Opportunities and pitfalls of molecular testing for detecting sexually transmitted pathogens

In the last 20 years, nucleic acid amplification tests (NAATs) have gradually replaced traditional methods for the detection of sexually transmitted infections. NAAT technology comes with some considerable benefits for diagnosis, including increased sensitivity, rapid result turnaround and suitability for high throughput screening of asymptomatic individuals using more-readily available specimens. However, the transition to NAAT has not come without its problems. False-negative and false-positive results have been reported owing to various technical issues. Furthermore, increased reliance on NAATs for diagnosis have created the need to develop NAAT-based methods to inform treatment, being an area that presents its own set of challenges. In this review article, we explore NAAT-based detection of Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma genitalium and Trichomonas vaginalis. In doing so, we consider the benefits and limitations of NAAT-based technology and highlight areas where further research and development is in need.

Most but not all laboratories can detect the recently emerged Neisseria gonorrhoeae porA mutants - results from the QCMD 2013 N. gonorrhoeae external quality assessment programme

We describe the results of the Quality Control for Molecular Diagnostics 2013 Neisseria gonorrhoeae external quality assessment programme that included an N. gonorrhoeae strain harbouring an N. meningitidis porA gene which causes false-negative results in molecular diagnostic assays targeting the gonococcal porA pseudogene. Enhanced awareness of the international transmission of such gonococcal strains is needed to avoid false-negative results in both in-house and commercial molecular diagnostic assays used in laboratories worldwide, but particularly in Europe.

A national quality assurance survey of Neisseria gonorrhoeae testing

The aims of this study were to (1) conduct a national survey of Neisseria gonorrhoeae identification by National Neisseria Network (NNN) reference laboratories contributing data to the Australian Gonococcal Surveillance Programme and (2) determine the prevalence in Australia of strains of N. gonorrhoeae lacking gene sequences commonly targeted by in-house PCR assays for confirmation of gonococcal nucleic acid amplification tests. Gonococcal clinical isolates referred to NNN laboratories for the first half of 2012 were screened using in-house real-time PCR assays targeting multicopy opa, porA pseudogene and cppB genes. There were 2455 clinical gonococcal isolates received in the study period; 98.6 % (2420/2455) of isolates harboured all three gene targets, 0.12 % (3/2455) were porA-negative, 0.04 % (1/2455) opa-negative and 1.14 % (28/2455) cppB-negative by PCR. Notably, no isolates were simultaneously negative for two targets. However, three isolates failed to be amplified by all three PCR methods, one isolate of which was shown to be a commensal Neisseria strain by 16S rRNA sequencing. Using PCR as the reference standard the results showed that (1) identification of N. gonorrhoeae isolates by NNN laboratories was highly specific (99.96 %) and (2) strains of N. gonorrhoeae lacking gene sequences commonly targeted by in-house PCR assays are present but not widespread throughout Australia at this point in time.

Purification of DNA eluates from the ProbeTec GC Q(x) assay on BD Viper™ XTR allows for further analysis and confirmation of gonorrhea

Low positive predictive values of Neisseria gonorrhoeae nucleic acid amplification tests in low-prevalence populations are a major challenge for accurate diagnostics. It is therefore necessary to verify all positive N. gonorrhoeae results with a different assay and target gene, preferably using the same sample. The BD ProbeTec™ Q(x) Collection Kit for Endocervical or Lesion Specimens, which is recommended for BD Viper™ XTR, is incompatible with other commercial platforms. Therefore, a confirmatory PCR has not been available for samples received on this transport medium. To be able to verify results from these samples with another assay, our objective was to establish a procedure for using the DNA eluates from BD Viper™ XTR for further analysis. DNA eluates from BD Viper™ XTR were collected and analyzed in two in-house confirmatory real-time PCRs targeting the porA pseudogene and the opa multicopy gene. BD Viper™ XTR DNA eluates were analyzed directly and also after purification with the nucleic acid extraction system NucliSENS® easyMag®. Purification of BD Viper™ XTR DNA eluates with the nucleic acid extraction system NucliSENS® easyMag® provided a sensitivity of the in-house PCR comparable to BD Viper™. With the inclusion of two target genes in the confirmatory PCR, specific and reliable verification of results were obtained. This study presents a simple, inexpensive procedure which allows for rapid verification of gonorrhea from samples received on the BD ProbeTec™ Q(x) Collection Kit for Endocervical or Lesion Specimens.

Whole-genome sequencing of bacterial sexually transmitted infections: implications for clinicians

PURPOSE OF REVIEW

Increasingly, genomics is being used to answer detailed clinical questions. Although genome analysis of bacterial sexually transmitted infections (STIs) lags far behind that of many other bacterial pathogens, genomics can reveal previously inaccessible aspects of pathogen biology.

RECENT FINDINGS

Comparative genomic studies on the most common bacterial STI, chlamydia, have revolutionized our understanding of this intracellular bacterium, demonstrating that it undergoes extensive recombination and that the traditional typing schemes can be misleading. Genome projects can also help us to understand the recently observed phenomenon of 'diagnostic escape' seen in both Chlamydia trachomatis and Neisseria gonorrhoeae.

SUMMARY

The routine use of genomics in clinical settings is becoming a reality. For STIs, a primary requirement is an understanding of the diversity of circulating strains and how they change over time. This can help to inform future studies and allow us to address real clinical issues such as outbreak identification, global spread of successful clones and antimicrobial resistance monitoring.