Chlamydia trachomatis Variants Escaping Detection in the Aptima Combo 2 Assay in the United States

Katz, Samantha S.; Danavall, Damien; Morris, Monica; Herrod, B; Dale, Suzanne E.; Nye, Melinda B.; Kersh, Ellen N.; Kirkcaldy, Robert D.; Raphael, Brian

doi:10.1097/olq.0000000000001617

Cited by 6 publications

(2 citation statements)

References 14 publications

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“…Nevertheless, with other samples, the performance was also excellent (sensitivity > 94%), highlighting the great advantage and superiority of the CT/NG molecular testing [54]. Thus, despite being the most reliable technique, it is important to keep in mind that NAATs are associated with some false negative results, and the smaller the sensitivity of the test chosen, the more missing infected individuals there will be [55]. Also, some CT variants were considered hard to detect using some NAATs, leading to false negatives.…”

Section: Gold Standard Diagnostic Methodsmentioning

confidence: 99%

Chlamydial and Gonococcal Genital Infections: A Narrative Review

Rodrigues

Vieira‐Baptista

Catalão

et al. 2023

JPM

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Sexually transmitted infections (STIs) constitute one of the leading causes of disease burden worldwide, leading to considerable morbidity, mortality, health expenditures, and stigma. Of note are the most common bacterial STIs, chlamydial and gonococcal infections, whose etiological agents are Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG), respectively. Despite being usually asymptomatic, in some cases these infections can be associated with long-term severe complications, such as pelvic inflammatory disease, chronic pelvic pain, infertility, ectopic pregnancy, and increased risk of other STIs acquisition. As the symptoms, when present, are usually similar in both infections, and in most of the cases these infections co-occur, the dual-test strategy, searching for both pathogens, should be preferred. In line with this, herein we focus on the main aspects of CT and NG infections, the clinical symptoms as well as the appropriate state-of-the-art diagnostic tests and treatment. Cost-effective strategies for controlling CT and NG infections worldwide are addressed. The treatment for both infections is based on antibiotics. However, the continuing global rise in the incidence of these infections, concomitantly with the increased risk of antibiotics resistance, leads to difficulties in their control, particularly in the case of NG infections. We also discuss the potential mechanism of tumorigenesis related to CT infections. The molecular bases of CT and NG infections are addressed, as they should provide clues for control or eradication, through the development of new drugs and/or effective vaccines against these pathogens.

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Section: Gold Standard Diagnostic Methodsmentioning

confidence: 99%

Chlamydial and Gonococcal Genital Infections: A Narrative Review

Rodrigues

Vieira‐Baptista

Catalão

et al. 2023

JPM

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“…Mutations impacting diagnostic NAATs are not unique to SARS-CoV-2 and have been reported for parasites ( 23 ), fungi ( 24 ), bacteria ( 2 , 25 ), and other viruses ( 26 – 29 ). With the potential to cause false negative results with molecular technologies ( 4 ), the need for NAAT target sites quality assurance is well justified.…”

Section: Introductionmentioning

confidence: 99%

Neglected SARS-CoV-2 variants and potential concerns for molecular diagnostics: a framework for nucleic acid amplification test target site quality assurance

McCracken,

Gaston,

Pettipas

et al. 2023

Microbiol Spectr

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During the COVID-19 pandemic, SARS-CoV-2 detection using nucleic acid amplification tests (NAATs) played a key role in clinical management and public health interventions. However, mutations could jeopardize NAAT-based detection if they occur in the NAAT target site, potentially resulting in false negative results. However, mutation monitoring is challenged as the exact location of commercial NAAT target sites is not divulged by manufacturers. This study sequenced commercial SARS-CoV-2 NAAT target sites to assess the impact of mutations occurring in these regions. The resulting sequences for the Xpert, Cobas, and ID NOW SARS-CoV-2 assays were queried against SARS-CoV-2 genome databases to identify mutations in circulating strains. Synthetic DNAs and clinical specimens harboring NAAT target site mutations were used to assess mutation impact. Of 17,600 NAAT target site mutation occurrences in a genome database, 269 compromised target detection. These represented 24 unique mutations that reduced NAAT target sensitivity and nine led to target detection failure. Only seven of these mutations were previously recognized. Overall, this reactive strategy along with passive surveillance identified 29 novel mutations that compromised detection with Xpert and Cobas targets. Knowledge of commercial NAAT target sites, paired with a strategy for mutation impact assessment and ongoing genetic surveillance, provided a robust framework for commercial NAAT target site quality assurance. The question remains of who should be responsible for NAAT target site quality assurance, but collaborative efforts between methods users, industry, and regulatory agencies would be ideal. Molecular tests like polymerase chain reaction were widely used during the COVID-19 pandemic but as the pandemic evolved, so did SARS-CoV-2. This virus acquired mutations, prompting concerns that mutations could compromise molecular test results and be falsely negative. While some manufacturers may have in-house programs for monitoring mutations that could impact their assay performance, it is important to promptly report mutations in circulating viral strains that could adversely impact a diagnostic test result. However, commercial test target sites are proprietary, making independent monitoring difficult. In this study, SARS-CoV-2 test target sites were sequenced to monitor and assess mutations impact, and 29 novel mutations impacting SARS-CoV-2 detection were identified. This framework for molecular test target site quality assurance could be adapted to any molecular test, ensuring accurate diagnostic test results and disease diagnoses.

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The diagnostic-escape Finnish new variant of Chlamydia trachomatis first described in 2019 remains present in Finland three years after the introduction of an updated Aptima Combo 2 assay

Puolakkainen¹,

Mannonen²,

Unemo³

2023

Clinical Microbiology and Infection

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Chlamydia trachomatis Variants Escaping Detection in the Aptima Combo 2 Assay in the United States

Abstract: Chlamydia trachomatis diagnostic-escape variants were detected in the United States using a redesigned Aptima Combo 2 assay, which also correctly identified specimens previously identified as false negative or equivocal.

Cited by 6 publications

References 14 publications

Chlamydial and Gonococcal Genital Infections: A Narrative Review

Chlamydial and Gonococcal Genital Infections: A Narrative Review

Neglected SARS-CoV-2 variants and potential concerns for molecular diagnostics: a framework for nucleic acid amplification test target site quality assurance

The diagnostic-escape Finnish new variant of Chlamydia trachomatis first described in 2019 remains present in Finland three years after the introduction of an updated Aptima Combo 2 assay

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