Comparison of an in-house real-time duplex PCR assay with commercial HOLOGIC® APTIMA assays for the detection of Neisseria gonorrhoeae and Chlamydia trachomatis in urine and extra-genital specimens

Abstract

BackgroundExtra-genital Neisseria gonorrhoeae and Chlamydia trachomatis infections are mostly asymptomatic, and important reservoir sites of infection as they often go undetected and may be more difficult to eradicate with recommended therapeutic regimens. Commercial nucleic acid amplification tests (NAATs) have not received regulatory approval for the detection of N. gonorrhoeae and C. trachomatis in extra-genital specimens. The HOLOGIC® APTIMA Combo2 assay for N. gonorrhoeae and C. trachomatis has performed well in evaluations using extra-genital specimens.MethodsWe assessed the performance of an in-house real-time duplex PCR assay for the detection of N. gonorrhoeae and C. trachomatis in urine and extra-genital specimens using the HOLOGIC® APTIMA assays as gold standard comparators. Urine, oropharyngeal and ano-rectal specimens were collected from each of 200 men-who-have-sex-with-men (MSM) between December 2011 and July 2012.ResultsFor N. gonorrhoeae detection, the in-house PCR assay showed 98.5–100% correlation agreement with the APTIMA assays, depending on specimen type. Sensitivity for N. gonorrhoeae detection was 82.4% for ano-rectal specimens, 83.3% for oropharyngeal specimens, and 85.7% for urine; and specificity was 100% with all specimen types. The positive predictive value (PPV) for N. gonorrhoeae detection was 100% and the negative predictive value (NPV) varied with sample type, ranging from 98.5–99.5%. For C. trachomatis detection, correlation between the assays was 100% for all specimen types. The sensitivity, specificity, PPV and NPV of the in-house PCR assay was 100% for C. trachomatis detection, irrespective of specimen type.ConclusionThe in-house duplex real-time PCR assay showed acceptable performance characteristics in comparison with the APTIMA® assays for the detection of extra-genital N. gonorrhoeae and C. trachomatis.

Molecular Epidemiology of Chlamydia Trachomatis Infection in the Genitourinary Tract

“…The current nucleic acid expansion test (NAAT) is considered to be the gold standard for the diagnosis of CT infection (15). NAAT has the advantages of high sensitivity (90%-97%) and high specificity (99%-100%).…”

“…Although NAAT is the primary basis for laboratory diagnosis, such techniques are limited by the speed of detection and equipment requirements, and cannot be quickly screened for a large number of target populations. An X-pert technology developed in recent years, combined with microfluidic technology and real-time PCR, can achieve ideal sensitivity and specificity in various target populations (15). X-pert technology allows patients to sample themselves and report results within 90 minutes (16).…”

Urine Tests for Diagnosis of Infectious Diseases and Antibiotic-Resistant Pathogens

“…However, it shows low positive predictive value. Furthermore Chlamydia trachomatis, Mycoplasma genitalium, and Neisseria gonorrhea can be detected with PCR and real-time duplex PCR from urine samples [55][56][57][58]. Using urine as a specimen for diagnosis of Gonococcal infections by molecular tests has eased out uncomfortable sample collection by urethral swab and hence increased the number of patients volunteering to give specimen for this disease of public health importance.…”

Performance assessment of the Allplex™ STI Essential real-time PCR assay for the diagnosis of Neisseria gonorrhoeae and Chlamydia trachomatis infections in genital and extra-genital sites

“…However, the assay is not validated for oropharyngeal and ano-rectal specimens, while recommendations, driven by a relatively poor sensitivity of culture, show that NAATs for CT/ NG are indicated for such sites [10][11][12]. So far, only the Aptima Combo2 method is EMEA-IVD cleared for extragenital specimens [13].…”