Comparison between conventional culture and NAATs for the microbiological diagnosis in gonococcal infection

Impact of time of culture specimen collection on the recovery of Neisseria gonorrhoeae after a positive nucleic acid amplification test

OBJECTIVES

Culture of Neisseria gonorrhoeae remains essential for antimicrobial resistance (AMR) surveillance. We evaluated the effect of time of specimen collection on culture yield following a positive nucleic acid amplification test (NAAT).

METHODS

We retrospectively assessed N. gonorrhoeae culture yield among asymptomatic individuals (largely men who have sex with men) who attended for sexual health screening and had a positive NAAT. Participants underwent either same-day testing and notification (Drassanes Exprés) or standard screening with deferred testing.

RESULTS

Among 10 423 screened individuals, 809 (7.7%) tested positive for N. gonorrhoeae. A total of 995 different anatomical sites of infection culture was performed in 583 of 995 (58.6%) of anatomical sites (Drassanes Exprés 278 of 347, 80.1%; standard screening 305 of 648, 47.1%; p<0.001). Recovery was highest when culture specimens were collected within 3-7 days of screening with only a slight drop in recovery when the interval extended to 7 days . Recovery from pharynx was 38 of 149 (25.5%) within 3 days, 19 of 81 (23.4%) after 4-7 days (p=0.7245), 11 of 102 (10.7%) after 8-14 days (p<0.0036) and 1 of 22 (4.5%) with longer delays (p=0.00287). Recovery from rectum was 49 of 75 (65.3%) within 3 days, 28 of 45 (62.2%) after 4-7 days (p=0.7318), 41 of 69 (59.4%) after 8-14 days (p=0.4651) and 6 of 18 (33.3%) with longer delays (p=0.0131). Median culture specimen collection time was 1 day within Drassanes Exprés vs 8 days within standard screening. Consequently, the overall culture yield was slightly higher within Drassanes Exprés (102/278, 36.6% vs 99/305, 32.5%; p=0.2934).

CONCLUSION

Reducing the interval between screening and collection of culture specimens increased N. gonorrhoeae recovery in extragenital samples. Implementing a same-day testing and notification programme increased collection of culture samples and culture yield in our setting, which may help AMR surveillance.

Comparison of analytical sensitivity of DNA-based and RNA-based nucleic acid amplification tests for reproductive tract infection pathogens: implications for clinical applications

Currently, DNA-based nucleic acid amplification tests (NAATs) and RNA-based NAATs are employed to detect reproductive tract infection (RTI) pathogens including Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), and Ureaplasma urealyticum (UU). Although evaluations of DNA-based NAATs have already existed, the comparison of the two methods is scarce. Thus, we compared the limits of detection (LODs) of DNA-based and RNA-based NAATs on the same experimental conditions. Inactivated culture supernatants of CT, NG, and UU with determined pathogen DNA and RNA load were used to evaluate LODs of seven DNA kits and one RNA kit. The LODs of the seven DNA kits for CT, NG, and UU ranged between 38-1,480, 94-20,011, and 132-2,011 copies/mL, respectively. As for RNA kits, they could detect samples at RNA concentrations of 3,116, 2,509, and 2,896 copies/mL, respectively. The RNA concentrations of CT, NG, and UU were 40, 885, and 42 times that of corresponding pathogen DNA concentrations in the employed supernatants, so RNA kits could detect pathogen DNA concentrations as low as 78 copies/mL, 3 copies/mL, and 69 copies/mL, respectively, but the level of pathogen load that the RNA tests could detect was primarily dependent on the infectious phase and transcriptional level of RNA. Thus, a schematic of bacterial dynamics during the period of reproductive tract infections was provided, which suggests that in terms of the analytical sensitivity of pathogen detection, RNA tests are more suitable for detecting active infection and recovery phase, while DNA tests are more suitable for detection in the early stage of infection. IMPORTANCE Reproductive tract infections have considerable effects on the health of humans. CT, NG , and UU are common pathogens. Although evaluation of DNA-based tests has already existed, the comparison between DNA-based and RNA-based tests is rare. Therefore, this study compared the limits of detection of the two tests on the same experimental conditions. Results suggested that most DNA-based NAATs could detect CT, NG, and UU at DNA concentrations lower than 1,000 copies/mL, while RNA-based NAATs could detect bacteria at RNA concentrations around 3,000 copies/mL. Considering the copy number of RNA per bacterium is dynamic through the growth cycle, further comparison is combined with a schematic of bacterial dynamics. Results suggested that in terms of the analytical sensitivity of pathogen detection, RNA tests are more suitable for detecting active infection and recovery phase, while DNA tests are more suitable for detection in the early stage of infection.

Challenges in Managing Gonorrhea and New Advances in Prevention

Gonorrhea is the second most common bacterial sexually transmitted infection in the United States. Rates are increasing, and multiple challenges compound management, including worsening antimicrobial resistance. New therapeutics, enhanced screening and partner notification, and treatment through point-of-care testing and expedited partner therapy, as well as primary prevention efforts provide opportunities for success in combating these trends.

Evaluation of Sexually Transmitted Disease Surveillance System Electronic Laboratory Processing in Florida: Automating Case Creation, Reporting, and Closure of Chlamydia and Gonorrhea Cases

BACKGROUND

Each year, Florida Department of Health staff process hundreds of thousands of electronically received laboratory results for chlamydia (CT) and gonorrhea (GC). These processing steps are currently performed manually in Florida's surveillance system and divert from other sexually transmitted disease prevention efforts. We developed processes that would automate these procedures and evaluated the impact on potential programmatic time savings.

METHODS

We evaluated 575,952 electronic CT/GC laboratory results from January 2019 to December 2021. Laboratory results were processed through the newly automated procedures and algorithms. Expected time savings were projected using conservative estimates of 1 minute saved every time an automated process replaced a current manual procedure: profile matching, profile creation, event record creation, case review, and case reporting. Exceptions to automatic case reporting applied to certain higher-priority populations needing intervention.

RESULTS

During this period, 297,348 electronic CT/GC laboratory results were received for people with no previous recorded history of sexually transmitted diseases and required profile creation. In total, 386,763 new surveillance infection records were created for reporting. Of reported cases, 127,345 were from higher-priority groups. The proposed automations would have saved an estimated 33,121 hours of staff time, about 11,040 hours or the work of 5.3 full-time staff annually.

CONCLUSIONS

Automating current CT/GC laboratory processing would save thousands of personnel hours that could be redirected to higher-priority activities. Flexibility in prioritization criteria for automated case reporting allows programs to adjust automation to disease prevention priorities and resources. Similar automation procedures could be developed by other jurisdictions or health programs.

High-Resolution Melting Analysis to Detect Antimicrobial Resistance Determinants in South African Neisseria gonorrhoeae Clinical Isolates and Specimens

Background

Antimicrobial resistance is limiting treatment options for Neisseria gonorrhoeae infections. To aid or replace culture and the syndromic management approach, molecular assays are required for antimicrobial susceptibility testing to guide appropriate and rapid treatment.

Objective

We aimed to detect single-nucleotide polymorphisms and plasmids associated with antimicrobial resistance from N. gonorrhoeae isolates from a clinic population in South Africa, using real-time PCR as a rapid test for AMR detection.

Methods

N. gonorrhoeae isolates, from female and male patients presenting for care at a sexually transmitted infections clinic in Durban, South Africa, were analysed using phenotypic and genotypic methods for identification and antibiotic susceptibility testing (AST). Real-time PCR and high-resolution melting analysis were used to detect porA pseudogene (species-specific marker) and resistance-associated targets. Whole-genome sequencing was used as the gold standard for the presence of point mutations.

Results

The real-time porA pseudogene assay identified all N. gonorrhoeae-positive isolates and specimens. Concordance between molecular detection (real-time PCR and HRM) and resistance phenotype was ≥92% for bla_TEM (HLR penicillin), rpsJ_V57M (tetracycline), tetM (tetracycline), and gyrA_S91F (ciprofloxacin). Resistance determinants 16SrRNA_C1192U (spectinomycin), mtrR_G45D (azithromycin), and penA_D545S, penA_mosaic (cefixime/ceftriaxone) correlated with the WHO control isolates.

Conclusions

Eight resistance-associated targets correlated with phenotypic culture results. The porA pseudogene reliably detected N. gonorrhoeae. Larger cohorts are required to validate the utility of these targets as a convenient culture-free diagnostic tool, to guide STI management in a South African population.

Impact of Anatomic Site, Specimen Collection Timing, and Patient Symptom Status on Neisseria gonorrhoeae Culture Recovery

BACKGROUND

Neisseria gonorrhoeae culture is required for antimicrobial susceptibility testing, but recovering isolates from clinical specimens is challenging. Although many variables influence culture recovery, studies evaluating the impact of culture specimen collection timing and patient symptom status are limited. This study analyzed urogenital and extragenital culture recovery data from Centers for Disease Control and Prevention's Strengthening the US Response to Resistant Gonorrhea (SURRG) program, a multisite project, which enhances local N. gonorrhoeae culture and antimicrobial susceptibility testing capacity.

METHODS

Eight SURRG jurisdictions collected gonococcal cultures from patients with N. gonorrhoeae-positive nucleic acid amplification test (NAAT) results attending sexually transmitted disease and community clinics. Matched NAAT and culture specimens from the same anatomic site were collected, and culture recovery was assessed. Time between NAAT and culture specimen collection was categorized as same day, 1 to 7 days, 8 to 14 days, or ≥15 days, and patient symptoms were matched to the anatomic site where culture specimens were collected.

RESULTS

From 2018 to 2019, among persons with N. gonorrhoeae-positive NAAT, urethral infections resulted in the highest culture recovery (5927 of 6515 [91.0%]), followed by endocervical (222 of 363 [61.2%]), vaginal (63 of 133 [47.4%]), rectal (1117 of 2805 [39.8%]), and pharyngeal (1019 of 3678 [27.7%]) infections. Culture recovery was highest when specimens were collected on the same day as NAAT specimens and significantly decreased after 7 days. Symptoms were significantly associated with culture recovery at urethral (P = <0.0001) and rectal (P = <0.0001) sites of infection but not endocervical, vaginal, or pharyngeal sites.

CONCLUSIONS

Culture specimen collection timing and patient symptomatic status can impact culture recovery. These findings can guide decisions about culture collection protocols to maximize culture recovery and strengthen detection of antimicrobial-resistant infections.

Detection and Drug Susceptibility Testing of Neisseria gonorrhoeae Using Isothermal Microcalorimetry

Background: Gonorrhea is a frequently encountered sexually transmitted disease that results in urethritis and can further lead to pelvic inflammatory disease, infertility, and possibly disseminated gonococcal infections. Thus, it must be diagnosed promptly and accurately. In addition, drug susceptibility testing should be performed rapidly as well. Unfortunately, Neisseria gonorrhoea is a fastidious microorganism that is difficult to grow and requires culturing in an opaque medium. Methods: Here, we used isothermal microcalorimetry (IMC) to monitor the growth and the antimicrobial susceptibility of N. gonorrhoea. Results: Using IMC, concentrations of N. gonorrhoea between 2000 and 1 CFU·mL⁻¹ were detected within 12 to 33 h. In addition, drug susceptibility could be monitored easily. Conclusions: The use of isothermal microcalorimetry provides an interesting and useful tool to detect and characterize fastidious microbes such as N. gonorrhoea that require media incompatible with optical detection conventionally used in many commercial systems.

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.

Bacterial sexually transmitted infections

Worldwide, the incidence of bacterial sexually transmitted infections (STIs) has shown a significant increase in recent years. In Germany, this circumstance is reflected by a rise in the number of reported syphilis cases. There has also been an uptick in the incidence of non-notifiable STIs such as gonorrhea and infections caused by Chlamydia trachomatis and Mycoplasma genitalium. A key factor in the spread of these infections is their varied clinical presentation, which includes urogenital, pharyngeal and rectal involvement as well as a large number of asymptomatic cases. New real-time multiplex PCR methods allow for rapid and targeted detection of STI pathogens. The most common bacterial STI is urogenital chlamydial infection caused by serovars D-K, which affects young adults in particular. Lymphogranuloma venereum (LGV) caused by L serovars often presents as chlamydial proctitis. In recent years, Neisseria (N.) gonorrhoeae has shown a significant development of resistance, with high-level monoresistance and multiresistance to antibiotics commonly used for treatment. It is therefore imperative that sensitivity testing of N. gonorrhoeae be performed in addition to nucleic acid amplification tests (NAATs). Increased drug resistance has also been observed for Mycoplasma genitalium, a fact that complicates treatment.

The Laboratory Diagnosis of Neisseria gonorrhoeae: Current Testing and Future Demands

The ideal laboratory test to detect Neisseria gonorrhoeae (Ng) should be sensitive, specific, easy to use, rapid, and affordable and should provide information about susceptibility to antimicrobial drugs. Currently, such a test is not available and presumably will not be in the near future. Thus, diagnosis of gonococcal infections presently includes application of different techniques to address these requirements. Microscopy may produce rapid results but lacks sensitivity in many cases (except symptomatic urogenital infections in males). Highest sensitivity to detect Ng was shown for nucleic acid amplification technologies (NAATs), which, however, are less specific than culture. In addition, comprehensive analysis of antibiotic resistance is accomplished only by in vitro antimicrobial susceptibility testing of cultured isolates. As a light at the end of the tunnel, new developments of molecular techniques and microfluidic systems represent promising opportunities to design point-of-care tests for rapid detection of Ng with high sensitivity and specificity, and there is reason to hope that such tests may also provide antimicrobial resistance data in the future.

Bakterielle sexuell übertragbare Infektionen

Bakterielle sexuell übertragbare Infektionen (STI) zeigen seit Jahren weltweit eine deutliche Zunahme. In Deutschland wird diese Tatsache durch steigende Meldezahlen für Syphilis bestätigt. Auch für die nicht meldepflichtigen STI Gonorrhoe, Chlamydia-trachomatis- und Mycoplasma-genitalium-Infektionen wird eine zunehmende Inzidenz beobachtet. Entscheidend für die Weiterverbreitung ist, dass das breite klinische Spektrum, welches neben Urogenitalsitus auch Pharynx und Rektum einbezieht, durch eine hohe Zahl asymptomatischer Verläufe ergänzt wird. Neue Real-Time-Multiplex-Diagnostikverfahren ermöglichen einen schnellen und gezielten Nachweis von STI-Erregern. Die häufigste bakterielle STI ist die urogenitale Chlamydieninfektion mit den Serovaren D-K, die besonders bei jungen Erwachsenen auftritt. Einer Chlamydien-Proktitis kann eine Infektion mit L-Serovaren und damit eine Lymphogranuloma-venereum (LGV)-Infektion zugrunde liegen. Neisseria (N.) gonorrhoeae zeigte in den letzten Jahren eine starke Resistenzentwicklung mit Ausbildung von Einzel- und Multiresistenzen gegenüber bisher gängigen Antibiotika. Daher ist für N. gonorrhoeae zusätzlich zum nucleic acid amplification test (NAAT) eine kulturelle Empfindlichkeitstestung durchzuführen. Auch für Mycoplasma genitalium sind Resistenzentwicklungen bekannt, die eine Therapie erschweren können.

Comparison of rRNA-based and DNA-based nucleic acid amplifications for detection of Chlamydia trachomatis, Neisseria gonorrhoeae, and Ureaplasma urealyticum in urogenital swabs

Background

Nucleic acid amplification tests (NAAT) are well-accepted in diagnosis and surveillance of sexually infectious pathogens worldwide. However, performance differences between a RNA-based NAAT and DNA-based NAAT are rarely reported. This study compares the performances of the RNA-based SAT (simultaneous amplification and testing) assay and the DNA-based quantitative real-time polymerase chain reaction (qPCR) assay.

Methods

A total of 123 urogenital swabs were collected from outpatients with suspected genital infections in our hospital. Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), and Ureaplasma urealyticum (UU) in these swabs were simultaneously tested by SAT and qPCR. Any swabs were positive in the qPCR assay were further verified by following cloning and sequencing. All statistical analysis was performed using the SPSS software.

Results

When the concentrations of CT, NG, or UU were more than 1 × 10³ copies/ml, 100% agreements between SAT and qPCR were observed regardless of the pathogen. No discrepancy was found. However, the sensitivity of SAT is significantly higher than qPCR in samples with concentration less than 1 × 10³ copies/ml. When tested by SAT and qPCR, 57.14 and 28.57% were positive for CT, 46.15% and 0 were positive for NG, 80% and 0 were positive for UU, respectively.

Conclusions

The SAT assay has better agreements and higher sensitivities when compared with the qPCR assay, and thus could be a better choice for screening, diagnosis, and surveillance of sexually transmitted diseases, especially for CT and NG.

A Case of Persistent and Possibly Treatment Resistant Pharyngeal Gonorrhea

An HIV-negative man with pharyngeal gonorrhea had a positive test-of-cure (nucleic acid amplification test) result 7 days after treatment with ceftriaxone/azithromycin. Neisseria gonorrhoeae Multi-Antigen Sequencing Type 1407 and mosaic pen A (XXXIV) gene were identified in the test-of-cure specimen, and culture was negative. Retreatment with ceftriaxone 500 mg intramuscularly plus azithromycin 2 g orally yielded a negative test-of-cure result.