{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T06:13:39Z","timestamp":1790144019787,"version":"4.0.1"},"reference-count":24,"publisher":"American Society for Microbiology","issue":"3","license":[{"start":{"date-parts":[[2016,3,1]],"date-time":"2016-03-01T00:00:00Z","timestamp":1456790400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"name":"The Centre Hospitalier Universitaire de Nimes"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["J Clin Microbiol"],"published-print":{"date-parts":[[2016,3]]},"abstract":"<jats:title>ABSTRACT<\/jats:title><jats:p>Pneumonia due to<jats:named-content content-type=\"genus-species\">Pneumocystis jirovecii<\/jats:named-content>(PCP) is a frequent infection among HIV-positive or other immunocompromised patients. In the past several years, PCR on pulmonary samples has become an essential element for the laboratory diagnosis of PCP. Nevertheless, very few comparative studies of available PCR assays have been published. In this work, we evaluated the concordance between four real-time PCR assays, including three commercial kits, AmpliSens, MycAssay, and Bio-Evolution PCR, and an in-house PCR (J. Fillaux et al. 2008, J Microbiol Methods 75:258\u2013261, doi:<jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"doi\" xlink:href=\"http:\/\/dx.doi.org\/10.1016\/j.mimet.2008.06.009\">http:\/\/dx.doi.org\/10.1016\/j.mimet.2008.06.009<\/jats:ext-link>), on 148 pulmonary samples. The results showed concordance rates ranging from 81.6% to 96.6% (kappa, 0.64 to 0.93). Concordance was excellent between three assays: the in-house assay, AmpliSens, and the MycAssay PCR (kappa, &gt;0.8). The performances of these PCR assays were also evaluated according to the classification of the probability of PCP (proven, probable, possible, or no final diagnosis of PCP) based on clinical and radiological signs as well as on the direct examination of bronchoalveolar lavage samples. In the proven PCP category,<jats:named-content content-type=\"genus-species\">Pneumocystis jirovecii<\/jats:named-content>DNA was detected with all four assays. In the probable PCP category, the in-house PCR, AmpliSens, and the MycAssay PCR were positive for all samples, while the Bio-Evolution PCR failed to detect<jats:named-content content-type=\"genus-species\">Pneumocystis jirovecii<\/jats:named-content>DNA in two samples. In the possible PCP category, the percentage of positive samples according to PCR varied from 54.5% to 86.4%. Detection of colonized patients is discussed. Finally, among the four evaluated PCR assays, one was not suitable for colonization detection but showed good performance in the proven and probable PCP groups. For the three other assays, performances were excellent and allowed detection of a very low fungal burden.<\/jats:p>","DOI":"10.1128\/jcm.02876-15","type":"journal-article","created":{"date-parts":[[2015,12,31]],"date-time":"2015-12-31T03:03:08Z","timestamp":1451530988000},"page":"625-630","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":45,"title":["Performances of Four Real-Time PCR Assays for Diagnosis of Pneumocystis jirovecii Pneumonia"],"prefix":"10.1128","volume":"54","author":[{"given":"Mil\u00e8ne","family":"Sasso","sequence":"first","affiliation":[{"name":"Laboratoire de Parasitologie-Mycologie, CHU de N\u00eemes et Facult\u00e9 de M\u00e9decine de Montpellier-N\u00eemes, N\u00eemes, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elsa","family":"Chastang-Dumas","sequence":"additional","affiliation":[{"name":"Laboratoire de Parasitologie-Mycologie, CHU de N\u00eemes et Facult\u00e9 de M\u00e9decine de Montpellier-N\u00eemes, N\u00eemes, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sophie","family":"Bastide","sequence":"additional","affiliation":[{"name":"BESPIM (Biostatistique, Epid\u00e9miologie Clinique, Sant\u00e9 Publique et Information M\u00e9dicale), CHU de N\u00eemes, N\u00eemes, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sandrine","family":"Alonso","sequence":"additional","affiliation":[{"name":"BESPIM (Biostatistique, Epid\u00e9miologie Clinique, Sant\u00e9 Publique et Information M\u00e9dicale), CHU de N\u00eemes, N\u00eemes, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Catherine","family":"Lechiche","sequence":"additional","affiliation":[{"name":"Service de Maladies Infectieuses et Tropicales, CHU de N\u00eemes, N\u00eemes, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nathalie","family":"Bourgeois","sequence":"additional","affiliation":[{"name":"D\u00e9partement de Parasitologie-Mycologie, CHU de Montpellier, Montpellier, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laurence","family":"Lachaud","sequence":"additional","affiliation":[{"name":"Laboratoire de Parasitologie-Mycologie, CHU de N\u00eemes et Facult\u00e9 de M\u00e9decine de Montpellier-N\u00eemes, N\u00eemes, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_3_2_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.idc.2009.10.010"},{"key":"e_1_3_3_3_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid2009.131668"},{"key":"e_1_3_3_4_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid1903.121151"},{"key":"e_1_3_3_5_2","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.00013-12"},{"key":"e_1_3_3_6_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.02390-10"},{"key":"e_1_3_3_7_2","doi-asserted-by":"publisher","DOI":"10.1183\/09031936.00095811"},{"key":"e_1_3_3_8_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.diagmicrobio.2012.03.001"},{"key":"e_1_3_3_9_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.05880-11"},{"key":"e_1_3_3_10_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.diagmicrobio.2015.03.006"},{"key":"e_1_3_3_11_2","first-page":"75","article-title":"Detection of Pneumocystis jirovecii and Aspergillus spp. DNA in bronchoalveolar lavage fluids by commercial real-time PCR assays: comparison with conventional diagnostic tests","volume":"38","author":"Orsi CF","year":"2015","unstructured":"Orsi CF, Bettua C, Pini P, Venturelli C, La Regina A, Morace G, Luppi M, Forghieri F, Bigliardi S, Luppi F, Codeluppi M, Girardis M, Blasi E. 2015. Detection of Pneumocystis jirovecii and Aspergillus spp. DNA in bronchoalveolar lavage fluids by commercial real-time PCR assays: comparison with conventional diagnostic tests. New Microbiol 38:75\u201384.","journal-title":"New Microbiol"},{"key":"e_1_3_3_12_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.mimet.2008.06.009"},{"key":"e_1_3_3_13_2","unstructured":"Lachaud L Sasso M Dumas-Chastang E Boutet-Dubois A Bourgeois A Lechiche C. 2013. Abstr 6th Trends in Medical Mycology abstr P061."},{"key":"e_1_3_3_14_2","doi-asserted-by":"publisher","DOI":"10.2307\/2529310"},{"key":"e_1_3_3_15_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0073099"},{"key":"e_1_3_3_16_2","doi-asserted-by":"crossref","first-page":"1965","DOI":"10.3760\/cma.j.issn.0366-6999.20122506","article-title":"Use of real-time polymerase chain reaction for the diagnosis of Pneumocystis pneumonia in immunocompromised patients: a meta-analysis","volume":"126","author":"Summah H","year":"2013","unstructured":"Summah H, Zhu Y-G, Falagas ME, Vouloumanou EK, Qu J-M. 2013. Use of real-time polymerase chain reaction for the diagnosis of Pneumocystis pneumonia in immunocompromised patients: a meta-analysis. Chin Med J (Engl) 126:1965\u20131973.","journal-title":"Chin Med J (Engl)"},{"key":"e_1_3_3_17_2","doi-asserted-by":"publisher","DOI":"10.1007\/s10096-013-1960-3"},{"key":"e_1_3_3_18_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1469-0691.2010.03400.x"},{"key":"e_1_3_3_19_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01480-14"},{"key":"e_1_3_3_20_2","doi-asserted-by":"publisher","DOI":"10.1086\/523814"},{"key":"e_1_3_3_21_2","doi-asserted-by":"publisher","DOI":"10.1051\/parasite\/2011182121"},{"key":"e_1_3_3_22_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01554-13"},{"key":"e_1_3_3_23_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1469-0691.2011.03605.x"},{"key":"e_1_3_3_24_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1440-1843.2008.01457.x"},{"key":"e_1_3_3_25_2","doi-asserted-by":"publisher","DOI":"10.1099\/jmm.0.45528-0"}],"container-title":["Journal of Clinical Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JCM.02876-15","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JCM.02876-15","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,5,31]],"date-time":"2025-05-31T23:55:58Z","timestamp":1748735758000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/JCM.02876-15"}},"subtitle":[],"editor":[{"given":"D. W.","family":"Warnock","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2016,3]]},"references-count":24,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2016,3]]}},"alternative-id":["10.1128\/JCM.02876-15"],"URL":"https:\/\/doi.org\/10.1128\/jcm.02876-15","relation":{},"ISSN":["0095-1137","1098-660X"],"issn-type":[{"value":"0095-1137","type":"print"},{"value":"1098-660X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,3]]},"assertion":[{"value":"2015-10-27","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2015-12-15","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2016-02-25","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}