{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T00:54:06Z","timestamp":1789088046913,"version":"build-2803163510"},"reference-count":15,"publisher":"American Society for Microbiology","issue":"2","license":[{"start":{"date-parts":[[2018,1,24]],"date-time":"2018-01-24T00:00:00Z","timestamp":1516752000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2018,2,1]],"date-time":"2018-02-01T00:00:00Z","timestamp":1517443200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["J Clin Microbiol"],"published-print":{"date-parts":[[2018,2]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>\n            Available methods for the diagnosis of coccidioidomycosis have significant shortcomings relative to accuracy and timeliness. We retrospectively and prospectively evaluated the diagnostic performance and reproducibility of a new cartridge-based real-time PCR assay for\n            <jats:named-content content-type=\"genus-species\">Coccidioides<\/jats:named-content>\n            spp. directly in lower respiratory secretions and compared them to today's \u201cgold standard,\u201d fungal culture. The GeneSTAT\n            <jats:named-content content-type=\"genus-species\">Coccidioides<\/jats:named-content>\n            assay uses a 106-bp target sequence repeated multiple times (\u223c60\u00d7) per genome, thus lowering the limit of detection (LOD) for extracted DNA to 10 genome equivalents\/ml. A total of 332 prospective and retrospective individual patient specimens were tested. The retrospective samples consisted of 100 bronchoalveolar lavage or bronchial wash (BAL\/BW) (51 positive and 49 negative by culture) specimens that had been collected previously and stored at \u221270\u00b0C. These samples were tested by the GeneSTAT\n            <jats:named-content content-type=\"genus-species\">Coccidioides<\/jats:named-content>\n            assay across three clinical test sites. The sensitivity was 100%, and the specificity ranged between 93.8% and 100%. There was minimal variance in the percent agreement across the three sites, 95.6% to 100%. Additionally, a total of 232 fresh (prospective) deidentified BAL\/BW specimens were tested across the three clinical sites, which included a number of specimens from Southern California to provide a diversity of isolates. Specimens were tested by fungal culture, with any isolates of\n            <jats:named-content content-type=\"genus-species\">Coccidioides<\/jats:named-content>\n            , except for one, being confirmed by molecular means (AccuProbe). The sensitivity of the GeneSTAT\n            <jats:named-content content-type=\"genus-species\">Coccidioides<\/jats:named-content>\n            assay across the three sites was 100% (4\/4) for positive fresh specimens, and the overall specificity of the assay was 99.6% (227\/228), ranging from 98.1% to 100%. In testing for cross-reactivity, the assay was 100% specific when screened against 47 different bacterial, viral, and fungal species.\n          <\/jats:p>","DOI":"10.1128\/jcm.01277-17","type":"journal-article","created":{"date-parts":[[2017,12,6]],"date-time":"2017-12-06T16:20:14Z","timestamp":1512577214000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":46,"title":["Multicenter Clinical Validation of a Cartridge-Based Real-Time PCR System for Detection of Coccidioides spp. in Lower Respiratory Specimens"],"prefix":"10.1128","volume":"56","author":[{"given":"Michael A.","family":"Saubolle","sequence":"first","affiliation":[{"name":"Laboratory Sciences of Arizona\/Sonora Quest Laboratories, Banner University Medical Center-Phoenix, University of Arizona, Phoenix, Arizona, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bette R.","family":"Wojack","sequence":"additional","affiliation":[{"name":"Laboratory Sciences of Arizona\/Sonora Quest Laboratories, Banner University Medical Center-Phoenix, University of Arizona, Phoenix, Arizona, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anne M.","family":"Wertheimer","sequence":"additional","affiliation":[{"name":"The BIO5 Institute and the Applied Biosciences Graduate Interdisciplinary Program, University of Arizona, Tucson, Arizona, USA"},{"name":"Division of Geriatrics General Internal Medicine and Palliative Medicine, University of Arizona, Tucson, Arizona, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Atehkeng Z.","family":"Fuayagem","sequence":"additional","affiliation":[{"name":"The BIO5 Institute and the Applied Biosciences Graduate Interdisciplinary Program, University of Arizona, Tucson, Arizona, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen","family":"Young","sequence":"additional","affiliation":[{"name":"TriCore Reference Laboratories, Albuquerque, New Mexico, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brian A.","family":"Koeneman","sequence":"additional","affiliation":[{"name":"Laboratory Sciences of Arizona\/Sonora Quest Laboratories, Tempe, Arizona, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_3_2_2","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciw360"},{"key":"e_1_3_3_3_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.02230-06"},{"key":"e_1_3_3_4_2","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/cis1028"},{"key":"e_1_3_3_5_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid1206.060028"},{"key":"e_1_3_3_6_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid1407.070832"},{"key":"e_1_3_3_7_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid1563.081007"},{"key":"e_1_3_3_8_2","unstructured":"Arizona Department of Health Services. 2007. Valley fever 2007 annual report. Arizona Department of Health Services Phoenix AZ. http:\/\/www.azdhs.gov\/documents\/preparedness\/epidemiology-disease-control\/valley-fever\/reports\/valley-fever-2007.pdf."},{"key":"e_1_3_3_9_2","first-page":"217","article-title":"Increase in reported coccidioidomycosis\u2014United States, 1998\u20132011","volume":"62","author":"Centers for Disease Control and Prevention","year":"2013","unstructured":"Centers for Disease Control and Prevention. 2013. Increase in reported coccidioidomycosis\u2014United States, 1998\u20132011. MMWR Morb Mortal Wkly Rep 62:217\u2013221.","journal-title":"MMWR Morb Mortal Wkly Rep"},{"key":"e_1_3_3_10_2","unstructured":"Arizona Department of Health Services. 2014. Valley fever 2014 annual report. Arizona Department of Health Services Phoenix AZ. http:\/\/www.azdhs.gov\/documents\/preparedness\/epidemiology-disease-control\/valley-fever\/reports\/valley-fever-2014.pdf."},{"key":"e_1_3_3_11_2","doi-asserted-by":"publisher","DOI":"10.1196\/annals.1406.049"},{"key":"e_1_3_3_12_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01776-06"},{"key":"e_1_3_3_13_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.02731-14"},{"key":"e_1_3_3_14_2","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciu681"},{"key":"e_1_3_3_15_2","unstructured":"Engelthaler D Driebe E Keim P. 5 July 2012. Method for detecting Coccidioides species. US patent application no. 61\/668 203."},{"key":"e_1_3_3_16_2","doi-asserted-by":"publisher","DOI":"10.1378\/chest.12-1312"}],"container-title":["Journal of Clinical Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JCM.01277-17","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JCM.01277-17","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,3,5]],"date-time":"2022-03-05T10:12:39Z","timestamp":1646475159000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/JCM.01277-17"}},"subtitle":[],"editor":[{"given":"David W.","family":"Warnock","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2018,2]]},"references-count":15,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2018,2]]}},"alternative-id":["10.1128\/JCM.01277-17"],"URL":"https:\/\/doi.org\/10.1128\/jcm.01277-17","relation":{},"ISSN":["0095-1137","1098-660X"],"issn-type":[{"value":"0095-1137","type":"print"},{"value":"1098-660X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,2]]},"assertion":[{"value":"2017-08-22","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2017-11-28","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2018-01-24","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e01277-17"}}