Surveillance for Chlamydia trachomatis variants escaping detection with the Aptima Combo 2 assay in Canada from 2019 to 2021

ABSTRACT Nucleic acid amplification tests (NAATs) are the method of choice for Chlamydia trachomatis diagnosis, but these strategies are susceptible to target site mutations. C. trachomatis variants escaping detection with the Aptima Combo 2 (AC2) assay on the Hologic Panther instrument from 23S rRNA mutations have been reported in Nordic countries, England, Japan, and the United States. Given the potential for false negative results, this study investigated whether strains of C. trachomatis with AC2 target site mutations were present in Canada. Surveillance was conducted in Canadian laboratories from 2019 to 2021. Specimens suspected of AC2 target site mutations included those with low-value detections on the AC2 assay, with subsequent high-value detections on the Aptima Chlamydia Trachomatis (ACT) assay used for confirmatory testing. Specimens with AC2/ACT discrepant results were subjected to sequencing of the AC2 target (i.e., 23S rRNA). Sequencing revealed 15 (4.8%) diagnostic escape variants which were carrying either C1514T, G1523A, or G1526A mutations. All specimens with a diagnostic escape mutation were detected with a reformulated version of the AC2 assay. Overall, while the prevalence of C. trachomatis variants was rare, their presence in the Canadian population supports the use of the new AC2 kit formulation and the need for ongoing genetic surveillance for NAAT-based assays.IMPORTANCEMolecular tests are commonly used for the detection of sexually transmitted infections (STIs) like Chlamydia trachomatis. Mutations impacting C. trachomatis molecular target detection on the Hologic Panther AC2 assay have been reported in several countries, raising concerns about potential false negative results. This study showed C. trachomatis target detection failures in specimens submitted for C. trachomatis testing in Canadian laboratories from 2019 to 2021. A reformulated version of the AC2 molecular test is now available that can identify C. trachomatis strains harboring target site mutations that were impacted by the previous test formulation. While target site mutations were rare in Canada, revealing their presence is important to ensure accurate molecular detection of C. trachomatis with existing testing methods. This study supports ongoing genetic monitoring of C. trachomatis molecular test target sites, as well as the use of the reformulated test to avoid false negative results and subsequent transmissions.