Nucleic acid amplification testing for Neisseria gonorrhoeae: an ongoing challenge

Relative Cost and Infectious Days Averted Associated With Rapid Gonorrhea and Chlamydia Testing Among Men Who Have Sex With Men

BACKGROUND

Standard-of-care nucleic acid amplification tests (routine NAATs) for Neisseria gonorrhoeae (GC) and Chlamydia trachomatis (CT) can take several days to result and therefore delay treatment. Rapid point-of-care GC/CT NAAT (rapid NAAT) could reduce the time to treatment and therefore onward transmission. This study evaluated the incremental cost per infectious day averted and overall cost of implementation associated with rapid compared with routine NAAT.

METHODS

Prospective sexually transmitted infection (STI) treatment data from men who have sex with men and transgender women in San Diego who received rapid NAAT between November 2018 and February 2021 were evaluated. Historical time from testing to treatment for routine NAAT was abstracted from the literature. Costs per test for rapid and routine NAAT were calculated using a micro-costing approach. The incremental cost per infectious day averted comparing rapid to routine NAAT and the costs of rapid GC/CT NAAT implementation in San Diego Public Health STI clinics were calculated.

RESULTS

Overall, 2333 individuals underwent rapid NAAT with a median time from sample collection to treatment of 2 days compared with 7 to 14 days for routine NAAT equating to a reduction of 5 to 12 days. The cost of rapid and routine GC/CT NAAT was $57.86 and $18.38 per test, respectively, with a cost-effectiveness of between $2.43 and $5.82 per infectious day averted. The incremental cost of rapid NAAT improved when at least 2000 tests were performed annually.

CONCLUSIONS

Although rapid GC/CT NAAT is more expensive than routine testing, the reduction of infectious days between testing and treatment may reduce transmission and provide improved STI treatment services to patients.

Development of advanced control material for reverse transcription-mediated bacterial nucleic acid amplification tests

Detection of bacterial RNA by nucleic acid amplification tests (NAATs), such as reverse transcription PCR (RT-PCR) and reverse transcription loop-mediated isothermal amplification (RT-LAMP), offers distinct advantages over DNA-based methods. However, such assays also present challenges in ascertaining positive and internal control material that can reliably monitor success over all phases of testing (bacterial lysis, nucleic acid recovery, reverse transcription, amplification, and signal detection): since they are unable to distinguish between amplification of bacterial RNA transcripts and the DNA templates that encode them, using intact organisms as controls can inform cell lysis but not successful detection of RNA. We developed a control strategy for RNA-based bacterial NAATs that allows ready discrimination of RNA from DNA templates using self-splicing bacterial introns, such that those nucleic acids ultimately encode different sequences. We engineered two vectors encoding synthetic transgenes based on this principle, one that is active in the Gram-negative bacterium Escherichia coli and one that functions in both E. coli and the Gram-positive organism Staphylococcus aureus. We subsequently designed RT-LAMP assays that either target RNA and DNA from transgenic organisms or target RNA exclusively and demonstrated the specificity of amplification using purified nucleic acids. Using multiplex fluorescent RT-LAMP of heat-lysed specimens, we showed the practicality of deploying such transgenic organisms as an internal control to ascertain sample integrity and assay performance during clinical diagnostic testing. Our approach has broad utility for RNA-based bacterial NAATs, especially point-of-care assays and other applications where nucleic acids are nonspecifically liberated for testing.

Analytical and clinical validation of a multiplex PCR assay for detection of Neisseria gonorrhoeae and Chlamydia trachomatis including simultaneous LGV serotyping on an automated high-throughput PCR system

For effective infection control measures for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG), a reliable tool for screening and diagnosis is essential. Here, we aimed to establish and validate a multiplex PCR assay on an automated system using a dual-target approach for the detection of CT/NG and differentiation between lymphogranuloma venereum (LGV) and non-LGV from genital and extra-genital specimens. Published primer/probe sets (CT: pmpH, cryptic plasmid; NG: porA, opa) were modified for the cobas 5800/6800/8800. Standards quantified by digital PCR were used to determine linearity and lower limit of detection (LLoD; eSwab, urine). For clinical validation, prospective samples (n = 319) were compared with a CE-marked in vitro diagnostics (CE-IVD) assay. LLoDs ranged from 21.8 to 244 digital copies (dcp)/mL and 10.8 to 277 dcp/mL in swab and urine, respectively. A simple linear regression analysis yielded slopes ranging from -4.338 to -2.834 and Pearson correlation coefficients from 0.956 to 0.994. Inter- and intra-run variability was <0.5 and <1 cycle threshold (ct), respectively. No cross-reactivity was observed (n = 42). Clinical validation showed a sensitivity of 94.74% (95% confidence interval (CI): 87.23%-97.93%) and 95.51% (95% CI: 89.01%-98.24%), a specificity of 99.59% (95% CI: 97.71%-99.98%) and 99.57% (95% CI: 97.58%-99.98%), positive predictive values of 89.91% (estimated prevalence: 3.7%; 95% CI: 80.91%-95.6%) and 88.61% (estimated prevalence: 3.4%; 95% CI: 80.18%-94.34%), and negative predictive values of 99.81% (95% CI: 98.14%-100%) and 99.85% (95% CI: 98.14%-100%) for the detection of CT and NG, respectively. In conclusion, we established a dual-target, internally controlled PCR on an automated system for the detectiwon of CT/NG from genital and extra-genital specimens. Depending on local regulations, the assay can be used as a screening or a confirmatory/typing assay.IMPORTANCEChlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) represent a major global health burden, with the World Health Organization estimating that >128 million and >82 million people, respectively, were newly infected in 2020. For effective infection control measures, a reliable tool for sensitive diagnosis and screening of CT/NG is essential. We established a multiplex PCR assay for the detection of CT/NG and simultaneous discrimination between lymphogranuloma venereum (LGV) and non-LGV strains, which has been validated for genital and extra-genital specimens on a fully automated system. To increase assay sensitivity, a dual-target approach has been chosen for both pathogens. This strategy reduces false-positive results in oropharyngeal swabs due to the detection of commensal N. species that may harbor NG DNA fragments targeted in the PCR due to horizontal gene transmission following previous infection. In sum, the established assay provides a powerful tool for use as either a screening/diagnostic or a typing/confirmatory assay.

Rapid Minimum Inhibitory Concentration (MIC) Analysis Using Lyophilized Reagent Beads in a Novel Multiphase, Single-Vessel Assay

Antimicrobial resistance (AMR) is a global threat fueled by incorrect (and overuse) of antibiotic drugs, giving rise to the evolution of multi- and extreme drug-resistant bacterial strains. The longer time to antibiotic administration (TTA) associated with the gold standard bacterial culture method has been responsible for the empirical usage of antibiotics and is a key factor in the rise of AMR. While polymerase chain reaction (PCR) and other nucleic acid amplification methods are rapidly replacing traditional culture methods, their scope has been restricted mainly to detect genotypic determinants of resistance and provide little to no information on phenotypic susceptibility to antibiotics. The work presented here aims to provide phenotypic antimicrobial susceptibility testing (AST) information by pairing short growth periods (~3-4 h) with downstream PCR assays to ultimately predict minimum inhibitory concentration (MIC) values of antibiotic treatment. To further simplify the dual workflows of the AST and PCR assays, these reactions are carried out in a single-vessel format (PCR tube) using novel lyophilized reagent beads (LRBs), which store dried PCR reagents along with primers and enzymes, and antibiotic drugs separately. The two reactions are separated in space and time using a melting paraffin wax seal, thus eliminating the need to transfer reagents across different consumables and minimizing user interactions. Finally, these two-step single-vessel reactions are multiplexed by using a microfluidic manifold that allows simultaneous testing of an unknown bacterial sample against different antibiotics at varying concentrations. The LRBs used in the microfluidic system showed no interference with the bacterial growth and PCR assays and provided an innovative platform for rapid point-of-care diagnostics (POC-Dx).

Challenges and Solutions to STI Control in the Era of HIV and STI Prophylaxis

PURPOSE OF REVIEW

This article reviews current efforts to control bacterial sexually transmitted infections (STIs) among HIV pre-exposure prophylaxis (PrEP) users and outlines the opportunities and challenges to controlling STIs within HIV PrEP programs.

RECENT FINDINGS

The incidence of STIs continues to rise globally especially among HIV PrEP users, with an estimated 1 in 4 PrEP users having a curable bacterial STI. STIs and HIV comprise a syndemic needing dual interventions. The majority of STIs are asymptomatic, and when testing is available, many STIs occur in extragenital sites that are missed when relying on urine testing or genital swabs. Optimal testing and treatment, including testing for antimicrobial resistance, pose difficulties in high income countries and is essentially non-existent in most low- and middle-income countries. Novel STI primary prevention strategies, like doxycycline post-exposure prophylaxis (PEP) for STI prevention, have proven to be highly efficacious in some populations. A few jurisdictions have issued normative guidelines and position statements for doxycycline PEP; however, clinical standards for implementation and data on public health impact are limited. STI incidence rates are high and rising in sexually active populations. Sexual health programs should leverage the expansion of HIV PrEP delivery services to integrate STI testing, surveillance, and novel STI prevention services.

Disseminated Gonococcal Infection With Dermatitis-Arthritis Syndrome

Gonorrhea is a sexually transmitted infection caused by gram-negative diplococci, Neisseria gonorrhoeae. Disseminated gonorrhea is diagnosed infrequently, partly due to low suspicion at the time of presentation, and at times, due to overlapping symptoms associated with non-infectious conditions like systemic lupus erythematosus (SLE). In this article, we present a 42-year-old sexually active female with knee pain and swelling, fever, and rash. Knee aspirate showed the presence of monosodium urate crystals, and the synovial culture grew gram-negative diplococci, requiring multiple joint washouts. The urine nucleic acid amplification test (NAAT) was indeterminate. She was treated with high-dose intravenous ceftriaxone for one week post-joint washout with rapid improvement in her condition and resolution of the rash.

PivNG primers and probes set used in the cobas omni Utility Channel is a reliable supplemental test for detection of Neisseria gonorrhoeae in oropharyngeal, urogenital and rectal specimens collected in cobas PCR Media

OBJECTIVE

To evaluate the clinical performance of the novel PivNG primers and probes set (PivNG test) used in the cobas omni Utility Channel for supplemental testing of Neisseria gonorrhoeae (NG).

METHODS

Oropharyngeal, urogenital and rectal samples were self-collected during routine testing at Barts Health sexual health clinics, London, UK. Samples were tested by the cobas CT/NG test and PivNG cobas omni Utility Channel test on cobas 6800/8800 Systems. Supplemental testing was carried out with the Xpert CT/NG test. PivNG overall percent agreements, positive percent agreements (PPAs)/negative percent agreements (NPAs) and positive/negative predictive values were calculated for each sample type. Microscopy and/or culture data were included for a randomised subset of concordant/discordant results, and a composite reference standard (cobas CT/NG, Xpert CT/NG and culture results) adjusted for partial verification bias was used to determine PivNG PPA and NPA.

RESULTS

Of 447 evaluable samples with valid results from all three assays (cobas CT/NG, PivNG and Xpert CT/NG), 288 (64.4%) were NG-positive by both PivNG and cobas CT/NG; 117 (26.2%) were NG-negative in both tests; and 42 (9.4%) had discordant results (with NG-negative supplementary Xpert) CT/NG results in 40/42 instances). Of 19 PivNG/Xpert CT/NG-discordant samples, 11 were confirmed NG-positive by microscopy and/or culture results. PivNG PPA and NPA were 100% and 91% for oropharyngeal swabs, 100% and 100% for vaginal swabs, 100% and 100% for male urine samples, and 100% and 97% for rectal swabs, respectively, compared with the partially adjusted composite reference standard.

CONCLUSIONS

PivNG is a reliable supplementary test with high sensitivity for confirming NG infection when used in conjunction with the cobas CT/NG test and samples collected in cobas PCR Media. Moreover, the PivNG test offers a convenient, high-throughput solution for supplemental NG testing of various sample types, with the potential to reduce the number of indeterminate reports.

A Review of Recent Advances in Our Understanding of Neisseria gonorrhoeae

Gonorrhoea is an infection caused by bacteria that has recently been detected in humans and typically spreads through sexual contact. It leads to significant health issues in both prosperous and impoverished countries, culminating in significant yearly expenditures for diagnosis and treatment. Young adults who are involved in unprotected sexual activity and are promiscuous are particularly susceptible to gonorrhoea. It has been estimated that approximately 86.95 million individuals globally acquire the virus each year. Gonorrhoea has been reported to affect a variety of body parts, including the cervix in women and the urethra in males, as well as other areas such as the eyes, anus, throat, and, on rare occasions, the joints. It is momentarily the second most frequently reported sexually transmitted disease (STD) by the Centers for Disease Control and Prevention (CDC), trailing only chlamydia. Since the early 2000s, gonorrhoea cases have been on the rise globally, especially across many European nations, with an elevated prevalence among populations at higher risk of getting sexually transmitted infections (STIs), such as men who have sex with men and young heterosexual individuals. The fundamental objectives of gonorrhoea management techniques are to prevent, identify, and cure infections in patients and their partners in addition to minimizing the disease's stigma. It additionally involves monitoring antibiotic resistance and treatment failures, and it also involves advocating appropriate antimicrobial medication usage and stewardship.

The changing epidemiology of Neisseria gonorrhoeae genogroups and antimicrobial resistance in Queensland, Australia, 2010-15: a case series analysis of unique Neisseria gonorrhoeae isolates

BACKGROUND

Neisseria gonorrhoeae (NG) can lead to serious reproductive and sexual health outcomes, and the annual number of NG notifications in Australia increased steadily from 10329 in 2010 to 29549 by 2020. Australian populations most affected are urban men who have sex with men and First Nations peoples living in remote areas, and a resurgence in urban heterosexuals has been observed since 2012.

METHODS

A case series analysis of Queensland NG isolates (2010-15) exploring temporal trends and antimicrobial resistance by demographic and geographic distribution and genotype was performed. Proportions describe age, sex, strain, genogroup (NG multi-antigen sequence typing), region, swab site, antimicrobial sensitivity and isolate rates per 100000 population. Dominant genogroups were identified.

RESULTS

Among 3953 isolates, the median age was 25years (IQR 20-34years) and most (n =2871/3915, 73%) were men. Brisbane city (68.8) and Far North Queensland (54.1) excluding Cairns showed the highest rates. Forty-six genogroups were documented, seven (G2992, G6876, G1415, G4186, G5, G1407 and G6937) comprised half of all isolates. The predominant male genogroup was G2992 (16%), and G6876 (20%) for females; G5 was predominantly male from 2010 to 2011, but equal in both sexes from 2012 to 2015.

CONCLUSION

Considerable temporal, geographical and demographical diversity was observed in Queensland NG isolates, which has public health implications. Certain genogroups are more transient than others, and evidence suggests bridging from male-dominant networks to heterosexual networks. Molecular surveillance can enhance tracking the epidemiology and movement of NG in Australia, highlighting the necessity of genotyping to expose potentially prevalent strains circulating in undetected or underrepresented networks by current screening methods.

The prevalence of Mycoplasma genitalium (MG) and Trichomonas vaginalis (TV) at testing centers in Belgium, Germany, Spain, and the UK using the cobas TV/MG molecular assay

Mycoplasma genitalium (MG) and Trichomonas vaginalis (TV) can lead to long-term sequelae in males and females; however, global prevalence data vary between geographical regions, as these sexually transmitted infections are not included in routine screening. The objective of this study was to use the cobas^® TV/MG assay to assess the point prevalence of TV and MG in specimens from men and women over a broad European geographical area. Urine, vaginal, endocervical, and rectal samples were collected from patients aged ≥ 18 years receiving Chlamydia trachomatis (CT) and/or Neisseria gonorrhoeae (NG) screening as per local standard of care at sites in Belgium, Germany, Spain, and the UK (Wales). Remnant samples were assessed using the cobas TV/MG assay. Analysis of 2795 samples showed that MG prevalence varied slightly across female sample types (range: 1.7-5.8%; p = 0.0042). MG prevalence was higher in male rectal samples (12.5%) than in male urine samples (3.9%; p < 0.0001). TV prevalence was low in male (0.8%; 12/1535) and female (1.3%; 16/1260) samples across all sites. Co-infection of TV/MG with CT or NG was 10.0% (19/190) and 9.6% (7/73), respectively, in both male and female samples. MG and TV prevalence rates were comparable to the published literature in Europe. MG prevalence was highest in male rectal samples; as rectal testing is an off-label use of the cobas TV/MG assay, the clinical utility of this assay for rectal testing should be further investigated.

Near-infrared spectroscopy as a feasible method for the differentiation of Neisseria gonorrhoeae from Neisseria commensals and antimicrobial resistant from susceptible gonococcal strains

Rapid and cost-effective diagnosis of Neisseria gonorrhoeae (NG) are important measures for the control and management of gonococcal infection. Current diagnostic tools such as nucleic acid amplification tests and bacterial culture are not feasible in many resource-poor settings, and so syndromic patient management is commonplace. Alternative cost-effective diagnostic tools are therefore needed. Here, we sought to explore the utility and feasibility of Near Infrared Spectroscopy (NIRS) to (1) identify and differentiate NG from Neisseria commensals and (2) to differentiate fully susceptible NG from resistant NG. NIRS correctly classified NG from Neisseria commensals (R²= 0.89; SECV 0.164) and to a lesser capacity, susceptible NG from resistant (R² = 0.60; SECV 0.32). To the best our knowledge, this is the first proof of concept study in the field. Further evaluations are now warranted to enhance capacity and accuracy of this diagnostic approach.

Rapid Detection of Neisseria gonorrhoeae Genomic DNA Using Gold Nanoprobes Which Target the Gonococcal DNA Uptake Sequence

The rapid spread of antimicrobial resistant Neisseria gonorrhoeae continues to pose a serious threat to global health. To successfully treat and control gonococcal infections, rapid diagnosis is critical. Currently, nucleic acid amplification tests are the recommended diagnostic, however, these are both technically demanding and time consuming, making them unsuitable for resource-poor clinics. Consequently, there is a substantial need for an affordable, point-of-care diagnostic to use in these settings. In this study, DNA-functionalised gold nanoparticles (gold nanoprobes), with the ability to specifically detect the DNA Uptake Sequence (DUS) of Neisseria gonorrhoeae, were prepared. Using complementary annealing, the gold nanoprobes were shown to hybridise to genomic gonococcal DNA, causing a significant shift in their salt stability. By exploiting the shift in nanoprobe stability under the presence of target DNA, a solution-based colorimetric diagnostic for gonococcal DNA was prepared. Detection of purified genomic DNA was achieved in under 30 minutes, with a detection limit of 15.0 ng. Significantly, testing with DNA extracted from an off-target control organism suggested specificity for Neisseria. These results highlight the potential of DUS-specific gold nanoprobes in the rapid point-of-care diagnosis of gonococcal infections.

Pediatric Emergency Department Testing for Gonorrhea and Chlamydia in Children

OBJECTIVE

This study aimed to describe trends in the utilization of nucleic acid amplification (NAAT) testing for gonorrhea and chlamydia in US pediatric emergency departments. Nucleic acid amplification has been recommended over genital culture by the American Academy of Pediatrics and Centers for Disease Control and Prevention for children evaluated for sexual abuse.

METHODS

We conducted a multicenter study of children aged 12 months to 11 years tested for gonorrhea and chlamydia between 2004 and 2018 at 22 hospitals in the Pediatric Health Information System. We included patients diagnosed with maltreatment concerns and/or genitourinary (GU) symptoms. The primary outcome was prevalence of testing with NAAT, culture, or both. We analyzed groups based on patient sex, as well as diagnoses of maltreatment versus GU symptoms.

RESULTS

A total of 36,312 visits were analyzed. Visits were 73.4% girls and 26.6% boys. During the study period, there was an increase in use of NAAT-only testing for girls (49.3% to 94.3%; P < 0.001) and boys (54.5% to 96.1%; P < 0.001). There was a decrease in use of culture alone for girls (40% to 1.6%; P < 0.001) and boys (38.7% to 0.8%; P < 0.001). Use of both tests in the same encounter was higher among children diagnosed with maltreatment than GU symptoms, regardless of sex (P < 0.001).

CONCLUSIONS

Over a 14-year period, downtrend of culture use with increase in NAAT was observed, suggesting general adherence to evidence-based guidelines. Almost 10% of children diagnosed with maltreatment continued to be tested with culture. This could indicate provider concerns regarding test accuracy, legal admissibility, or lack of test availability.

Time to Clearance of Neisseria gonorrhoeae RNA at the Pharynx following Treatment

The number of days until pharyngeal Neisseria gonorrhoeae nucleic acid amplification test (NAAT) results become negative after treatment remains unknown. Between March 2019 and April 2021, we enrolled men who have sex with men (MSM) who had a clinical positive pharyngeal N. gonorrhoeae Aptima Combo 2 test result but had not yet been treated in a prospective longitudinal cohort study. MSM were enrolled on their day of treatment and self-collected daily pharyngeal specimens for 21 days at home. We used Kaplan-Meier estimates to determine the median time to clearance and the >95% time to clearance and the log rank test for equality to evaluate factors associated with time to clearance. Sixty-four men were enrolled in the study. Analyses excluded 8 men (12.5%) who were N. gonorrhoeae negative by NAAT at enrollment and 11 (17%) who failed to return any home-collected specimens. Among the 45 men included in the analysis, the median time to N. gonorrhoeae NAAT clearance was 3 days (95% confidence interval [CI], 2 to 5 days). Time to clearance for >95% of the cohort was 12 days (95% CI, 10 days to an undefined time). Men with a history of N. gonorrhoeae infection cleared faster than men without such history (8 days versus 17 days for >95% time to clearance; P = 0.03). In the absence of reexposure, positive N. gonorrhoeae Aptima Combo 2 assay results obtained prior to 12 days after treatment are likely false-positive results.

Molecular Detection of Sexually Transmitted Infections in Women with and without Human Papillomaviruses Infection Who Referred to Tehran West Hospitals in Iran

Background

According to the studies, many pathogens function as cofactors interacting with Human papillomavirus in the development of pre-cancer or cancer of the cervix. The aim of this study was to investigate the prevalence rate of Sexually Transmitted Infections (STIs) pathogens including Mycoplasma hominis, Ureaplasma urealyticum, Chlamydia trachomatis, Neisseria gonorrhoeae, Gardnerella vaginalis, and Streptococcus agalactiae in people with HPV and without HPV infection, and frequency rate of these pathogens in high and low risk of HPV.

Methods

Cervical samples of 280 women who referred to Tehran west hospitals in Iran, between 2019 and 2020, were collected. After DNA extraction of samples, identification of HPV and genotyping was performed, and then, to detect each microorganism, the PCR was carried out with specific primers. Finally, the results were analyzed using descriptive statistics tests.

Results

The mean age of patients was 37 years. Two groups of patients were identified based on positivity or negativity of HPV. In HPV-positive group (118 cases), the prevalence of U. urealyticum, M. hominis, N. gonorrhoeae, G. vaginalis, and S. agalactiae was 38 (13%), 7 (62%), 5.93%, 19.49%, 0.84% respectively. In HPV-negative group (162 cases), rate of infection with U. urealyticum, M. hominis, N. gonorrhoeae, G. vaginalis, and S. agalactiae was 29.62%, 6.17%, 3.08%, 16.04%, 0.61% respectively. Among the two groups, there was only 1 patient with C. trachomatis (0.84%), seen in HPV-positive group.

Conclusion

In this study no significant association was found between HPV and bacteria such as G. vaginalis and S. agalactiae, and it was found that C. trachomatis, and especially N. gonorrhoeae are strongly associated with HPV infection.

Neisseria gonorrhoeae: An Unexpected Cause of Polyarthritis and Meningitis

Neisseria gonorrhoeae, a gram-negative coccus, is a major cause of morbidity among sexually active individuals. Hematogenous spread of N gonorrhoeae from the initial site of infection is thought to occur in only 0.5% to 3% of infected patients. Disseminated gonococcal infections can rarely lead to serious sequelae, such as endocarditis or meningitis. In this article, we present a case that demonstrates a rare finding of disseminated gonococcal infection leading to N gonorrhoeae meningitis, complicated by hydrocephalus. The patient in this case initially presented with intermittent polyarthralgias for two years and later developed a rash. Cultures from blood and joint aspirate were negative. Urine nucleic acid amplification test for N gonorrhoeae was also negative. He was initially started on steroids for what was believed at first to be an autoimmune polyarthritis. The patient later developed acute encephalopathy. Head imaging revealed hydrocephalus. Cerebrospinal fluid analysis was consistent with bacterial meningitis. Blood, joint, and mucosal membrane studies failed to isolate the causative organism, but his cerebrospinal fluid grew N gonorrhoeae. He was treated with high-dose intravenous ceftriaxone for two weeks with rapid improvement in his mental status and resolution of his joint pains and rash.

Biodiagnostics in an era of global pandemics-From biosensing materials to data management

The novel corona virus SARS‐CoV‐2 (COVID‐19) has exposed the world to challenges never before seen in fast diagnostics, monitoring, and prevention of the outbreak. As a result, different approaches for fast diagnostic and screening are made and yet to find the ideal way. The current mini‐review provides and examines evidence‐based innovative and rapid chemical sensing and related biodiagnostic solutions to deal with infectious disease and related pandemic emergencies, which could offer the best possible care for the general population and improve the approachability of the pandemic information, insights, and surrounding contexts. The review discusses how integration of sensing devices with big data analysis, artificial Intelligence or machine learning, and clinical decision support system, could improve the accuracy of the recorded patterns of the disease conditions within an ocean of information. At the end, the mini‐review provides a prospective on the requirements to improve our coping of the pandemic‐related biodiagnostics as well as future opportunities.

SERS-based sensor for the detection of sexually transmitted pathogens in the male swab specimens: A new approach for clinical diagnosis

The surface-enhanced Raman scattering (SERS) has been widely tested for its usefulness in microbiological studies, providing many information-rich spectra which are a kind of 'whole-organism fingerprint' and enabling identification of bacterial species. Here we show, previously not considered, the comprehensive SERS-chemometric analysis of five bacterial pathogens, namely Neisseria gonorrhoeae, Mycoplasma hominis, Mycoplasma genitalium, Ureaplasma urealyticum, and Haemophilus ducreyi, all being responsible for sexually transmitted diseases (STDs). In the designed biosensor, the direct, intrinsic format of the spectroscopic analysis was adopted for the SERS-based screening of gonorrhea and chlamydiosis due to vibrational analysis of men's urethra swabs. Our experiments demonstrated that the applied method enables identification the individual species of the Neisseria genus with high accuracy. In order to differentiate the sexually transmitted pathogens and to classify the clinical samples of male urethra swabs, three multivariate methods were used. In the external validation the created models correctly classified the men's urethra swabs with prediction accuracy reaching 89% for SIMCA and 100% for PLS-DA. As a result, the developed protocol enables: (i) simple and non-invasive analysis of clinical samples (the collection of urethra swabs specimens could be carried out at different points of care, such as doctor's office); (ii) fast analysis (<15 min); (iii) culture-free identification; (iv) sensitive and reliable SERS-based diagnosis of STD. The simplicity of the developed detection procedure, supported by high sensitivity, reproducibility, and specificity, open a new path in the improvement of the point-of-care applications.

A pilot study to determine Neisseria gonorrhoeae-Chlamydia trachomatis coinfection rates in symptomatic patients attending STI Clinics, New Delhi, India

BACKGROUND

Neisseria gonorrhoeae and Chlamydia trachomatis are the two most prevalent bacterial sexually transmitted infections. For over two decades, treatment guidelines have recommended empirical co-treatment for N.gonorrhoeae and C.trachomatis as symptoms overlap and co-infection is common. Studies from India estimating the same are limited and mostly based on conventional techniques.

AIM AND OBJECTIVE

The aim of this study was to determine the frequency of N.gonorrhoeae and C.trachomatis coinfection using nucleic acid amplification tests. Further, we assessed the utility of pus cell estimation in Gram stained smears as a screening tool for inclusion of samples for molecular diagnosis.

METHODS

This was a prospective study conducted at two tertiary care hospitals; 100 patients (55 females and 45 males) with genitourinary discharge attending STI clinics were recruited, and endocervical or urethral swabs were collected. PCRs for N.gonorrhoeae and C.trachomatis were put up. In addition, microscopy and culture for gonococcus was performed followed by antimicrobial susceptibility testing. Statistical analysis was performed using the SPSS 16 software.

RESULTS

N.gonorrhoeae infection was more common than C.trachomatis. A total of 14 patients were positive by PCR (9 males and 5 females) for gonococcus. However, culture was positive only in 8 male patients. PCR for C.trachomatis was positive in 9 (4 males and 5 females) and the co-infection rate was 5%. The sensitivity and negative predictive value of pus cell estimation was 100% for males and 64% and 94.6% respectively for females. All isolates were susceptible to extended spectrum cephalosporins and azithromycin.

LIMITATION

The sample size of the study was small.

CONCLUSION

Frequency of N.gonorrhoeae/C.trachomatis coinfection in symptomatic STI patients is low. Coinfection is considerably overestimated and necessary confirmation of etiological diagnosis could reduce widespread empirical administration of broad-spectrum antibiotics.

HIV, Sexually Transmitted Infections and Sexual Practices Among Male Sex Workers Attending a Sexual Health Clinic in Melbourne, Australia: 2010 to 2018

BACKGROUND

There are limited data on HIV/sexually transmitted infection (STI) positivity and sexual practices among male sex workers (MSWs) both globally and particularly in Australia. This study aimed to explore demographic characteristics, sexual practices, and HIV/STI positivity among MSWs attending a sexual health clinic in Melbourne.

METHODS

We analyzed computerized medical records of all first-visit consultations with men 18 years or older who self-identified as current sex workers and attended the Melbourne Sexual Health Centre (MSHC) between 2010 and 2018. Demographic data, sexual behavior data, and laboratory results for HIV, syphilis, chlamydia, and gonorrhea were collected as part of routine clinical care at Melbourne Sexual Health Centre.

RESULTS

Of the 190 MSWs included in the analysis, the median age was 28 years (interquartile range, 23-30 years), 30.4% (52/171) reported having condomless penile-anal sex with their clients, and 59.6% (102/171) reported having condomless penile-oral sex with their clients since their last STI screening. Most (85.6%) MSWs had noncommercial sex partners, including 56.5% with male partners only, 30.6% with female partners only, and 12.9% with both. Approximately half of MSWs used condoms consistently with noncommercial sex partners (regardless of partner gender). The positivity for incident HIV was 1.7% (95% confidence interval [CI], 0.0%-5.0%), that for syphilis was 6.1% (95% CI, 2.6%-10.5%), that for chlamydia was 9.6% (95% CI, 5.6%-14.9%), and that for gonorrhea was 10.8% (95% CI, 4.4%-20.9%). Male sex workers who exclusively had sex with women had a lower any HIV/STI positivity (0%) compared with MSW who had sex with men (15.7%; P = 0.013).

CONCLUSIONS

Male sex workers fall into 2 groups: those who had male clients and/or noncommercial partners who have a relatively high HIV/STI positivity and those who only had female partners or clients whose HIV/STI positivity is low. Both have a high proportion of condomless sex with clients and noncommercial sex partners. Strategies to increase condom use during sex work are needed.

The attachment of a DNA-binding Sso7d-like protein improves processivity and resistance to inhibitors of M-MuLV reverse transcriptase

Reverse transcriptases (RTs) are a standard tool in both fundamental studies and diagnostics. RTs should possess elevated temperature optimum, high thermal stability, processivity and tolerance to contaminants. Here, we constructed a set of chimeric RTs, based on the combination of the Moloney murine leukaemia virus (M-MuLV) RT and either of two DNA-binding domains: the DNA-binding domain of the DNA ligase from Pyrococcus abyssi or the DNA-binding Sto7d protein from Sulfolobus tokodaii. The processivity and efficiency of cDNA synthesis of the chimeric RT with Sto7d at the C-end are increased several fold. The attachment of Sto7d enhances the tolerance of M-MuLV RT to the most common amplification inhibitors: NaCl, urea, guanidinium chloride, formamide, components of human whole blood and human blood plasma. Thus, fusing M-MuLV RT with an additional domain results in more robust and efficient RTs.

Evaluation of the ResistancePlus GC (beta) assay: a commercial diagnostic test for the direct detection of ciprofloxacin susceptibility or resistance in Neisseria gonorrhoeae

OBJECTIVES

To evaluate the performance of the ResistancePlus GC (beta) assay for the simultaneous detection of Neisseria gonorrhoeae and gyrA S91 markers of resistance (S91F) and susceptibility (WT) to ciprofloxacin, from both clinical specimens and isolates.

METHODS

Performance was assessed on several sample banks, including N. gonorrhoeae isolates (n = 822), non-gonococcal isolates (n = 110), N. gonorrhoeae-positive clinical specimens (n = 402) and N. gonorrhoeae-negative specimens (n = 290). Results were compared with previous testing data, including S91 genotyping and phenotypic resistance profiles.

RESULTS

Overall, the assay demonstrated 100% sensitivity for N. gonorrhoeae detection in clinical isolates. For gyrA S91 mutation detection in clinical isolates, the assay showed 100% sensitivity/specificity compared with the genotype, and >99%/>97% sensitivity/specificity when compared with phenotype. For positive clinical specimens, the assay demonstrated >96% sensitivity for N. gonorrhoeae detection and 100% sensitivity/specificity for gyrA S91 mutation detection. The assay demonstrated >99% specificity for N. gonorrhoeae detection against non-gonococcal isolates and 100% specificity for negative clinical specimens.

CONCLUSIONS

The ResistancePlus GC (beta) assay is suitable for the detection of N. gonorrhoeae and gyrA markers associated with resistance/susceptibility to ciprofloxacin directly in clinical samples. This assay could be implemented for the individualized treatment of gonorrhoea infections as well as to enhance current antimicrobial resistance surveillance methods.

The frontiers of addressing antibiotic resistance in Neisseria gonorrhoeae

The sexually transmitted infection gonorrhea, caused by the Gram-negative bacterium Neisseria gonorrhoeae, can cause urethritis, cervicitis, and systemic disease, among other manifestations. N. gonorrhoeae has rapidly rising incidence along with increasing levels of antibiotic resistance to a broad range of drugs including first-line treatments. The rise in resistance has led to fears of untreatable gonorrhea causing substantial disease globally. In this review, we will describe multiple approaches being undertaken to slow and control this spread of resistance. First, a number of old drugs have been repurposed and new drugs are being developed with activity against Neisseria gonorrhoeae. Second, vaccine development, long an important goal, is advancing. Third, new diagnostics promise rapid detection of antibiotic resistance and a shift from empiric to tailored treatment. The deployment of these new tools for addressing the challenge of antibiotic resistance will require careful consideration to provide optimal care for all patients while extending the lifespan of treatment regimens.

Evaluation of the prevalence of sexually transmitted bacterial pathogens in Northern Cyprus by nucleic acid amplification tests, and investigation of the relationship between these pathogens and cervicitis

Objective:

To evaluate the prevalence of pathogens, Chlamydia trachomatis, Neisseria gonorrhea and Trichomonas vaginalis, Mycoplasma hominis, Mycoplasma genitalium, Ureaplasma urealyticum, and Ureaplasma parvum in women via multiplex-polymerase chain reaction (PCR)-deoxyribonucleic acid (DNA).

Materials and Methods:

Cervical swabs of 273 women in reproductive age who underwent gynecologic examination in our outpatient clinic were evaluated using the multiplex-PCR-DNA method. The presence of cervicitis, contraceptive methods, marital status, and the number of partners were evaluated.

Results:

One hundred six (39%) of the 273 women had at least one bacterium, 25 women (9.8%) had two bacteria, and three women (1%) had three bacteria. U. urealyticum was the most frequently encountered bacterium (13.9%), followed by M. hominis (12.8%), U. parvum (12.4%), C. trachomatis (5.4%), M. genitalium (2.9%), N. gonorrhea (2.5%), and T. vaginalis (0.3%). Bacterial infection was detected more frequently in women aged <25 years, single, who had multiple partners, and clinically diagnosed with cervicitis. The cervicitis rate was 39% in our study. M. genitalium was significantly more frequent in women with cervicitis than in women without cervicitis (5.6 vs. 1.2%, p=0.005). C. trachomatis and N. gonorrhea, which are often associated with cervicitis, were comparable in women with and without cervicitis.

Conclusion:

Women with clinically diagnosed cervicitis or even with a normal-appearing cervix should be tested using multiplex-real-time PCR-nucleic-acidamplification tests on suspicion of such an infection. M. genitalium is an emerging bacterial agent for cervicitis along with C. trachomatis and N. gonorrhea.

Gonorrhoea

The bacterium Neisseria gonorrhoeae causes the sexually transmitted infection (STI) gonorrhoea, which has an estimated global annual incidence of 86.9 million adults. Gonorrhoea can present as urethritis in men, cervicitis or urethritis in women, and in extragenital sites (pharynx, rectum, conjunctiva and, rarely, systemically) in both sexes. Confirmation of diagnosis requires microscopy of Gram-stained samples, bacterial culture or nucleic acid amplification tests. As no gonococcal vaccine is available, prevention relies on promoting safe sexual behaviours and reducing STI-associated stigma, which hinders timely diagnosis and treatment thereby increasing transmission. Single-dose systemic therapy (usually injectable ceftriaxone plus oral azithromycin) is the recommended first-line treatment. However, a major public health concern globally is that N. gonorrhoeae is evolving high levels of antimicrobial resistance (AMR), which threatens the effectiveness of the available gonorrhoea treatments. Improved global surveillance of the emergence, evolution, fitness, and geographical and temporal spread of AMR in N. gonorrhoeae, and improved understanding of the pharmacokinetics and pharmacodynamics for current and future antimicrobials in the treatment of urogenital and extragenital gonorrhoea, are essential to inform treatment guidelines. Key priorities for gonorrhoea control include strengthening prevention, early diagnosis, and treatment of patients and their partners; decreasing stigma; expanding surveillance of AMR and treatment failures; and promoting responsible antimicrobial use and stewardship. To achieve these goals, the development of rapid and affordable point-of-care diagnostic tests that can simultaneously detect AMR, novel therapeutic antimicrobials and gonococcal vaccine(s) in particular is crucial.

Spontaneous Clearance of Pharyngeal Gonococcal Infections: A Retrospective Study in Patients of the Sexually Transmitted Infections Clinic; Amsterdam, the Netherlands; 2012 to 2015

INTRODUCTION

Pharyngeal Neisseria gonorrhoeae infections are mostly asymptomatic, yet sustain ongoing gonococcal transmission. We assessed the proportion of pharyngeal gonorrhea that spontaneously clears and identified determinants of clearance.

METHODS

At the sexually transmitted infections clinic Amsterdam, at-risk women and men who have sex with men were routinely screened for pharyngeal N. gonorrhoeae using an RNA-based nucleic acid amplification test (NAAT; Aptima Combo 2).We retrospectively examined medical records of pharyngeal gonorrhea patients (January 2012-August 2015). We included patients who returned for antibiotic treatment and had a new sample taken for NAAT before treatment. Spontaneous clearance was defined as a negative NAAT result at the follow-up visit.

RESULTS

During the study period, 1266 cases with a pharyngeal gonorrhea were not treated at the first consultation and returned for a follow-up visit. Median (interquartile range) time between the first consultation and follow-up was 10 (7-14) days. Spontaneous clearance was found in 139 cases (11.0%) and was associated with age at least 45 years (vs. 16-24 years; adjusted odds ratio, 2.02 [95% confidence interval, 1.09-3.75]) and with time from the first consultation to follow-up (adjusted odds ratio, 1.08 [1.06-1.10], per extra day).

CONCLUSIONS

Eleven percent of pharyngeal gonorrhea cases cleared spontaneously. Spontaneous clearance of pharyngeal gonorrhea was more often seen among older patients.

Genomic epidemiology and antimicrobial resistance of Neisseria gonorrhoeae in New Zealand

Background

Antimicrobial-resistant Neisseria gonorrhoeae is a major threat to public health. No studies to date have examined the genomic epidemiology of gonorrhoea in the Western Pacific Region, where the incidence of gonorrhoea is particularly high.

Methods

A population-level study of N. gonorrhoeae in New Zealand (October 2014 to May 2015). Comprehensive susceptibility testing and WGS data were obtained for 398 isolates. Relatedness was inferred using phylogenetic trees, and pairwise core SNPs. Mutations and genes known to be associated with resistance were identified, and correlated with phenotype.

Results

Eleven clusters were identified. In six of these clusters, >25% of isolates were from females, while in eight of them, >15% of isolates were from females. Drug resistance was common; 98%, 32% and 68% of isolates were non-susceptible to penicillin, ciprofloxacin and tetracycline, respectively. Elevated MICs to extended-spectrum cephalosporins (ESCs) were observed in 3.5% of isolates (cefixime MICs ≥ 0.12 mg/L, ceftriaxone MICs ≥ 0.06 mg/L). Only nine isolates had penA XXXIV genotypes, three of which had decreased susceptibility to ESCs (MIC = 0.12 mg/L). Azithromycin non-susceptibility was identified in 43 isolates (10.8%); two of these isolates had 23S mutations (C2611T, 4/4 alleles), while all had mutations in mtrR or its promoter.

Conclusions

The high proportion of females in clusters suggests transmission is not exclusively among MSM in New Zealand; re-assessment of risk factors for transmission may be warranted in this context. As elevated MICs of ESCs and/or azithromycin were found in closely related strains, targeted public health interventions to halt transmission are urgently needed.

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

Real-time polymerase chain reaction (PCR) assays to detect antimicrobial resistance-associated mutations were tested on Neisseria gonorrhoeae-positive clinical samples with matched isolates. Of the nucleic acid amplification tests/cultures, 87.7% (64/73), 98.6% (72/73), and 98.4% (62/63) predicted cephalosporin, ciprofloxacin, and azithromycin susceptibilities, respectively. N. gonorrhoeae multiantigen sequence type was correctly predicted for 98.7% (79/80), and 13 of 58 N. gonorrhoeae-negative specimens showed false-positive results.

Genital and Extragenital Gonorrhea and Chlamydia in Children and Adolescents Evaluated for Sexual Abuse

OBJECTIVE

The aim of this study was to describe the use of a nucleic acid amplification test in detecting genital and extragenital Neisseria gonorrhoeae (NG) and Chlamydia trachomatis (CT) in children and adolescents assessed for sexual abuse/assault.

METHODS

The charts of children aged 0 to 17 years, consecutively evaluated for sexual victimization, in emergency department and outpatient settings were reviewed. Data extracted included age, sex, type of sexual contact, anogenital findings, previous sexual contact, toxicology results, and sites tested for NG and CT.

RESULTS

Of the 1319 patients who were tested, 579 were tested at more than 1 site, and 120 had at least 1 infected site. Chlamydia trachomatis was identified in 104 patients, and NG was found in 33. In bivariate analysis, a positive test was associated with female sex, age older than 11 years, previous sexual contact, acute or healed genital injury, drug/alcohol intoxication, and examination within 72 hours of sexual contact. Fifty-one patients had positive anal tests, and 24 had positive oral tests. More than 75% of patients with positive extragenital tests had additional positive tests or anogenital injury. Most with a positive anal (59%) or oral (77%) test did not report that the assailant's genitals came into contact with that site.

CONCLUSIONS

Positive tests for NG and CT in patients evaluated for sexual victimization may represent infection from sexual contact, contiguous spread of infection, or the presence of infected assailant secretions. Relying on patient reports of symptoms, or types of sexual contact, to determine need for testing may miss NG and CT infections in patients evaluated for sexual victimization.

Surface enhanced Raman spectroscopy of Chlamydia trachomatis and Neisseria gonorrhoeae for diagnostics, and extra-cellular metabolomics and biochemical monitoring

SERS spectra excited at 785 nm of the bacteria Chlamydia trahomatis (elementary bodies, EB) and Neisseria gonorrheoae, the causative pathogens for the two most common sexually transmitted diseases (STD), chlamydia and gonorrhea, respectively, are reported. Although both are Gram-negative bacteria, the SERS signatures of C. trachomatis and N. gonorrheoae are completely different. N. gonorrheoae SERS spectra are due to the starvation induced nucleotide metabolites adenine and guanine, and the surface associated co-enzyme nicotinamide adenine dinucleotide and are very similar on Au and Ag although the spectrum appears more rapidly on Ag. The C. trachomatis SERS spectrum is dominated by the vibrational features of cell surface proteins. While features attributable to specific residues and the amide backbone characterize the C. trachomatis spectrum on Ag, the corresponding SERS spectrum on Au substrates displays vibrational characteristics of aggregated proteins. The prospects for the development of a SERS based platform for rapid (<one hour), low-cost bacterial STD diagnostics are promising based on these initial studies. Furthermore, this biomedical application demonstrates the potential for SERS to be a sensitive real time probe of the dynamics of biochemical activity in the cell wall and extracellular regions of microorganisms.

Loop-mediated isothermal amplification of Neisseria gonorrhoeae porA pseudogene: a rapid and reliable method to detect gonorrhea

BACKGROUND AND OBJECTIVE

Gonorrhea is a sexually transmitted disease caused by the bacterium Neisseria gonorrhoeae. Rapid detection is crucial for effective prevention and treatment. This study developed and tested a low-cost effective method for detecting N. gonorrhoeae, especially in developing countries.

METHODS

DNA from a N. gonorrhoeae standard strain, as well as from 26 genital secretion samples of gonorrhea patients, were isolated and used for loop-mediated isothermal amplification (LAMP) assay, which was conducted using either an automatic real-time PCR analyzer or a water bath. The amplified porA pseudogene sequence was compared with the NCBI database and the LAMP results were compared with that of the traditional culture method for its sensitivity and specificity.

RESULTS

LAMP was able to detect Neisseria DNA at a concentration as low as 1 pg/µL (1 × 10³ CFU/mL cells). The LAMP assay results obtained using an automatic real-time PCR analyzer was similar to that of the water bath. Relative to traditional culture, the sensitivity and specificity of the LAMP assay were 94.7 and 85.7%, respectively.

CONCLUSION

LAMP was sensitive and reliable for detecting the porA gene of N. gonorrhoeae. It could be used as a rapid, low cost, and effective method for detecting N. gonorrhoeae.

Value of light microscopy to diagnose urogenital gonorrhoea: a diagnostic test study in Indonesian clinic-based and outreach sexually transmitted infections services

INTRODUCTION

Gonorrhoea is a common sexually transmitted disease caused by Neisseria gonorrhoeae (Ng) infection. Light microscopy of urogenital smears is used as a simple tool to diagnose urogenital gonorrhoea in many resource-limited settings. We aimed to evaluate the accuracy of light microscopy to diagnose urogenital gonorrhoea as compared with a PCR-based test.

METHODS

In 2014, we examined 632 male urethral and 360 endocervical smears in clinic-based and outreach settings in Jakarta, Yogyakarta and Denpasar, Indonesia. Using the detection of Ng DNA by a validated PCR as reference test, we evaluated the accuracy of two light microscopic criteria to diagnose urogenital gonorrhoea in genital smears: (1) the presence of intracellular Gram-negative diplococci (IGND) and (2) ≥5 polymorphonuclear leucocytes (PMNL)/oil-immersion field (oif) in urethral or ≥20 PMNL/oif in endocervical smears.

RESULTS

In male urethral smears, IGND testing had a sensitivity (95% CI), specificity (95% CI) and kappa±SE of 59.0% (50.1 to 67.4), 89.4% (86.3 to 91.9) and 0.49±0.04, respectively. For PMNL count, these were 59.0% (50.1 to 67.4), 83.7% (80.2 to 86.9) and 0.40±0.04, respectively. The accuracy of IGND in the clinic-based settings (72.0% (57.5 to 83.3), 95.2% (91.8 to 97.5) and 0.68±0.06, respectively) was better than in the outreach settings (51.2% (40.0 to 62.3), 83.4% (78.2 to 87.8) and 0.35±0.06, respectively). In endocervical smears, light microscopy performed poorly regardless of the setting or symptomatology, with kappas ranging from -0.09 to 0.24.

CONCLUSION

Light microscopy using IGND and PMNL criteria can be an option with moderate accuracy to diagnose urethral gonorrhoea among males in a clinic-based setting. The poor accuracy in detecting endocervical infections indicates an urgent need to implement advanced methods, such as PCR. Further investigations are needed to identify the poor diagnostic outcome in outreach services.

Detection of antibiotic resistance is essential for gonorrhoea point-of-care testing: a mathematical modelling study

BACKGROUND

Antibiotic resistance is threatening to make gonorrhoea untreatable. Point-of-care (POC) tests that detect resistance promise individually tailored treatment, but might lead to more treatment and higher levels of resistance. We investigate the impact of POC tests on antibiotic-resistant gonorrhoea.

METHODS

We used data about the prevalence and incidence of gonorrhoea in men who have sex with men (MSM) and heterosexual men and women (HMW) to calibrate a mathematical gonorrhoea transmission model. With this model, we simulated four clinical pathways for the diagnosis and treatment of gonorrhoea: POC test with (POC+R) and without (POC-R) resistance detection, culture and nucleic acid amplification tests (NAATs). We calculated the proportion of resistant infections and cases averted after 5 years, and compared how fast resistant infections spread in the populations.

RESULTS

The proportion of resistant infections after 30 years is lowest for POC+R (median MSM: 0.18%, HMW: 0.12%), and increases for culture (MSM: 1.19%, HMW: 0.13%), NAAT (MSM: 100%, HMW: 99.27%), and POC-R (MSM: 100%, HMW: 99.73%). Per 100 000 persons, NAAT leads to 36 366 (median MSM) and 1228 (median HMW) observed cases after 5 years. Compared with NAAT, POC+R averts more cases after 5 years (median MSM: 3353, HMW: 118). POC tests that detect resistance with intermediate sensitivity slow down resistance spread more than NAAT. POC tests with very high sensitivity for the detection of resistance are needed to slow down resistance spread more than by using culture.

CONCLUSIONS

POC with high sensitivity to detect antibiotic resistance can keep gonorrhoea treatable longer than culture or NAAT. POC tests without reliable resistance detection should not be introduced because they can accelerate the spread of antibiotic-resistant gonorrhoea.

A multicentre double-blind randomised controlled trial evaluating the efficacy of daily use of antibacterial mouthwash against oropharyngeal gonorrhoea among men who have sex with men: the OMEGA (Oral Mouthwash use to Eradicate GonorrhoeA) study protocol

BACKGROUND

Gonorrhoea is one of the most common sexually transmissible infections in men who have sex with men (MSM). Gonorrhoea rates have increased substantially in recent years. There is concern that increasing gonorrhoea prevalence will increase the likelihood of worsening antibiotic resistance in Neisseria gonorrhoeae. A recent randomised controlled trial (RCT) demonstrated that a single-dose of mouthwash has an inhibitory effect against oropharyngeal gonorrhoea. We are conducting the first RCT to evaluate whether daily use of mouthwash could reduce the risk of acquiring oropharyngeal gonorrhoea.

METHODS/DESIGN

The OMEGA (Oral Mouthwash use to Eradicate GonorrhoeA) study is a double-blind RCT and will be conducted at several sexual health clinics and high caseload General Practice (GP) clinics in Melbourne and Sydney, Australia. A total of 504 MSM attending the participating sites will be recruited. Participants will be randomised to either using 'Study mouthwash A' or 'Study mouthwash B' for 12 weeks. Study mouthwash A was inhibitory against N. gonorrhoeae in vitro, whereas study mouthwash B was not. Participants will be instructed to rinse and gargle the study mouthwash for 60 seconds every day. The primary outcome is the proportion of participants with oropharyngeal gonorrhoea detected by nucleic acid amplification test by 12 weeks.

DISCUSSION

The results from this trial may provide a novel way to reduce gonorrhoea prevalence and transmission without the use of antibiotics that may be associated with development of resistance. If shown to be effective, the widespread use of mouthwash will reduce the prevalence of oropharyngeal gonorrhoea, which plays key role in driving the emergence of gonococcal antimicrobial resistance through DNA exchange with oral commensal bacteria. The anticipated net effect will be interruption of onward transmission of N. gonorrhoeae within high density sexual networks within MSM populations.

TRIAL REGISTRATION

Australian New Zealand Clinical Trials Registry ACTRN12616000247471 , registered on 23rd February 2016.

Simultaneous detection and identification of STI pathogens by multiplex Real-Time PCR in genital tract specimens in a selected area of Apulia, a region of Southern Italy

PURPOSE

Genital tract infections are globally a major cause of morbidity in sexually active individuals. The aim of this study was to investigate the prevalence and associations of co-infections of Chlamydia trachomatis, Neisseria gonorrhoeae, Trichomonas vaginalis, Mycoplasma hominis (MH), Mycoplasma genitalium, Ureaplasma urealyticum (UU) and Ureaplasma parvum (UP) in specimens collected from female (SF) and male (SM) patients.

METHODS

1575 samples from 1575 individuals from the geographical area around Bari, Apulia region in Southern Italy, were collected and analyzed by a multiplex Real-Time PCR (mRT-PCR) (Anyplex^TM II STI-7, Seegene, Inc., Seoul, Korea) assay.

RESULTS

455/1575 (28.89%) samples resulted positive for at least one of the targets named above. Statistically significant differences in prevalence of the pathogens between SF and SM were not detected except for UP (24.92% in SF vs 8.91% in SM). Prevalence of co-infections was 6.84 and 3.96% in SF and SM, respectively. Moreover, MH presence in SF, but not in SM, was associated with UU and UP.

CONCLUSIONS

Our data suggest different patterns of infections between females and male and the importance of an increased vigilance of sexually transmitted pathogens to reduce the burden on general population and the sequelae or the complications on reproductive organs.

Antimicrobial-resistant sexually transmitted infections: gonorrhoea and Mycoplasma genitalium

The emergence of antimicrobial resistance (AMR) is a major concern worldwide and already compromises treatment effectiveness and control of several bacterial sexually transmitted infections (STIs). Neisseria gonorrhoeae and Mycoplasma genitalium are evolving into so-called superbugs that can become resistant, both in vitro and clinically, to essentially all antimicrobials available for treatment, causing exceedingly difficult-to-treat or untreatable STIs and threatening global public health. Widespread AMR in these bacteria is likely to persist and even worsen in the future, owing to the high number of infections, widespread and uncontrolled use of antimicrobials, limited surveillance of AMR and clinical failures, as well as the extraordinary capacity of these bacteria to develop AMR. This development would not only result in an increased prevalence of N. gonorrhoeae and M. genitalium infections but also in a considerably increasing number of severe complications affecting reproductive health. To combat this threat, clinicians need to be aware of the current guidelines on diagnostic procedures, recommended treatment regimens, as well as therapeutic options for multidrug-resistant bacteria. AMR testing needs to be more frequently performed, inform treatment decisions and elucidate how AMRs compromise treatment effectiveness, guiding research for effective future therapies.

Gonorrhoea diagnostics: An update

Diagnosis of gonorrhoea is an ongoing challenge. The organism is fastidious requiring meticulous collection and transport for successful cultivation. Asymptomatic infections are common which go undetected by conventional methods thereby leading to continued transmission and the risk of complications. The nucleic acid amplification tests, now increasingly used in developed countries, offer improved sensitivity compared to bacterial culture. However, these continue to suffer sequence related problems leading to false positive and false negative results. Further, these cannot be used for generation of data on antibiotic susceptibility because genetic markers of antibiotic resistance to recommended therapies have not been fully characterised. They are unaffordable in a setting like ours where reliance is placed on syndromic approach for sexually transmitted infection (STI) management. The use of syndromic approach has resulted in a considerable decline in the number of Neisseria gonorrhoeae isolates that have been cultured for diagnostic purposes. Many laboratories formerly doing so are no longer performing culture for gonococci, and the basic skills have been lost. There is a need to not only revive this skill but also adopt newer technologies that can aid in accurate diagnosis in a cost-effective manner. There is room for innovation that can facilitate the development of a point-of-care test for this bacterial STI.

Extragenital Infections Caused by Chlamydia trachomatis and Neisseria gonorrhoeae: A Review of the Literature

In the United States, sexually transmitted diseases due to Chlamydia trachomatis and Neisseria gonorrhoeae continue to be a major public health burden. Screening of extragenital sites including the oropharynx and rectum is an emerging practice based on recent studies highlighting the prevalence of infection at these sites. We reviewed studies reporting the prevalence of extragenital infections in women, men who have sex with men (MSM), and men who have sex only with women (MSW), including distribution by anatomical site. Among women, prevalence was found to be 0.6–35.8% for rectal gonorrhea (median reported prevalence 1.9%), 0–29.6% for pharyngeal gonorrhea (median 2.1%), 2.0–77.3% for rectal chlamydia (median 8.7%), and 0.2–3.2% for pharyngeal chlamydia (median 1.7%). Among MSM, prevalence was found to be 0.2–24.0% for rectal gonorrhea (median 5.9%), 0.5–16.5% for pharyngeal gonorrhea (median 4.6%), 2.1–23.0% for rectal chlamydia (median 8.9%), and 0–3.6% for pharyngeal chlamydia (median 1.7%). Among MSW, the prevalence was found to be 0–5.7% for rectal gonorrhea (median 3.4%), 0.4–15.5% for pharyngeal gonorrhea (median 2.2%), 0–11.8% for rectal chlamydia (median 7.7%), and 0–22.0% for pharyngeal chlamydia (median 1.6%). Extragenital infections are often asymptomatic and found in the absence of reported risk behaviors, such as receptive anal and oral intercourse. We discuss current clinical recommendations and future directions for research.

Multiplex Real-Time PCR Assay with High-Resolution Melting Analysis for Characterization of Antimicrobial Resistance in Neisseria gonorrhoeae

Resistance to antibiotics used against Neisseria gonorrhoeae infections is a major public health concern. Antimicrobial resistance (AMR) testing relies on time-consuming culture-based methods. Development of rapid molecular tests for detection of AMR determinants could provide valuable tools for surveillance and epidemiological studies and for informing individual case management. We developed a fast (<1.5-h) SYBR green-based real-time PCR method with high-resolution melting (HRM) analysis. One triplex and three duplex reactions included two sequences for N. gonorrhoeae identification and seven determinants of resistance to extended-spectrum cephalosporins (ESCs), azithromycin, ciprofloxacin, and spectinomycin. The method was validated by testing 39 previously fully characterized N. gonorrhoeae strains, 19 commensal Neisseria species strains, and an additional panel of 193 gonococcal isolates. Results were compared with results of culture-based AMR determination. The assay correctly identified N. gonorrhoeae and the presence or absence of the seven AMR determinants. There was some cross-reactivity with nongonococcal Neisseria species, and the detection limit was 10(3) to 10(4) genomic DNA (gDNA) copies/reaction. Overall, the platform accurately detected resistance to ciprofloxacin (sensitivity and specificity, 100%), ceftriaxone (sensitivity, 100%; specificity, 90%), cefixime (sensitivity, 92%; specificity, 94%), azithromycin (sensitivity and specificity, 100%), and spectinomycin (sensitivity and specificity, 100%). In conclusion, our methodology accurately detects mutations that generate resistance to antibiotics used to treat gonorrhea. Low assay sensitivity prevents direct diagnostic testing of clinical specimens, but this method can be used to screen collections of gonococcal isolates for AMR more quickly than current culture-based AMR testing.

Multiplex Strand Invasion Based Amplification (mSIBA) assay for detection of Chlamydia trachomatis and Neisseria gonorrhoeae

Nucleic acid amplification tests have become a common method for diagnosis of STIs due to their improved sensitivity over immunoassays and traditional culture-based methods. Isothermal nucleic acid amplification methods offer significant advantages over polymerase chain reaction (PCR) because they do not require sophisticated instruments needed for thermal cycling of PCR. We recently reported a novel isothermal nucleic acid amplification method, Strand Invasion-Based Amplification (SIBA), which exhibited high analytical sensitivity and specificity for amplification of DNA. However, because the reactions were detected using an intercalating dye, this method was only suitable for amplifying a single genomic target. Here, we report the development of multiplexed SIBA (mSIBA) that allows simultaneous detection of Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), and an internal control in the same reaction tube. SIBA is compatible with probes, allowing the detection of multiple DNA targets in the same reaction tube. The IC was developed to assess the quality of the isolated DNA and the integrity of the enzyme system, as well as to test oligonucleotides. The mSIBA assay retained high analytical sensitivity and specificity for the detection of CT and NG. The development of mSIBA enables rapid screening for CT and NG within point-of-care or central laboratory settings.

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.

Substantial increases in chlamydia and gonorrhea positivity unexplained by changes in individual-level sexual behaviors among men who have sex with men in an Australian sexual health service from 2007 to 2013

BACKGROUND

To determine the risk-adjusted temporal trend of gonorrhea and chlamydia positivity and associated risk behaviors among men who have sex with men (MSM) attending a sexual health clinic in Melbourne in Australia.

METHODS

Gonorrhea and chlamydia positivity by anatomical site adjusted for year of test, age, number of sexual partners, and condom use among MSM attending Melbourne Sexual Health Centre from 2007 to 2013 were calculated using generalized estimating equation regression models.

RESULTS

A total of 12,873 MSM were included with a median age of 30.0 years. The proportion with pharyngeal, urethral, and anal gonorrhea was 1.7%, 2.3%, and 2.9%, respectively. The adjusted odds of gonorrhea positivity increased by 9% (95% confidence interval [CI], 3%-15%), 11% (95% CI, 6%-17%), and 12% (95% CI, 7%-17%) per year, respectively. The proportion of MSM who were infected with anal chlamydia was 5.6%, with an average increase of 6% (95% CI, 3%-10%) per year; however, no significant change was observed in urethral chlamydia positivity (adjusted odds ratio, 1.02; 95% CI, 0.98-1.06). Increases in gonorrhea and chlamydia positivity were primarily restricted to MSM who reported more than 10 partners in 12 months. The number of partners in the last 12 months fell from 16.6 to 10.5, whereas consistent condom use with casual partners decreased from 64.6% to 58.9% over the study period.

CONCLUSIONS

Gonorrhea and chlamydia have increased among MSM despite the decrease in the number of sexual partners and are occurring primarily in MSM with high numbers of partners and persist after adjusting for known risk factors, suggesting that unmeasured factors (e.g., more assortative mixing patterns) may explain the observed changes.

Performance of the NG OligoGen kit for the diagnosis of Neisseria gonorrhoeae: comparison with cobas 4800 assay

PCR assays are nowadays between the most sensitive and reliable methods for screening and diagnosing sexually transmitted infections (STIs). The aim of this study was to analyze the reliability, accuracy, and usefulness of the new NG OligoGen kit in comparison with the cobas 4800 assay for the detection of Neisseria gonorrhoeae in clinical samples. A prospective study was designed for detection of N. gonorrhoeae including urine samples (n=152), rectal (n=80), endocervical (n=67), pharyngeal (n=41), and urethral swabs (n=5) that were sent from a regional STI clinic in Seville, Spain. Samples were collected from 255 (73.9%) men and 90 women. Sensitivity, specificity, positive and negative predicative values, and kappa value for N. gonorrhoeae detection using the NG OligoGen kit were 99.6%, 100%, 100%, 99.1%, and 0.99, respectively. Statistical data obtained in this study confirm the usefulness and reliable results of this new assay.

Analytical specificity and sensitivity of the novel dual-target GeneProof Neisseria gonorrhoeae PCR kit for detection of N. gonorrhoeae

Detection of Neisseria gonorrhoeae relies increasingly on nucleic acid amplification tests (NAATs). The specificity of many gonococcal NAATs has been suboptimal and supplementary testing remains recommended in Europe and several additional countries. The novel dual-target GeneProof Neisseria gonorrhoeae PCR kit, targeting porA pseudogene and 16S rRNA gene, showed a high specificity and sensitivity when isolates of non-gonococcal Neisseria and related species (n = 144), and gonococci (n = 104) were tested. However, rare gonococcal porA mutants were only detected in the 16S rRNA gene target and two non-gonococcal isolates showed a low-level cross-reactivity in the 16S rRNA gene target. The detection limit for both targets was 1.5 copies per reaction.

Molecular Assay for Detection of Ciprofloxacin Resistance in Neisseria gonorrhoeae Isolates from Cultures and Clinical Nucleic Acid Amplification Test Specimens

We developed a real-time PCR assay to detect single nucleotide polymorphisms associated with ciprofloxacin resistance in specimens submitted for nucleic acid amplification testing (NAAT). All three single nucleotide polymorphism (SNP) targets produced high sensitivity and specificity values. The presence of ≥2 SNPs was sufficient to predict ciprofloxacin resistance in an organism.

Will targeting oropharyngeal gonorrhoea delay the further emergence of drug-resistant Neisseria gonorrhoeae strains?

Gonorrhoea is an important sexually transmitted infection associated with serious complications and enhanced HIV transmission. Oropharyngeal infections are often asymptomatic and will only be detected by screening. Gonococcal culture has low sensitivity (<50%) for detecting oropharyngeal gonorrhoea, and, although not yet approved commercially, nucleic acid amplification tests (NAAT) are the assay of choice. Screening for oropharyngeal gonorrhoea should be performed in high-risk populations, such as men-who-have-sex-with-men(MSM). NAATs have a poor positive predictive value when used in low-prevalence populations. Gonococci have repeatedly thwarted gonorrhoea control efforts since the first antimicrobial agents were introduced. The oropharyngeal niche provides an enabling environment for horizontal transfer of genetic material from commensal Neisseria and other bacterial species to Neisseria gonorrhoeae. This has been the mechanism responsible for the generation of mosaic penA genes, which are responsible for most of the observed cases of resistance to extended-spectrum cephalosporins (ESC). As antimicrobial-resistant gonorrhoea is now an urgent public health threat, requiring improved antibiotic stewardship, laboratory-guided recycling of older antibiotics may help reduce ESC use. Future trials of antimicrobial agents for gonorrhoea should be powered to test their efficacy at the oropharynx as this is the anatomical site where treatment failure is most likely to occur. It remains to be determined whether a combination of frequent screening of high-risk individuals and/or laboratory-directed fluoroquinolone therapy of oropharyngeal gonorrhoea will delay the further emergence of drug-resistant N. gonorrhoeae strains.