Simultaneous Detection of Neisseria gonorrhoeae and Fluoroquinolone Resistance Mutations to Enable Rapid Prescription of Oral Antibiotics

Syndromic approaches for sexually transmitted infections: added value of molecular diagnosis

PURPOSE OF REVIEW

Sexually transmitted infections (STIs) are a significant global health concern, with many cases going undiagnosed due to asymptomatic infections. Traditional diagnostic methods, such as culture and serology, have limitations in sensitivity, specificity, and turnaround time. Molecular diagnostics, particularly PCR-based approaches, offer significant advantages, including improved detection rates and the potential for syndromic testing. This review examines the role of syndromic PCR diagnostics in improving STI detection and management.

RECENT FINDINGS

Recent studies highlight the utility in detecting common STIs, such as Chlamydia trachomatis , Neisseria gonorrhoeae , and Trichomonas vaginalis , as well as emerging pathogens. PCR-based syndromic panels allow for the simultaneous detection of multiple pathogens from a single sample, improving diagnostic accuracy and efficiency. Syndromic PCR approaches streamline diagnosis, aid in early detection, and support efficient treatment, addressing both common and emerging infections.

SUMMARY

Syndromic PCR diagnostics streamline STI detection, addressing the limitations of conventional methods. They enable faster, more accurate, and comprehensive diagnosis, leading to targeted treatment and improved patient outcomes. Expanding syndromic panels to include emerging pathogens and ensuring cost-effective implementation remain key areas for future research.

Mutational alterations in the QRDR regions associated with fluoroquinolone resistance in Pseudomonas aeruginosa of clinical origin from Savar, Dhaka

Bacterial DNA gyrase and topoisomerase IV are the major targets of quinolone antibiotic, and mutational alterations in quinolone resistance determining regions (QRDR) serve as major mechanism of resistance in most bacterial species, including P. aeruginosa. The present investigation was aimed to study the molecular mechanism of fluoroquinolone resistance among clinical P. aeruginosa isolated from Dhaka, Bangladesh, including alterations in target sites of the antimicrobial action. Laboratory collection of 53 P. aeruginosa were subjected to conventional cultural and biochemical characterization, followed by molecular identification using 16S rDNA sequencing. Susceptibility to ciprofloxacin and levofloxacin was tested by disc diffusion method followed by MIC assay. Resistant isolates were analyzed for mutation in their QRDR regions of gyrA and parC, and subjected to PCR detection of plasmid mediated quinolone resistance (PMQR) genes qnrA, qnrS and qnrB. Among the isolates, 28% were found to be resistant to both fluoroquinolones tested. All of the fluoroquinolone resistant isolates carried a single mutation in gyrA (Thr-83-Ile), while 20% carried a single parC mutation (Ser-87-Leu). Higher level of MIC was observed in isolates carrying alterations at both sites. None of the isolates harbored any PMQR genes investigated, suggesting that chromosomal mutations in QRDR regions to be the major contributing factor for quinolone resistance in P. aeruginosa under investigation.

Self-actuated microfluidic chiplet for two-stage multiplex nucleic acid amplification assay

Effective diagnosis of comorbidities and infectious diseases that present similar symptoms requires point-of-need assays capable of co-detecting and differentiating among multiple co-endemic pathogens to enable timely, precision medicine and effective control measures. We previously developed a two-stage isothermal amplification assay dubbed Penn-RAMP to address this need. Penn-RAMP's first stage comprises a recombinase polymerase amplification (RPA), which amplifies all targets of interest in a single reaction chamber for a short duration. The RPA amplicons are then aliquoted into multiple loop-mediated isothermal amplification (LAMP) reaction chambers, each customized with pre-dried primers to amplify a single target or a group of targets. To enable Penn-RAMP at the point of need, we describe here a self-actuated Penn-RAMP chiplet that accommodates the Penn-RAMP assay. Our chiplet employs temperature-controlled phase change valves and capillary valves to self-aliquot first-stage amplicons into multiple (five) second-stage reaction chambers and to seal these chambers. The functionality of our device is demonstrated by co-detecting plant pathogens. The analytical performance of our chiplet is comparable to that of the benchtop Penn-RAMP assay and surpasses that of standalone LAMP assays. Our self-actuated chiplet can be operated standalone with purified nucleic acids or as the downstream amplification module of a sample preparation cassette.

Detection of Chlamydia trachomatis and Neisseria gonorrhoeae (and Its Resistance to Ciprofloxacin): Validation of a Molecular Biology Tool for Rapid Diagnosis and Treatment

Background and Objectives: Neisseria gonorrhoeae and Chlamydia trachomatis can cause similar clinical syndromes and may coexist in infections. In emergency medicine, empirical treatment targeting both pathogens is often employed, potentially contributing to antibiotic resistance. Gonococcal resistance has emerged against first-line antimicrobials, necessitating prior testing for fluoroquinolone susceptibility. Certest Biotec developed two molecular diagnostic products for simultaneous detection: VIASURE C. trachomatis & N. gonorrhoeae Real-Time PCR Detection Kit and VIASURE Neisseria gonorrhoeae Ciprofloxacin-Resistant Real-Time PCR Detection Kit. To evaluate these products, clinical performance assessments were conducted at the Clinical Microbiology Laboratory of Miguel Servet University Hospital in Zaragoza, Spain. Results and Conclusions: Both VIASURE assays under study demonstrated high clinical sensitivity and specificity compared to reference molecular assays and Sanger sequencing. These kits offer an accurate diagnosis, facilitating appropriate treatment choices while addressing concerns about emerging antibiotic resistance. Methods: A total of 540 clinical samples from 540 patients already characterized as positive or negative for CT and NG by a molecular assay and by antibiotic susceptibility testing for ciprofloxacin using a concentration gradient diffusion method were used for the clinical evaluation. In cases where sensitivity results were unavailable, conventional PCR and Sanger sequencing were employed.

Promoting molecular diagnostic equity: assessing in-house real-time PCR for Neisseria gonorrhoeae in anal samples from MSM recruited in an outpatient setting in Morocco

Objectives

Gonorrhea is a prevalent sexually transmitted infection among men who have sex with men (MSM). In Morocco, the basic laboratory diagnosis of Neisseria gonorrhoeae (NG) is based on microscopy and, in some settings, on culture. However, no nucleic acid amplification test (NAAT) has been implemented for routine diagnosis of gonorrhoeae.The aim of this study is to assess the effectiveness of an in-house real-time PCR test for detecting N. gonorrhoeae DNA in anal swabs samples collected during an Integrated Behavioral and Biological survey.

Patients and methods

Samples from 245 MSM, recruited using a Respondent Driven Sampling, were collected and tested for NG infection using GeneXpert CT/NG assay (Cepheid, USA). An In-House real-time PCR technique targeting the pseudo gene porA was developed and used for a parallel investigation of the same infection. The reliability of the in-house RT-PCR was validated through tests of reproducibility, repeatability, limit of detection, and cross-reactivity with other bacteria. The intrinsic performance characteristics of the qRT-PCR were assessed, namely, the sensitivity, the specificity, the positive predictive value (PPV), and the negative predictive value (NPV). The GeneXpert CT/NG assay was adopted as a reference method.

Results

For N. gonorrhoeae detection, the in-house real-time PCR assay showed a sensitivity and specificity of 80% and 100%, respectively. The PPV of the assay was 100% and the NPV was 97.3%.

Conclusion

The in-house real-time PCR assay has high specificity and sensitivity, and it emerges as a promising approach for detecting N. gonorrhoeae in clinical specimens, particularly in decentralized settings such as regional laboratories.

Extra-genital Neisseria gonorrhoeae infections with genetic mutations conferring ciprofloxacin resistance among men who have sex with men and transgender women in Lima, Peru

BACKGROUND

The increasing prevalence of drug-resistant Neisseria gonorrhoeae (NG) infections has caused great concern. Ciprofloxacin remains the empiric antimicrobial recommended to treat NG infections in Peru disregarding the susceptibility profile of circulating NG strains. We report the prevalence of individuals infected with NG strains presenting mutations in the gyrA gene that confers ciprofloxacin resistance.

METHODS

We conducted a descriptive study assessing extragenital swab samples collected from a cohort of men who have sex with men and transgender women in Lima, Peru. Anal and pharyngeal NG positive swabs for Aptima Combo 2 assay (Hologic Inc., USA) were used for DNA extraction. We performed TaqMan real time PCR assays to detect a point mutation at codon Ser91 of the gyrase A (gyrA) gene.

RESULTS

From 156 individuals who had at least one positive sample for NG reported by the Aptima assay, 80 individuals had at least one amplified DNA for the gyrA gene. We found that 67 of them (84.0%) were infected with a gyrA-mutated NG strain at the Ser91 codon.

CONCLUSIONS

We report a high prevalence of gyrA mutation conferring ciprofloxacin resistance among individuals with extragenital NG infection. Empirical treatment of NG needs to be urgently updated in Peru in concordance with international guidelines.

Development of diagnostic tests for pathogen identification and detection of antimicrobial resistance on WHO global priority pathogens using modular real-time nucleic acid amplification test

BACKGROUND

Concerns regarding antimicrobial resistance (AMR) have resulted in the World Health Organization (WHO) designating so-called global priority pathogens (GPPs). However, little discussion has focused on the diagnosis of GPPs. To enable the simultaneous identification of pathogens and AMR, we developed a modular real-time nucleic acid amplification test (MRT-NAAT).

METHODS

Sequence-specific primers for each modular unit for MRT-NAAT pathogen identification and AMR sets were designed. The composition of the reaction mixture and the real-time PCR program were unified irrespective of primer type so to give MRT-NAAT modularity. Standard strains and clinical isolates were used to evaluate the performance of MRT-NAAT by real-time PCR and melting curve analysis. Probit analysis for the MRT-NAAT pathogen identification set was used to assess the limit of detection (LoD).

RESULTS

The MRT-NAAT pathogen identification set was made up of 15 modular units 109-199 bp in product size and with a T_ms of 75.5-87.5 °C. The LoD was < 15.548 fg/μL, and nine modular units successfully detected the target pathogens. The MRT-NAAT AMR set included 24 modular units 65-785 bp in product size with a T_ms of 75.5-87.5 °C; it showed high performance for detecting GPP target genes and variants.

CONCLUSIONS

MRT-NAAT enables pathogen identification and AMR gene detection and is time-effective. By unifying the reaction settings of each modular unit, the modularity where combinations of primers can be used according to need could be achieved. This would greatly help in reflecting the researcher's need and the AMR status of a certain region while successfully detecting pathogens and AMR genes.

Worryingly high prevalence of resistance-associated mutations to macrolides and fluoroquinolones in Mycoplasma genitalium among men who have sex with men with recurrent sexually transmitted infections

Background

Men who have sex with men (MSM) using pre-exposure prophylaxis (PrEP) recurrently infected with STIs are playing a pivotal role in contemporary Sexually transmitted infections (STI) epidemics. Our aim was to assess whether these individuals had more Mycoplasma genitalium ( M. genitalium) infections and more resistance to macrolides and fluoroquinolones of M. genitalium compared to those who were not recurrently infected with STIs.

Methods

The study was performed on 179 Belgian MSM PrEP users that were followed up for 18 months. STIs including M. genitalium were detected quarterly. Detection of resistance-associated mutations (RAMs) to macrolides and fluoroquinolones was performed via Sanger sequencing of the 23S rRNA gene and parC gene (conferring mutations at position 83/87 in ParC). Differences in M. genitalium positivity rate and presence of RAMs between both groups were assessed using mixed-effects logistic regression.

Results

A total of 91 new M. genitalium infections were detected among 70 participants. MSM experiencing recurrent STIs have significantly more M. genitalium infections compared to those without (11.7% vs. 4.7% OR: 2.69). Importantly, the prevalence of RAMs to macrolides (95.2% vs. 77.4%) and fluoroquinolones (35.7% vs. 12.9%) was much higher among individuals with recurrent STIs. The difference was only statistically significant for macrolides (OR 5.83, p = .036).

Conclusions

MSM recurrently infected with STIs play a central role in the emergence of antimicrobial resistance in M. genitalium. The use of macrolides and fluoroquinolones should preferably be minimized in this population in order to avoid further emergence of multi-resistant M. genitalium.

Single gene targeted nanopore sequencing enables simultaneous identification and antimicrobial resistance detection of sexually transmitted infections

OBJECTIVES

To develop a simple DNA sequencing test for simultaneous identification and antimicrobial resistance (AMR) detection of multiple sexually transmitted infections (STIs).

METHODS

Real-time PCR (qPCR) was initially performed to identify Neisseria gonorrhoeae (NG), Chlamydia trachomatis (CT), Mycoplasma genitalium (MG) and Trichomonas vaginalis (TV) infections among a total of 200 vulvo-vaginal swab samples from female sex workers in Ecuador. qPCR positive samples plus qPCR negative controls for these STIs were subjected to single gene targeted PCR MinION-nanopore sequencing using the smartphone operated MinIT.

RESULTS

Among 200 vulvo-vaginal swab samples 43 were qPCR positive for at least one of the STIs. Single gene targeted nanopore sequencing generally yielded higher pathogen specific read counts in qPCR positive samples than qPCR negative controls. Of the 26 CT, NG or MG infections identified by qPCR, 25 were clearly distinguishable from qPCR negative controls by read count. Discrimination of TV qPCR positives from qPCR negative controls was poorer as many had low pathogen loads (qPCR cycle threshold >35) which produced few specific reads. Real-time AMR profiling revealed that 3/3 NG samples identified had gyrA mutations associated with fluoroquinolone resistance, 2/10 of TV had mutations related to metronidazole resistance, while none of the MG samples possessed 23S rRNA gene mutations contributing to macrolide resistance.

CONCLUSIONS

Single gene targeted nanopore sequencing for diagnosing and simultaneously identifying key antimicrobial resistance markers for four common genital STIs shows promise. Further work to optimise accuracy, reduce costs and improve speed may allow sustainable approaches for managing STIs and emerging AMR in resource poor and laboratory limited settings.

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.

Genomic Analysis of the Predominant Strains and Antimicrobial Resistance Determinants Within 1479 Neisseria gonorrhoeae Isolates From the US Gonococcal Isolate Surveillance Project in 2018

BACKGROUND

The prevalence of Neisseria gonorrhoeae (GC) isolates with elevated minimum inhibitory concentrations to various antibiotics continues to rise in the United States and globally. Genomic analysis provides a powerful tool for surveillance of circulating strains, antimicrobial resistance determinants, and understanding of transmission through a population.

METHODS

Neisseria gonorrhoeae isolates collected from the US Gonococcal Isolate Surveillance Project in 2018 (n = 1479) were sequenced and characterized. Whole-genome sequencing was used to identify sequence types, antimicrobial resistance profiles, and phylogenetic relationships across demographic and geographic populations.

RESULTS

Genetic characterization identified that (1) 80% of the GC isolates were represented in 33 multilocus sequence types, (2) isolates clustered in 23 major phylogenetic clusters with select phenotypic and demographic prevalence, and (3) common antimicrobial resistance determinants associated with low-level or high-level decreased susceptibility or resistance to relevant antibiotics.

CONCLUSIONS

Characterization of this 2018 Gonococcal Isolate Surveillance Project genomic data set, which is the largest US whole-genome sequence data set to date, sets the basis for future prospective studies, and establishes a genomic baseline of GC populations for local and national monitoring.

In vitro antimicrobial effect and mechanism of action of plasma-activated liquid on planktonic Neisseria gonorrhoeae

Neisseria gonorrhoeae (Ng) is highly resistant to treatment, and there is an urgent need for new treatments to alleviate gonococcal resistance caused by antibiotic monotherapy. The antimicrobial effect and mechanism of plasma-activated liquid (PAL) on Ng were evaluated in this study. Upon PAL treatment, extensively analyses on cell culturability, metabolic capacity, intracellular reactive oxygen species (ROS),membrane integrity and nucleic acids for Ng were carried out and significant antimicrobial effects observed.PAL exerted antibacterial effect on Ng and induced bacterial death (6.71-log) following immersion for 30 min and treatment for 120 s. However, bacterial viability test revealed that after immersion in the same PAL, 10.17% of bacteria retained their metabolic capacity. This indicates that bacteria enter a physiological viable but non-culturable state to protect themselves from environmental stress. Confocal fluorescence microscopy and transmission electron microscopy demonstrated that PAL exerts bactericidal effect on Ng and disrupts its morphological structure. PAL may upregulate inflammatory factors and genes to modulate the resistance of Ng and affect the immune status of the host during infection.

Prevalence of Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma genitalium and Trichomonas vaginalis including relevant resistance-associated mutations in a single center in the Netherlands

PURPOSE

In this study, we report the prevalence of Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), Mycoplasma genitalium (MG) and Trichomonas vaginalis (TV) amongst clinical specimens of patients suspected for sexually transmitted infections received at our laboratory and in addition report the prevalence of resistance-associated mutations (RAM) for ciprofloxacin in NG and azithromycin and moxifloxacin in MG.

METHODS

All specimens received from December 2018 to May 2019 were tested for the four pathogens. In addition, the presence of RAM associated with resistance to ciprofloxacin in NG and to azithromycin and moxifloxacin in MG was determined by different real-time PCR assays on all NG- and MG-positive specimens.

RESULTS

CT was detected most often (267/2613, 10.2%), followed by MG (106/2592, 4.1%), NG (41/2613, 1.6%) and TV (10/2592, 0.4%) amongst all specimens. The prevalence of ciprofloxacin RAM in NG was 21.2%, and the prevalence of RAM in MG was 40.6% for azithromycin and 8.1% for moxifloxacin. Nearly all specimens containing moxifloxacin-resistant MG also contained azithromycin-resistant MG.

CONCLUSION

CT is found most often in our population followed by MG and NG. By using molecular assays to detect RAM supplementary to pathogen identification of NG and MG, optimal therapy can be advised.