{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T06:09:52Z","timestamp":1775628592173,"version":"3.50.1"},"reference-count":42,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T00:00:00Z","timestamp":1775606400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:sec>\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>Determining the etiology of community-acquired pneumonia (CAP) is essential for targeted treatment and optimal care. Reliable results require selection of the appropriate sampling site.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      Paired nasopharyngeal (NP) and oropharyngeal (OP) swabs were collected from 484 patients with CAP between September 2016 and September 2018. The samples were analyzed by PCRs for\n                      <jats:italic>Streptococcus pneumoniae<\/jats:italic>\n                      ,\n                      <jats:italic>Haemophilus influenzae<\/jats:italic>\n                      , 6 atypical bacterial species, and 14 viral agents.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      The most common pathogen was\n                      <jats:italic>S. pneumoniae<\/jats:italic>\n                      (24%), followed by\n                      <jats:italic>H. influenzae<\/jats:italic>\n                      (23%). Both were more frequently detected in the oropharynx, with 29% and 40% respectively, identified only in OP swabs. Respiratory viruses were found in 32% of the patients; of these, 65% were present in both NP and OP samples. Notably, 21% were detected only in NP samples, and 15% only in OP samples.\n                      <jats:italic>Mycoplasma pneumoniae<\/jats:italic>\n                      was identified in 6% of all patients, predominantly in OP samples (89%) compared with NP samples (70%). Cq-values were lower in NP swabs for all pathogens except\n                      <jats:italic>M. pneumoniae<\/jats:italic>\n                      , suggesting a higher microbial load in the nasopharynx.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Discussion<\/jats:title>\n                    <jats:p>\n                      This study highlights the importance of sampling site selection in the diagnosis and management of CAP. Nasopharyngeal sampling was more effective for detecting respiratory viruses, whereas OP samples yielded more cases of\n                      <jats:italic>S. pneumoniae<\/jats:italic>\n                      ,\n                      <jats:italic>H. influenzae<\/jats:italic>\n                      and\n                      <jats:italic>M. pneumoniae<\/jats:italic>\n                      . To maximize the diagnostic yield, a combined NP\/OP-sampling strategy can thus be recommended.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fmicb.2026.1774447","type":"journal-article","created":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T05:32:51Z","timestamp":1775626371000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Combined nasopharyngeal and oropharyngeal sampling improves pathogen detection in community-acquired pneumonia"],"prefix":"10.3389","volume":"17","author":[{"given":"Karin","family":"Hansen","sequence":"first","affiliation":[{"name":"Clinical Microbiology, Department of Translational Medicine, Faculty of Medicine, Lund University","place":["Malm\u00f6, Sweden"]},{"name":"Infectious Diseases, Department of Translational Medicine, Faculty of Medicine, Lund University","place":["Malm\u00f6, Sweden"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lisa","family":"Wasserstrom","sequence":"additional","affiliation":[{"name":"Clinical Microbiology, Department of Translational Medicine, Faculty of Medicine, Lund University","place":["Malm\u00f6, Sweden"]},{"name":"Department of Clinical Microbiology, Infection Control and Prevention, Sk\u00e5ne University Hospital","place":["Lund, Sweden"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jonas","family":"Ahl","sequence":"additional","affiliation":[{"name":"Clinical Microbiology, Department of Translational Medicine, Faculty of Medicine, Lund University","place":["Malm\u00f6, Sweden"]},{"name":"Infectious Diseases, Department of Translational Medicine, Faculty of Medicine, Lund University","place":["Malm\u00f6, Sweden"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yu-Ching","family":"Su","sequence":"additional","affiliation":[{"name":"Clinical Microbiology, Department of Translational Medicine, Faculty of Medicine, Lund University","place":["Malm\u00f6, Sweden"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anna C.","family":"Nilsson","sequence":"additional","affiliation":[{"name":"Infectious Diseases, Department of Translational Medicine, Faculty of Medicine, Lund University","place":["Malm\u00f6, Sweden"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kristian","family":"Riesbeck","sequence":"additional","affiliation":[{"name":"Clinical Microbiology, Department of Translational Medicine, Faculty of Medicine, Lund University","place":["Malm\u00f6, Sweden"]},{"name":"Department of Clinical Microbiology, Infection Control and Prevention, Sk\u00e5ne University Hospital","place":["Lund, Sweden"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2026,4,8]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"1191","DOI":"10.1016\/S1473-3099(18)30310-4","article-title":"Estimates of the global, regional, and national morbidity, mortality, and aetiologies of lower respiratory infections in 195 countries, 1990-2016: A systematic analysis for the Global Burden of Disease Study 2016.","volume":"18","year":"2018","journal-title":"Lancet Infect. 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