestamp":1745287253000},"page":"400","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Diagnosis of Community-Acquired Pneumonia Due to Influenza or Respiratory Syncytial Virus: Evaluation of RT-PCR Sensitivity in Nasopharyngeal, Saliva, and Sputum Samples"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7801-5374","authenticated-orcid":false,"given":"Julio","family":"Ramirez","sequence":"first","affiliation":[{"name":"Norton Infectious Diseases Institute, Norton Healthcare, Louisville, KY 40202, USA"},{"name":"Division of Infectious Diseases, University of Louisville, Louisville, KY 40202, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9112-2860","authenticated-orcid":false,"given":"Stephen","family":"Furmanek","sequence":"additional","affiliation":[{"name":"Norton Infectious Diseases Institute, Norton Healthcare, Louisville, KY 40202, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2284-6213","authenticated-orcid":false,"given":"Thomas","family":"Chandler","sequence":"additional","affiliation":[{"name":"Norton Infectious Diseases Institute, Norton Healthcare, Louisville, KY 40202, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4319-7694","authenticated-orcid":false,"given":"Ruth","family":"Carrico","sequence":"additional","affiliation":[{"name":"Norton Infectious Diseases Institute, Norton Healthcare, Louisville, KY 40202, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8459-0025","authenticated-orcid":false,"given":"Ashley","family":"Wilde","sequence":"additional","affiliation":[{"name":"Norton Infectious Diseases Institute, Norton Healthcare, Louisville, KY 40202, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-3871-3653","authenticated-orcid":false,"given":"Alan","family":"Junkins","sequence":"additional","affiliation":[{"name":"Norton Infectious Diseases Institute, Norton Healthcare, Louisville, KY 40202, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anupama","family":"Raghuram","sequence":"additional","affiliation":[{"name":"Norton Infectious Diseases Institute, Norton Healthcare, Louisville, KY 40202, USA"},{"name":"Division of Infectious Diseases, University of Louisville, Louisville, KY 40202, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,4,22]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1806","DOI":"10.1093\/cid\/cix647","article-title":"Adults Hospitalized with Pneumonia in the United States: Incidence, Epidemiology, and Mortality","volume":"65","author":"Ramirez","year":"2017","journal-title":"Clin. Infect. Dis."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"632","DOI":"10.1056\/NEJMcp2303286","article-title":"Community-acquired pneumonia","volume":"389","author":"File","year":"2023","journal-title":"N. Engl. J. Med."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1056\/NEJMoa1500245","article-title":"Community-acquired pneumonia requiring hospitalization among US adults","volume":"373","author":"Jain","year":"2015","journal-title":"N. Engl. J. Med."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1183\/16000617.0076-2015","article-title":"Viral infection in community-acquired pneumonia: A systematic review and meta-analysis","volume":"25","author":"Burk","year":"2016","journal-title":"Eur. Respir. Rev."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Kim, C., Ahmed, J.A., Eidex, R.B., Nyoka, R., Waiboci, L.W., Erdman, D., Tepo, A., Mahamud, A.S., Kabura, W., and Nguhi, M. (2011). Comparison of nasopharyngeal and oropharyngeal swabs for the diagnosis of eight respiratory viruses by real-time reverse transcription-PCR assays. PLoS ONE, 6.","DOI":"10.1371\/journal.pone.0021610"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"3439","DOI":"10.1128\/JCM.00886-09","article-title":"Identification of respiratory viruses in adults: Nasopharyngeal versus oropharyngeal sampling","volume":"47","author":"Lieberman","year":"2009","journal-title":"J. Clin. Microbiol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1016\/j.jiac.2020.09.027","article-title":"Comparative evaluation of nasopharyngeal swab and saliva specimens for the molecular detection of SARS-CoV-2 RNA in Japanese patients with COVID-19","volume":"27","author":"Sakanashi","year":"2021","journal-title":"J. Infect Chemother."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1016\/j.ehmc.2015.08.004","article-title":"Isolation precautions in the inpatient setting","volume":"5","author":"Gottenborg","year":"2015","journal-title":"Hosp. Med. Clin."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1593","DOI":"10.1007\/s40121-023-00805-1","article-title":"Diagnosis of Respiratory Syncytial Virus in Adults Substantially Increases When Adding Sputum, Saliva, and Serology Testing to Nasopharyngeal Swab RT-PCR","volume":"12","author":"Ramirez","year":"2023","journal-title":"Infect. Dis. Ther."},{"key":"ref_10","unstructured":"Federal Drug Administration (2025, April 09). 510(k) Substantial Equivalence Determination Decision Summary, Available online: https:\/\/www.accessdata.fda.gov\/cdrh_docs\/reviews\/K161220.pdf."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1016\/j.jcv.2017.08.018","article-title":"The Performance of Luminex ARIES Flu A\/B & RSV and Cepheid Xpert Flu\/RSV XC for the detection of influenza A, influenza B, and respiratory syncytial virus in prospective patient samples","volume":"95","author":"McMullen","year":"2017","journal-title":"J. Clin. Virol."},{"key":"ref_12","unstructured":"Luminex Corporation (2025, April 11). ARIES System Operation Manual, Revision E. Available online: https:\/\/us.diasorin.com\/sites\/default\/files\/products-documentation-tool\/89-00002-00-425.pdf."},{"key":"ref_13","unstructured":"R Core Team (2025). R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing. Available online: https:\/\/www.R-project.org\/."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"372","DOI":"10.1016\/j.cmi.2018.06.009","article-title":"Saliva as a diagnostic specimen for testing respiratory virus by a point-of-care molecular assay: A diagnostic validity study","volume":"25","author":"To","year":"2019","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"2122","DOI":"10.1002\/jmv.23937","article-title":"Comparison of sputum and nasopharyngeal swabs for detection of respiratory viruses","volume":"86","author":"Jeong","year":"2014","journal-title":"J. Med. Virol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"942.e1","DOI":"10.1016\/j.cmi.2022.12.024","article-title":"Agreement of respiratory viruses\u2019 detection between nasopharyngeal swab and bronchoalveolar lavage in adults admitted for pneumonia: A retrospective study","volume":"29","author":"Bouzid","year":"2023","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1387","DOI":"10.1016\/j.chest.2020.10.017","article-title":"Paired nasopharyngeal and deep lung testing for severe acute respiratory syndrome coronavirus-2 reveals a viral gradient in critically ill patients: A multicenter study","volume":"159","author":"Hamed","year":"2021","journal-title":"Chest"}],"container-title":["Pathogens"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-0817\/14\/5\/400\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T17:19:03Z","timestamp":1760030343000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-0817\/14\/5\/400"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,4,22]]},"references-count":17,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2025,5]]}},"alternative-id":["pathogens14050400"],"URL":"https:\/\/doi.org\/10.3390\/pathogens14050400","relation":{},"ISSN":["2076-0817"],"issn-type":[{"value":"2076-0817","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,4,22]]}}}