{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,4]],"date-time":"2025-11-04T23:30:53Z","timestamp":1762299053798,"version":"build-2065373602"},"reference-count":12,"publisher":"CSIRO Publishing","issue":"4","license":[{"start":{"date-parts":[[2025,8,18]],"date-time":"2025-08-18T00:00:00Z","timestamp":1755475200000},"content-version":"vor","delay-in-days":2237,"URL":"https:\/\/doi.org\/10.1071\/journalslicense"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,8,5]]},"abstract":"<jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>The 7.5-kb chlamydial cryptic plasmid remains a widely used sequence target for Chlamydia trachomatis nucleic acid amplification tests, but sequence variation in this plasmid, particularly a previously reported 377-bp deletion, can cause false-negative results. Here we report the presence in Australia of a C. trachomatis strain lacking the cryptic plasmid. Methods: A rectal swab from a male in his 50s provided a positive result for C. trachomatis using the Roche Cobas 4800 test, but a negative result in our confirmatory in-house polymerase chain reaction (PCR) method targeting the chlamydial cryptic plasmid. This result was unexpected given our in-house PCR assay targeted a region of sequence outside the recognised 377-bp deletion. To further investigate this discrepancy, the sample was retested using a second in-house PCR targeting a chromosomal (ompA) gene as well as six primer sets flanking various regions of the cryptic plasmid. Results: The sample provided positive results in the second in-house method, confirming the presence of C. trachomatis DNA. All other primer sets targeting the cryptic plasmid failed to amplify, indicating a lack of the chlamydial cryptic plasmid in this sample. Conclusions: The recognition of a plasmid-deficient strain of C. trachomatis within Australia highlights further limitations of using the chlamydial cryptic plasmid for C. trachomatis diagnostics and re-emphasises the benefits of using multitarget assays to avoid false-negative results.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1071\/sh18205","type":"journal-article","created":{"date-parts":[[2019,7,4]],"date-time":"2019-07-04T01:39:22Z","timestamp":1562204362000},"page":"394-396","source":"Crossref","is-referenced-by-count":5,"title":["False-negative Chlamydia polymerase chain reaction result caused by a cryptic plasmid-deficient Chlamydia trachomatis strain in Australia"],"prefix":"10.1071","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3199-6432","authenticated-orcid":true,"given":"Emma L.","family":"Sweeney","sequence":"first","affiliation":[{"name":"AUniversity of Queensland Centre for Clinical Research (UQ-CCR), The University of Queensland, Brisbane, Qld 4029, Australia."},{"name":"CCorresponding author. Email: e.l.sweeney@uq.edu.au"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cheryl","family":"Bletchly","sequence":"additional","affiliation":[{"name":"BPathology Queensland, Central Laboratory, Brisbane, Qld 4006, Australia."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rita","family":"Gupta","sequence":"additional","affiliation":[{"name":"BPathology Queensland, Central Laboratory, Brisbane, Qld 4006, Australia."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David M.","family":"Whiley","sequence":"additional","affiliation":[{"name":"AUniversity of Queensland Centre for Clinical Research (UQ-CCR), The University of Queensland, Brisbane, Qld 4029, Australia."},{"name":"BPathology Queensland, Central Laboratory, Brisbane, Qld 4006, Australia."}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"67","published-online":{"date-parts":[[2019,7,4]]},"reference":[{"key":"2025102615521860600_R1"},{"key":"2025102615521860600_R2","doi-asserted-by":"publisher","first-page":"96","DOI":"10.1093\/oxfordjournals.epirev.a036266","article-title":"Epidemiology of sexually transmitted Chlamydia trachomatis infections.","volume":"5","author":"Thompson","year":"1983","journal-title":"Epidemiol Rev"},{"key":"2025102615521860600_R3"},{"issue":"11","key":"2025102615521860600_R4","article-title":"A variant of Chlamydia trachomatis with deletion in cryptic plasmid: implications for use of PCR diagnostic tests.","volume":"11","author":"Ripa","year":"2006","journal-title":"Euro Surveill"},{"issue":"7","key":"2025102615521860600_R5","doi-asserted-by":"publisher","first-page":"607","DOI":"10.1136\/sextrans-2013-051018","article-title":"The new variant of Chlamydia trachomatis was present as early as 2003 in Orebro County, 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Chlamydia trachomatis using real-time and conventional detection methodologies.","volume":"37","author":"Whiley","year":"2005","journal-title":"Pathology"},{"issue":"4","key":"2025102615521860600_R9","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0195454","article-title":"CtGEM typing: discrimination of Chlamydia trachomatis ocular and urogenital strains and major evolutionary lineages by high resolution melting analysis of two amplified DNA fragments.","volume":"13","author":"Giffard","year":"2018","journal-title":"PLoS One"},{"issue":"2","key":"2025102615521860600_R10","doi-asserted-by":"publisher","first-page":"144","DOI":"10.1016\/0147-619X(90)90033-9","article-title":"The 7.5-kb plasmid present in Chlamydia trachomatis is not essential for the growth of this 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Health"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/connectsci.au\/sh\/article-pdf\/16\/4\/394\/799182\/sh18205.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/connectsci.au\/sh\/article-pdf\/16\/4\/394\/799182\/sh18205.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,26]],"date-time":"2025-10-26T19:52:21Z","timestamp":1761508341000},"score":1,"resource":{"primary":{"URL":"https:\/\/connectsci.au\/sh\/article\/16\/4\/394\/101972\/False-negative-Chlamydia-polymerase-chain-reaction"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,7,4]]},"references-count":12,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2019,8,5]]}},"URL":"https:\/\/doi.org\/10.1071\/sh18205","relation":{},"ISSN":["1448-5028","1449-8987"],"issn-type":[{"type":"print","value":"1448-5028"},{"type":"electronic","value":"1449-8987"}],"subject":[],"published":{"date-parts":[[2019,7,4]]}}}