{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T12:09:55Z","timestamp":1780315795107,"version":"3.54.1"},"reference-count":40,"publisher":"Wiley","issue":"4","license":[{"start":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T00:00:00Z","timestamp":1774915200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"},{"start":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T00:00:00Z","timestamp":1774915200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Pediatric Pulmonology"],"published-print":{"date-parts":[[2026,4]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>Fungal pathogens are frequently detected in the cystic fibrosis (CF) airways; however, limitations exist with culture\u2010based detection methods. Here, we apply a novel next generation sequencing (NGS) technique to identify fungal taxa in airway samples from CF and non\u2010CF disease controls (DC), comparing the results to traditional culture.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>Bronchoalveolar lavage fluid (BALF) and oropharyngeal (OP) swabs were collected concurrently from children; expectorated sputum (ES) was collected from adults with CF. Total fungal load (TFL) was quantified via quantitative polymerase chain reaction (qPCR). Fungal communities were determined using NGS (V6\/V8) and assessed for relative abundance, diversity, and richness. Wilcoxon rank\u2010sum tests compared TFL and diversity measures.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Seventy\u2010six samples (23 paired BALF\u2010OP swabs, 30 ES samples) from 52 individuals (69% CF) were collected as part of two\u00a0clinical research studies. Sequencing was successful in 90% of samples, including 78% of OP swabs, and identified more diverse fungal communities than culture. Predominant taxa included\n                      <jats:italic>Agaricomycetes<\/jats:italic>\n                      ,\n                      <jats:italic>Aspergillus<\/jats:italic>\n                      ,\n                      <jats:italic>Candida\u2010Lodderomyces\u2010<\/jats:italic>\n                      clade, and\n                      <jats:italic>Cladosporium<\/jats:italic>\n                      .\n                      <jats:italic>Aspergillus<\/jats:italic>\n                      was detected in all sequenced samples. Fungal richness and diversity varied by sample type with no notable difference between BALF and ES samples by culture result. Fungal community concordance, as assessed by beta diversity, between BALF\u2010OP swab specimen pairs was low, though richness and diversity were similar.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>NGS identified more distinct fungi in the airways of pwCF and OP swabs show potential for reliably detecting fungi in the airway, mitigating the need for ES. Future work will assess fungal\u2010bacterial interactions and associations with clinical outcomes.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1002\/ppul.71598","type":"journal-article","created":{"date-parts":[[2026,4,1]],"date-time":"2026-04-01T06:31:28Z","timestamp":1775025088000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Molecular Methods to Detect and Quantify Fungal Communities in Cystic Fibrosis Airway Specimens"],"prefix":"10.1002","volume":"61","author":[{"ORCID":"https:\/\/orcid.org\/0009-0009-9587-6681","authenticated-orcid":false,"given":"Matthew K.","family":"Fought","sequence":"first","affiliation":[{"name":"Division of Pulmonary and Sleep Medicine University of Washington and Seattle Children's Hospital Seattle Washington USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gina","family":"Hong","sequence":"additional","affiliation":[{"name":"Perelman School of Medicine at the University of Pennsylvania Philadelphia Pennsylvania USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexandra C.","family":"Quinn","sequence":"additional","affiliation":[{"name":"Division of Pulmonary and Sleep Medicine University of Washington and Seattle Children's Hospital Seattle Washington USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brandie D.","family":"Wagner","sequence":"additional","affiliation":[{"name":"Colorado School of Public Health University of Colorado Denver Aurora Colorado USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charles E.","family":"Robertson","sequence":"additional","affiliation":[{"name":"University of Colorado School of Medicine Aurora Colorado USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J. Kirk","family":"Harris","sequence":"additional","affiliation":[{"name":"University of Colorado School of Medicine Aurora Colorado USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Theresa A.","family":"Laguna","sequence":"additional","affiliation":[{"name":"Division of Pulmonary and Sleep Medicine University of Washington and Seattle Children's Hospital Seattle Washington 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