Diagnosis of Neisseria gonorrhoeae using molecular beacon

Alkhumra Hemorrhagic Fever Virus (AHFV): A Concise Overview

Alkhumra fever is a viral disease caused by the Alkhumra hemorrhagic fever virus (AHFV). It belongs to family Flaviviridae, genus Flavivirus. AHFV is primarily transmitted to humans through the bite of infected ticks, for example, Hyalomma. This disease was first identified in the Kingdom of Saudi Arabia (KSA) in 1995 and then reported in other countries of the Arabian Peninsula and the Middle East. The AHFV genome consists of a positive-sense, single-stranded RNA molecule of approximately 10.2 kilobases (kb) in length. The Open Reading Frame (ORF) encodes a polyprotein precursor that is processed by viral and host proteases to yield individual viral proteins. The polyprotein precursor is cleaved by viral proteases and host signal peptidases into three structural and seven non-structural proteins. AHFV can cause a range of clinical manifestations, from mild flu-like symptoms to severe hemorrhagic fever. In this review, we focus on insightful understanding of molecular biology, pathogenesis, and their potential therapeutic targets for AHFV.

Performance verification and clinical evaluation of the NAP-Fluo Cycler system for detecting five genital tract pathogens based on microfluidic technology

Introduction

Sexually transmitted infections (STIs) are among the most common infectious diseases worldwide, often leading to coinfections. Timely detection of genital tract pathogens in at-risk populations is crucial for preventing STIs. We evaluated the NAP-Fluo Cycler System, an innovative microfluidic nucleic acid detection platform, for its ability to simultaneously identify Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), Ureaplasma urealyticum (UU), Mycoplasma genitalium (MG), and Mycoplasma hominis (MH) in urethral or cervical secretions.

Materials and methods

The limits of detection (LODs), repeatability, specificity, and interference resistance of the system were evaluated using standard strains, a panel of 24 pathogens, and seven interferents. We used the system to analyze 302 clinical samples and compared the results with those of five approved commercial reference kits.

Results

The system achieved LODs of 500 IFU/mL, 500 CFU/mL, and 500 CCU/mL for CT, NG, and UU/MG/MH, respectively, demonstrating high stability (coefficient of variation <1.1 %), specificity, and resistance to interference. Among 302 clinical samples, 237 tested positive with single, dual, and triple infection rates of 35.6 %, 16.2 %, and 3.0 %, respectively. The reference kits detected 138 positive samples. The concordance rates with commercial reference kits were 100 % for UU, NG, and MH; 94.85 % for CT; and 80.00 % for MG.

Conclusions

This system offers a streamlined, rapid, and multiplex detection method that reduces testing time and complexity. Although it performs well with pure strains, it has limitations when using clinical samples of CT and MG, suggesting the need for further refinement before its widespread use in the clinic.

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.

Multiple sexually transmitted co-infections are associated with adverse reproductive outcomes in asymptomatic adolescent pregnant women; A Prospective cohort study

BACKGROUND

A prospective cohort was conducted to assess the prevalence of seven RTIs/STIs in adolescent asymptomatic pregnant women to find a significant correlation between infection and pregnancy.

METHODS

The study was restricted to 18-19 years of asymptomatic adolescent pregnant women attending Ante-Natal Care and the health status of the pregnant women were followed up to parturition. The health status of the infant was followed till 6 months post-delivery. The prevalence of the concerning pathogens and the significance of their association with adverse outcomes of pregnancy were determined.

RESULTS

Among 279 subjects, the most significant co-infections were observed for M. hominis with U. parvum (9.31%; p-value-0.0071/OR-2.6421) and U. urealyticum (7.88%; p-value-0.0119/OR-2.6455). Statistically significant associations were found between C. trachomatis [(p-value-0.0439); OR-2.9902] and M. genitalium [(p-value-0.0284); OR-3.442] with PTB, N. gonorrhoeae with LBW <2.5 kg [(p-value-0.0052);OR-4.9017], U. urealyticum with VLBW <2 kg [(p-value-0.0262);OR-3.0207], M. genitalium [(p-value-0.0184); OR-11.7976] and T. vaginalis with PROM [(p-value 0.0063); OR-19.4275] while M. genitalium [(p-value 0.0190); OR-12.9230] and U. urealyticum [(p-value 0.0063); OR-14.5149] with PPROM with 95% CI respectively.

CONCLUSIONS

Asymptomatic adolescents are at high risk of adverse pregnancy outcomes if infected with the concerned pathogens.

Improved management can be achieved by introducing additional parameters in the syndromic diagnosis of nonviral sexually transmitted infections at low-resource settings

BACKGROUND

The syndromic approach is a simple and affordable strategy for the management of sexually transmitted infections in countries with low-resource settings. However, because of the lack of specificity and accuracy, the risk of overuse and misuse of antibiotics is very high. Here, we proposed a more specific and accurate algorithm compared with the current algorithm used for syndromic case management of 3 common sexually transmitted pathogens and compared its precision with laboratory-based tests.

OBJECTIVE

This study aimed to report a comparative account of the accuracy of existing syndromic case management guidelines followed in mainstream hospitals, for taking care of patients with nonviral sexually transmitted infections, concerning an approach involving an alternative algorithm formulated in our laboratory followed by polymerase chain reaction testing.

STUDY DESIGN

This was an observational study that compared the data between 2 categories based on diagnostics accuracy and treatment. In category I, symptoms of infection were scored on the basis of the existing National AIDS Control Organization and National AIDS Control Programme guidelines, and patients were treated before testing by polymerase chain reaction. In category II, patients were recruited on the basis of the National AIDS Control Organization and National AIDS Control Programme guidelines with additional alternative syndromic case management parameters. All samples were tested by polymerase chain reaction for Chlamydia trachomatis, Neisseria gonorrhoeae, and Trichomonas vaginalis and clinically correlated before giving the treatment.

RESULTS

In category I, among 646 women with symptomatic infection, only 46 (7.82%) tested positive by polymerase chain reaction assay for at least 1 of the pathogens, and 600 (92.87%) tested negative for infection by any of the 3 pathogens. The total estimated percentages of the overuse and misuse of antibiotics were 92.87% and 8.69%, respectively. Correct and complete treatment based on laboratory outcome compared with National AIDS Control Programme guidelines was 42 of 46 (91.30%). The estimated overuse of azithromycin and cefixime (Gray Kit) was 29.69%, the estimated overuse of a combination of doxycycline, cefixime, and metronidazole (Yellow Kit) was 29.87%, and the estimated overuse of a combination of doxycycline, cefixime, metronidazole, and azithromycin (Gray with Yellow Kit) was 11.45%. In category II, wherein patients were treated using an alternative syndromic approach and polymerase chain reaction diagnostics, 243 of 319 patients (76.15%) were infected with either of the pathogens (Chlamydia trachomatis, Neisseria gonorrhoeae, and Trichomonas vaginalis), whereas 76 of 319 patients (23.82%) were negative for any of the 3 pathogens. Among 243 patients with infection, 99 of 243 (40.74%) were infected with a single pathogen, whereas 144 of 243 (59.20%) were coinfected. Of 144 coinfected patients, the percentage of Chlamydia trachomatis + Neisseria gonorrhoeae infection was the highest (51.38%), followed by coinfection with all 3 pathogens (30%). Coinfection with Chlamydia trachomatis + Trichomonas vaginalis was 9.72%, and coinfection with Neisseria gonorrhoeae + Trichomonas vaginalis was 9.03%. The estimated overuse of antibiotics was found to be 23.82% only.

CONCLUSION

The proposed alternative strategies of syndromic case management can reduce the percentage of misuse and overuse of antibiotics from 92.87% to 23.82%. Moreover, syndromic case management alone was insufficient for disease management.

A systematic review and meta-analysis of different diagnostic procedures to detect gonococcus infection in resource-limited scenario

Context

Neisseria gonorrhoeae is a Gram-negative diplococcus, an obligate human pathogen, and the etiologic agent of the sexually transmitted infection (STI), gonorrhoea. culture is the standard procedure for diagnosis, which may be supported by nucleic acid tests and microscopy.

Aims

To determine the best possible method of diagnosis for Gonococcus infection in resource-limited settings.

Settings and Design

The meta-analyses were designed to determine the difference in diagnosis between Culture and nucleic acid amplification tests (NAATs) and also between the different Amplification Tests and widely available Roche COBAS AMPLICOR test.

Subjects and Methods

Databases searched were Pubmed, Medline, Google Scholar and Cochrane reviews. Risk ratio (RR) with 95% confidence intervals was estimated for the dichotomous outcomes. The random-effect model was applied for all the studies in the analysis.

Statistical Analysis Used

The meta-analysis was computed in RevMan Version 5.3, Copenhagen, Denmark.

Results

In the first analysis, NAATs significantly improved the chances of detection in comparison to the standard culture and final RR was 1.24 (1.05-2.51), which put the diamond on the right of no-effect axis, indicating more positives by NAATs. In the second analysis, AMPLICOR had the more positive results, which may have indicated better detection rate, as well as less specificity and final RR was 0.809 (0.737-0.888), which put the diamond on the left of the non-effect axis, indicating more positives by AMPLICOR.

Conclusions

In a resource-limited scenario like India, the syndromic management of STIs are considered to be the norm. A positive diagnosis is only given if the tests are confirmed by Culture, as it is still considered to be the gold standard of diagnosis. However, in many cases, due to suboptimal transportation and lack of proper handling, culture in unable to grow even if the patient is infected. In such cases, Nucleic Acid Tests should be able to detect an infection.

Portable Infrared Isothermal PCR Platform for Multiple Sexually Transmitted Diseases Strand Detection

Rapid and portable PCR detection is essential for screening sexually transmitted infections regularly. We developed an infrared mediated RNA isothermal RT-PCR (IR-MERIT PCR) platform and its compatible multichamber microfluidic chip for simultaneous amplification and testing (SAT) detection. This microfluidic chip integrates RNA extraction, micropump, and multitarget detection function onto the same chip. By utilizing IR-light-emitting diode (LED) as heat source, this platform can fulfill isothermal amplification within 70 min.

Multi-centric validation of an in-house-developed beacon-based PCR diagnostic assay kit for Chlamydia and Neisseria and portable fluorescence detector

OBJECTIVE

The development of an accurate, sensitive, specific, rapid, reproducible, stable-at-room-temperature and cost-effective diagnostic kit, and a low-cost portable fluorescence detector to fulfil the requirements of diagnostic facilities in developing countries.

METHODS

We developed the 'Chlamy and Ness CT/NG kit' based on molecular beacons for the detection of Chlamydia trachomatis (CT) and Neisseriagonorrhoeae (NG). Multi-centric evaluation of the CT/NG kit was performed using the commercially available nucleic acid amplification test (NAAT)-based FTD Urethritis basic kit for comparison from December 2014 to November 2016. The stability of the kit reagents at 4 and 37 ˚C and the inter-day reproducibility of results were also analysed.

RESULTS

The sensitivity and specificity of the kit were found to be 95.83 and 100.00 % for the detection of C. trachomatis and 93.24 and 99.75 % for N. gonorrhoeae, respectively, when tested against the commercial kit. The positive predictive value (PPV) was 100.00 and 98.57 %, whereas the negative predictive value (NPV) was 99.54 and 98.79 % for C. trachomatis and N. gonorrhoeae, respectively. Analysis of the kappa statistics enhanced the 'inter-rater' κ=0.976 for Chlamydia and κ=0.943 for Neisseria.

CONCLUSION

Our kit was found to be as sensitive and specific as commercially available kits. Its low cost and ease of use will make it suitable for the routine diagnosis of C. trachomatis and N. gonorrhoeae in the resource-limited settings of developing countries.

Evaluating the utility of syndromic case management for three sexually transmitted infections in women visiting hospitals in Delhi, India

Utility of syndromic case management (SCM) in women visiting obstetrics & gynecology department needs to be evaluated as it is subjective and imperfect. Consequently, antibiotic resistance has accelerated along with increased risk of infection to the partners. To understand the effectiveness and/or inadequacies of SCM, 11000 women were recruited and examined by clinicians for infection by Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), Trichomonas vaginalis (TV), Bacterial vaginosis (BV) and others. Amongst these patients, 1797 (16.3%) reported vaginal discharge (VD). Other symptoms included: vaginitis (97%), cervicitis (75%), genital ulcers (60%), abnormal vaginal discharge (55%) and lower abdominal pain (48%). The patients were treated for single or co-infections using pre-packed National Aids Control Program III STI/RTI Kits. However, based on PCR diagnostics, 1453/1797 (81%) subjects were uninfected for NG/TV/CT. Amongst 344 (19%) infected patients, 257 (75%) carried infection with single pathogen (TV/NG/CT) while 87/344 (25%) were co-infected with multiple pathogens. Prevalence of TV, NG & CT was 4%, 7% and 8% respectively. Co-infection with CT + NG was highest, 51% (44/87), whereas, co-infection with CT + TV was 21% and NG + TV was 18% while co-infection with all three pathogens was 1.3%. We conclude that SCM is imprecise and successful intervention requires accurate and confirmatory diagnostic approach.