{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,19]],"date-time":"2026-02-19T02:07:14Z","timestamp":1771466834303,"version":"3.50.1"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2025,2,28]],"date-time":"2025-02-28T00:00:00Z","timestamp":1740700800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100005564","name":"Gilead","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100005564","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,2,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Bronchoalveolar lavage fluid (BALF) is the key sample type for diagnosing Pneumocystis jirovecii pneumonia, with quantitative PCR (qPCR) providing high sensitivity and specificity. However, sample processing varies considerably between laboratories, and optimal nucleic acid extraction method for BALF remains undetermined. This retrospective multicenter study, conducted in 12 centers as part of the fungal PCR initiative, assessed the efficacy of P. jirovecii detection by qPCR in different BALF fractions, including whole (WHO), pellet (PEL), and supernatant (SUP). Samples that were P. jirovecii-qPCR-positive during routine testing were divided into the three predefined fractions prior to nucleic acid extraction and qPCR, comparing detection rates and quantification cycle (Cq) values. Out of 113 P. jirovecii-qPCR-positive BALF samples, 339 qPCR measurements were analyzed. The PEL fraction demonstrated a similar detection rate to the WHO fraction, with positivity rates of 92.9% and 88.5%, respectively. The SUP fraction showed a lower positivity rate of 71.7%, dropping to 47% for high Cq values (Cq\u00a0&amp;gt;\u00a035). Quantitative analysis showed that the SUP fraction consistently yielded higher Cq values, trailing by 3.05 cycles compared to WHO, while PEL showed a smaller deviation (0.49 cycles), confirming its efficiency in retaining P. jirovecii genetic material for qPCR detection. The study concludes that the SUP fraction is suboptimal for P. jirovecii detection due to higher Cq values, suggesting lower fungal loads. The PEL and WHO fractions are comparable, suggesting that the PEL is a viable alternative, permitting the concentration of larger BALF volumes to levels that can be extracted across a range of platforms.<\/jats:p>","DOI":"10.1093\/mmy\/myaf023","type":"journal-article","created":{"date-parts":[[2025,3,7]],"date-time":"2025-03-07T18:10:31Z","timestamp":1741371031000},"source":"Crossref","is-referenced-by-count":4,"title":["Multicentric prospective evaluation of <i>Pneumocystis jirovecii<\/i> fungal load in bronchoalveolar lavage fluid fractions using qPCR"],"prefix":"10.1093","volume":"63","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7784-4434","authenticated-orcid":false,"suffix":"MD","given":"Th\u00e9o","family":"Ghelfenstein-Ferreira","sequence":"first","affiliation":[{"name":"Institut Pasteur, Universit\u00e9 Paris Cit\u00e9, National Reference Center for Invasive Mycoses and Antifungals, Translational Mycology research group, Mycology Department , F-75015 Paris ,","place":["France"]},{"name":"Laboratoire de parasitologie-mycologie, AP-HP, H\u00f4pital Saint-Louis , F-75010 Paris ,","place":["France"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"suffix":"PhD","given":"Lize","family":"Cuypers","sequence":"additional","affiliation":[{"name":"National reference centre for mycosis, Department of Laboratory Medicine, University Hospitals Leuven , 3000 Leuven ,","place":["Belgium"]},{"name":"Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical Microbiology , KU Leuven 3000 Leuven ,","place":["Belgium"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ana\u00efs","family":"Pinto","sequence":"additional","affiliation":[{"name":"Laboratoire de parasitologie-mycologie, AP-HP, H\u00f4pital Saint-Louis , F-75010 Paris ,","place":["France"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7945-9890","authenticated-orcid":false,"suffix":"MD, PhD","given":"Guillaume","family":"Desoubeaux","sequence":"additional","affiliation":[{"name":"Service de parasitologie-mycologie-m\u00e9decine tropicale, h\u00f4pital Bretonneau, F-37044 Tours, France; Centre d\u2019\u00e9tude des pathologies respiratoires (CEPR) \u2013 Inserm UMR1100, facult\u00e9 de m\u00e9decine , F-37032 Tours ,","place":["France"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"suffix":"PhD","given":"Vicente","family":"Friaza","sequence":"additional","affiliation":[{"name":"Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Roc\u00edo\/Consejo Superior de Investigaciones Cient\u00edficas\/Universidad de Sevilla , 41013 Seville ,","place":["Spain"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"suffix":"PhD","given":"Stefan","family":"Fuchs","sequence":"additional","affiliation":[{"name":"Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck , 6020 Innsbruck 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Universit\u00e9 de Picardie Jules Verne , F-80000 Amiens ,","place":["France"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1166-2563","authenticated-orcid":false,"suffix":"MD, PhD","given":"Sean","family":"Zhang","sequence":"additional","affiliation":[{"name":"Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine , Baltimore MD 21287-7093 ,","place":["USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1641-7367","authenticated-orcid":false,"suffix":"MD, PhD","given":"Mario","family":"Cruciani","sequence":"additional","affiliation":[{"name":"Infectious Diseases Unit, San Bonifacio Hospital , 37129 Verona ,","place":["Italy"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"suffix":"MD, PhD","given":"Rosemary","family":"Barnes","sequence":"additional","affiliation":[{"name":"Infection, Immunity and Biochemistry, School of Medicine, 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