{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,12]],"date-time":"2025-12-12T13:26:23Z","timestamp":1765545983292},"reference-count":14,"publisher":"American Society for Microbiology","issue":"3","license":[{"start":{"date-parts":[[2015,3,1]],"date-time":"2015-03-01T00:00:00Z","timestamp":1425168000000},"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":[[2015,3]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>\n            Rapid real-time PCR (RT-PCR) can be performed in a community hospital setting to identify\n            <jats:named-content content-type=\"genus-species\">Coccidioides<\/jats:named-content>\n            species using the new Becton Dickinson molecular instrument BD Max. Following sample preparation, DNA extraction and PCR were performed on the BD Max using the BD Max extraction kit ExK-DNA-1 test strip and a master mix prepared by BioGX (Birmingham, AL). Sample preparation took 2 h, and testing on the BD Max took an additional 2 h. Method sensitivity and specificity were evaluated along with the limits of detection to confirm that this convenient method would provide medically useful information. Using serial dilutions, the lower limit of detection was determined to be 1 CFU\/\u03bcl. Testing with this method was validated using samples from various body sites, including bronchial alveolar lavage (BAL) fluid; sputum and lung tissue samples; and pleural and spinal fluids. Safety protocols were established, and specimen preparation processes were developed for the various types of specimens. The range for the cycle threshold (\n            <jats:italic>\n              C\n              <jats:sub>T<\/jats:sub>\n            <\/jats:italic>\n            ) indicating adequate fluorescent signal to signify a positive result was established along with the acceptable range for the internal standard. Positive controls run with each batch were prepared by spiking a pooled BAL fluid specimen with a known dilution of\n            <jats:named-content content-type=\"genus-species\">Coccidioides immitis<\/jats:named-content>\n            organism. Our experience with testing &gt;330 patient samples shows that clinically relevant information can be available within 4 h using an RT-PCR method on the BD Max to identify\n            <jats:named-content content-type=\"genus-species\">Coccidioides<\/jats:named-content>\n            spp., with sensitivity equivalent to culture.\n          <\/jats:p>","DOI":"10.1128\/jcm.02731-14","type":"journal-article","created":{"date-parts":[[2015,1,15]],"date-time":"2015-01-15T06:40:15Z","timestamp":1421304015000},"page":"926-929","update-policy":"http:\/\/dx.doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":30,"title":["Development of a Real-Time PCR Assay for Identification of Coccidioides immitis by Use of the BD Max System"],"prefix":"10.1128","volume":"53","author":[{"given":"Marilyn","family":"Mitchell","sequence":"first","affiliation":[{"name":"Microbiology Department, Community Medical Centers\u2013Fresno, Fresno, California, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dominic","family":"Dizon","sequence":"additional","affiliation":[{"name":"University of California\u2013San Francisco, Fresno, California, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robert","family":"Libke","sequence":"additional","affiliation":[{"name":"University of California\u2013San Francisco, Fresno, California, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Peterson","sequence":"additional","affiliation":[{"name":"University of California\u2013San Francisco, Fresno, California, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David","family":"Slater","sequence":"additional","affiliation":[{"name":"Microbiology Department, Community Medical Centers\u2013Fresno, Fresno, California, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Akashdeep","family":"Dhillon","sequence":"additional","affiliation":[{"name":"Microbiology Department, Community Medical Centers\u2013Fresno, Fresno, California, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"235","reference":[{"key":"e_1_3_2_2_2","doi-asserted-by":"publisher","DOI":"10.1513\/pats.200907-080AL"},{"key":"e_1_3_2_3_2","first-page":"217","article-title":"Increase in reported coccidioidomycosis\u2013United States, 1998\u20132011","volume":"62","author":"Centers for Disease Control and Prevention (CDC)","year":"2013","unstructured":"Centers for Disease Control and Prevention (CDC). 2013. Increase in reported coccidioidomycosis\u2013United States, 1998\u20132011. MMWR Morb Mortal Wkly Rep 62:217\u2013221.","journal-title":"MMWR Morb Mortal Wkly Rep"},{"key":"e_1_3_2_4_2","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.00005-13"},{"key":"e_1_3_2_5_2","unstructured":"Centers for Disease Control and Prevention. 2014. Valley fever (coccidioidomycosis) statistics. http:\/\/www.cdc.gov\/fungal\/diseases\/coccidioidomycosis\/statistics.html."},{"key":"e_1_3_2_6_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid1206.060028"},{"key":"e_1_3_2_7_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.42.2.778-783.2004"},{"key":"e_1_3_2_8_2","unstructured":"Galgiani JN. 2014. Laboratory diagnosis of coccidioidomycosis. www.UpToDate.com."},{"key":"e_1_3_2_9_2","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.3.3.247"},{"key":"e_1_3_2_10_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01776-06"},{"key":"e_1_3_2_11_2","doi-asserted-by":"publisher","DOI":"10.4148\/1941-4765.1335"},{"key":"e_1_3_2_12_2","volume-title":"Reference method for broth dilution antifungal susceptibility testing of yeasts; approved standard","author":"Clinical and Laboratory Standards Institute","year":"2010","unstructured":"Clinical and Laboratory Standards Institute. 2010. Reference method for broth dilution antifungal susceptibility testing of yeasts; approved standard. CLSI M27-A3. Clinical and Laboratory Standards Institute, Wayne, PA."},{"key":"e_1_3_2_13_2","volume-title":"Reference method for broth dilution antifungal susceptibility testing of filamentous fungi; approved standard","author":"Clinical and Laboratory Standards Institute","year":"2010","unstructured":"Clinical and Laboratory Standards Institute. 2010. Reference method for broth dilution antifungal susceptibility testing of filamentous fungi; approved standard\u20142nd ed. CLSI M38-A2. Clinical and Laboratory Standards Institute, Wayne, PA.","edition":"2"},{"key":"e_1_3_2_14_2","doi-asserted-by":"publisher","DOI":"10.1128\/jcm.29.2.393-394.1991"},{"key":"e_1_3_2_15_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1469-0691.2006.01679.x"}],"container-title":["Journal of Clinical Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JCM.02731-14","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JCM.02731-14","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,3,5]],"date-time":"2022-03-05T12:06:34Z","timestamp":1646481994000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/JCM.02731-14"}},"subtitle":[],"editor":[{"given":"D. W.","family":"Warnock","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2015,3]]},"references-count":14,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2015,3]]}},"alternative-id":["10.1128\/JCM.02731-14"],"URL":"https:\/\/doi.org\/10.1128\/jcm.02731-14","relation":{},"ISSN":["0095-1137","1098-660X"],"issn-type":[{"value":"0095-1137","type":"print"},{"value":"1098-660X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,3]]},"assertion":[{"value":"2014-09-26","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2015-01-07","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2015-02-19","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}