False-negative Chlamydia polymerase chain reaction result caused by a cryptic plasmid-deficient Chlamydia trachomatis strain in Australia
Emma L. Sweeney
A C , Cheryl Bletchly B , Rita Gupta B and David M. Whiley A B
A University of Queensland Centre for Clinical Research (UQ-CCR), The University of Queensland, Brisbane, Qld 4029, Australia.
B Pathology Queensland, Central Laboratory, Brisbane, Qld 4006, Australia.
C Corresponding author. Email: e.l.sweeney@uq.edu.au
Sexual Health 16(4) 394-396 https://doi.org/10.1071/SH18205
Submitted: 25 October 2018 Accepted: 25 March 2019 Published: 4 July 2019
Abstract
Background: 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.
Additional keywords: sexually transmissible infection.
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