A Comparison of Real-Time Polymerase Chain Reaction Assays for the Detection of Antimicrobial Resistance Markers and Sequence Typing From Clinical Nucleic Acid Amplification Test Samples and Matched Neisseria gonorrhoeae Culture

Antimicrobial resistance prediction in Neisseria gonorrhoeae: Current status and future prospects

INTRODUCTION

Several nucleic acid amplification tests (NAATs), mostly real-time PCRs, to detect antimicrobial resistance (AMR) determinants and predict AMR in Neisseria gonorrhoeae are promising, and some may be ready to apply at the point-of-care (POC), but important limitations remain with most NAATs. Next-generation sequencing (NGS) can overcome many of these limitations.Areas covered: Recent advances, with main focus on publications since 2017, in the development and use of NAATs and NGS to predict gonococcal AMR for surveillance and clinical use, and pros and cons of these tests as well as future perspectives for appropriate use of molecular AMR prediction for N. gonorrhoeae.Expert Commentary: NAATs and/or NGS for AMR prediction should supplement culture-based AMR surveillance, which will remain because it detects also AMR due to unknown AMR determinants, and translation into POC tests is imperative for the end-goal of individualized treatment, sparing ceftriaxone±azithromycin. Several challenges for direct testing of clinical, especially pharyngeal, specimens and for accurate prediction of cephalosporins and azithromycin resistance, especially using NAATs, remain. The choice of AMR prediction assay needs to carefully consider the intended use of the assay; limitations intrinsic to the AMR prediction technology, algorithms and specific to chosen methodology; specimen types analyzed; and cost-effectiveness.

Mycoplasma genitalium, Chlamydia trachomatis, and Neisseria gonorrhoeae Detected With Aptima Assays Performed on Self-Obtained Vaginal Swabs and Urine Collected at Home and in a Clinic

Self-obtained vaginal swabs, first-void urine and pooled specimens were collected at home and in a clinic. Percent prevalence and collection site concordance was 30.3 and 100 for Mycoplasma genitalium (74.4% azithromycin resistant) 15.1 and 96.7 for Chlamydia trachomatis and 6.6 and 100 for Neisseria gonorrhoeae (27% ciprofloxacin-resistant).

Equations To Predict Antimicrobial MICs in Neisseria gonorrhoeae Using Molecular Antimicrobial Resistance Determinants

The emergence of Neisseria gonorrhoeae strains that are resistant to azithromycin and extended-spectrum cephalosporins represents a public health threat, that of untreatable gonorrhea infections. Multivariate regression modeling was used to determine the contributions of molecular antimicrobial resistance determinants to the overall antimicrobial MICs for ceftriaxone, cefixime, azithromycin, tetracycline, ciprofloxacin, and penicillin. A training data set consisting of 1,280 N. gonorrhoeae strains was used to generate regression equations which were then applied to validation data sets of Canadian (n = 1,095) and international (n = 431) strains. The predicted MICs for extended-spectrum cephalosporins (ceftriaxone and cefixime) were fully explained by 5 amino acid substitutions in PenA, A311V, A501P/T/V, N513Y, A517G, and G543S; the presence of a disrupted mtrR promoter; and the PorB G120 and PonA L421P mutations. The correlation of predicted MICs within one doubling dilution to phenotypically determined MICs of the Canadian validation data set was 95.0% for ceftriaxone, 95.6% for cefixime, 91.4% for azithromycin, 98.2% for tetracycline, 90.4% for ciprofloxacin, and 92.3% for penicillin, with an overall sensitivity of 99.9% and specificity of 97.1%. The correlations of predicted MIC values to the phenotypically determined MICs were similar to those from phenotype MIC-only comparison studies. The ability to acquire detailed antimicrobial resistance information directly from molecular data will facilitate the transition to whole-genome sequencing analysis from phenotypic testing and can fill the surveillance gap in an era of increased reliance on nucleic acid assay testing (NAAT) diagnostics to better monitor the dynamics of N. gonorrhoeae.

A profile of the cobas® CT/NG assay on the cobas® 6800/8800 system for detection of Chlamydia trachomatis and Neisseria gonorrhoeae

Introduction: Chlamydia trachomatis and Neisseria gonorrhoeae infection rates continue to rise worldwide. Increasing screening of the largely asymptomatic infections is critical for timely and effective disease control. Laboratory solutions that can handle increasing volumes and generate highly accurate test results are needed in reference labs that provide the majority of chlamydia/gonorrhea testing.Areas covered: This review will describe the Roche cobas CT/NG assay performed on the cobas 6800/8800 system. The instrument features will be described as will the performance of the assay.Expert opinion: The high throughput cobas 6800/8800 can be integrated with clinical chemistry, hematology and immunology systems which will increase reference lab efficiency. The broad menu, ease of expansion with lab developed tests, in combination with features that support lab efficiencies and cost management while assuring high sensitivity and specificity, make this a uniquely effective diagnostic tool.

Genetic Characterization and Enhanced Surveillance of Ceftriaxone-Resistant Neisseria gonorrhoeae Strain, Alberta, Canada, 2018

In July 2018, a case of Neisseria gonorrhoeae associated with ceftriaxone treatment failure was identified in Alberta, Canada. We identified the isolate and nucleic acid amplification testing (NAAT) specimen as the ceftriaxone-resistant strain multilocus sequence type 1903/NG-MAST 3435/NG-STAR 233, originally identified in Japan (FC428), with the same penA 60.001 mosaic allele and genetic resistance determinants. Core single-nucleotide variant (SNV) analysis identified 13 SNVs between this isolate and FC428. Culture-independent surveillance by PCR for the A311V mutation in the penA allele and N. gonorrhoeae multiantigen sequence typing directly from NAAT transport media positive for N. gonorrhoeae by NAAT did not detect spread of the strain. We identified multiple sequence types not previously detected in Alberta by routine surveillance. This case demonstrates the benefit of using culture-independent methods to enhance detection, public health investigations, and surveillance to address this global threat.

Multidrug-resistant and extensively drug-resistant Neisseria gonorrhoeae in Canada, 2012-2016

BACKGROUND

Neisseria gonorrhoeae have acquired resistance to many antimicrobials, including third generation cephalosporins and azithromycin, which are the current gonococcal combination therapy recommended by the Canadian Guidelines on Sexually Transmitted Infections.

OBJECTIVE

To describe antimicrobial susceptibilities for N. gonorrhoeae circulating in Canada between 2012 and 2016.

METHODS

Antimicrobial resistance profiles were determined using agar dilution of N. gonorrhoeae isolated in Canada 2012-2016 (n=10,167) following Clinical Laboratory Standards Institute guidelines. Data were analyzed by applying multidrug-resistant gonococci (MDR-GC) and extensively drug-resistant gonococci (XDR-GC) definitions.

RESULTS

Between 2012 and 2016, the proportion of MDR-GC increased from 6.2% to 8.9% and a total of 19 cases of XDR-GC were identified in Canada (0.1%, 19/18,768). The proportion of isolates with decreased susceptibility to cephalosporins declined between 2012 and 2016 from 5.9% to 2.0% while azithromycin resistance increased from 0.8% to 7.2% in the same period.

CONCLUSION

While XDR-GC are currently rare in Canada, MDR-GC have increased over the last five years. Azithromycin resistance in N. gonorrhoeae is established and spreading in Canada, exceeding the 5% level at which the World Health Organization states an antimicrobial should be reviewed as an appropriate treatment. Continued surveillance of antimicrobial susceptibilities of N. gonorrhoeae is necessary to inform treatment guidelines and mitigate the impact of resistant gonorrhea.

Addressing the rising rates of gonorrhea and drug-resistant gonorrhea: There is no time like the present

Increasing rates of gonococcal (GC) infection and antimicrobial resistant (AMR) GC, are a serious public health concern for Canada and around the world. Previously recommended treatments are ineffective against many of the gonorrhea strains circulating today. The current recommendation for combination therapy is now being threatened by globally emerging and increasingly resistant strains. It is important that coordinated efforts be made now to ensure these new global strains do not become established in Canada. Otherwise, we will be faced with the possibility of persistent GC infection which can lead to pelvic inflammatory disease, infertility and chronic pelvic pain in women; and epididymitis in men. The presence of GC can also increase the risk of HIV acquisition and transmission. There are a number of reasons why we are facing this public health threat. GC infection is often asymptomatic and it is highly transmissible. People may hesitate to seek testing (or to offer testing). Treatment is complex: recommendations vary by site of infection and risk of resistance. Sexual contact during travel is an important source of imported emerging resistant global strains. The new screening and diagnostic Nucleic Acid Amplification Test (NAAT) is excellent but has decreased the number of cultures being done and therefore our capacity to track AMR-GC. There are four key actions that clinicians and front-line public health professionals can take to stem the increase in rates of GC and drug resistant GC. First, normalize and increase GC screening based on risk factors and emphasize the need for safer sex practices. NAAT is useful for screening, but culture is still needed for extra-genital sites. Second, conduct pretravel counselling and include a travel history as part of the risk assessment. Third, use culture along with NAAT to establish the diagnosis and follow up for test-of-cure. Finally, refer to the most current Canadian Guidelines on Sexually Transmitted Infections or provincial/territorial recommendations on combination therapies for patients and their contacts as recommendations may have changed in response to evolving AMR-GC trends.