Use Of Nucleic Acid Amplification Tests Research Articles

Clinicoradiological Profile of Endobronchial Tuberculosis: A Cross-sectional Study

Introduction: Tuberculosis (TB) is a disease that causes severe mortality and morbidity worldwide, including India. Endobronchial Tuberculosis (EBTB) is an uncommon form of TB, which is often underdiagnosed due to the difficulty in diagnosis. This form of TB often has a poor prognosis and long-lasting sequelae. Aim: To study the proportion of EBTB in clinically diagnosed pulmonary TB and to study the clinicoradiological and bronchoscopic profile of EBTB. Materials and Methods: This study was a hospital-based recordbased cross-sectional study that included patients with sputum smear negative for Acid-Fast Bacilli (AFB) and Mycobacterium tuberculosis (M. tuberculosis) not detected on Nucleic Acid Amplification Test (NAAT), who were clinically diagnosed with TB. Bronchoscopy was performed on such patients, and samples were sent for investigations, including histopathology and NAAT. Demographic characteristics, bronchoscopy and radiology findings , and microbiology results were documented. Quantitative variables were summarised as means, and categorical variables were presented as percentages. Results: A total of 198 underwent bronchoscopy, of which 20 (10%) were diagnosed with EBTB. The mean age was 22 years, and 65% were females. The most common clinical feature in these patients was fever, the most common radiological presentation was lobar collapse, and the most common bronchoscopy feature was a tumorous lesion. NAAT detected M. tuberculosis in the bronchial wash in 50% of patients diagnosed with EBTB. A total of 45% of patients had TB which was diagnosed on histopathology. Conclusion: EBTB was diagnosed in 10% of smear-negative, NAAT-negative cases. The use of NAAT on bronchoscopy wash samples resulted in a high yield in diagnosis.

Comparison of Microscopy, Culture and Molecular Methods for Diagnosing Gonorrhea

Gonorrhea, a sexually transmitted infection caused by Neisseria gonorrhoeae, continues to be a significant global public health concern. The timely and accurate diagnosis of this infectious disease is crucial for its effective management. Traditional methods, especially culture, were historically considered the gold standard for diagnosing gonorrhea. However, the introduction of nucleic acid amplification tests (NAATs), such as Real-Time PCR, has revolutionized diagnostic approaches. Currently, the Center for Disease Control and Prevention (CDC) recommends NAAT as the primary diagnostic method, with culture reserved for specific cases, particularly for testing antimicrobial susceptibility in instances of suspected treatment failure. The International Union against Sexually Transmitted Infections (IUSTI) provides guidelines for the use of NAAT or culture, depending on clinical scenarios. This study conducted a retrospective comparative analysis of various diagnostic methods at the Apex Regional STD Centre in New Delhi, India, spanning from January 1, 2022, to December 31, 2022. Culture, Real-Time PCR, and smear examination were compared for the diagnosis of gonorrhea. A total of 33 samples were included in the analysis, with the following percentages: culture (92.02%), PCR (100%), and smear examination (100%). An intriguing finding was that 7.98% of samples were culture-negative but PCR-positive, highlighting a significant disparity between the two methods. This observation underscores the limitations of relying solely on culture for gonorrhea diagnosis and the potential consequences, including treatment delays, disease transmission, and the development of antibiotic-resistant strains. In summary, this study underscores the critical need for accurate and reliable diagnostic methods for gonorrhea. It emphasizes the evolving diagnostic landscape, with NAATs emerging as essential tools. The findings from multiple studies stress the complementary roles of different diagnostic methods and the necessity of adapting to evolving diagnostic techniques. This research highlights the importance of collaborative approaches to enhance accuracy and address the evolving challenges of gonorrhea diagnosis. Ultimately, the significance of laboratory testing extends beyond individual patient care to broader public health goals and the prevention of sexually transmitted infections.

Analysis of National Healthcare Safety Network Clostridioides difficile Infection Standardized Infection Ratio by Test Type

Background: The NHSN has used positive laboratory tests for surveillance of Clostridioides difficile infection (CDI) LabID events since 2009. Typically, CDIs are detected using enzyme immunoassays (EIAs), nucleic acid amplification tests (NAATs), or various test combinations. The NHSN uses a risk-adjusted, standardized infection ratio (SIR) to assess healthcare facility-onset (HO) CDI. Despite including test type in the risk adjustment, some hospital personnel and other stakeholders are concerned that NAAT use is associated with higher SIRs than are EIAs. To investigate this issue, we analyzed NHSN data from acute-care hospitals for July 1, 2017 through June 30, 2018. Methods: Calendar quarters for which CDI test type was reported as NAAT (includes NAAT, glutamate dehydrogenase (GDH)+NAAT and GDH+EIA followed by NAAT if discrepant) or EIA (includes EIA and GDH+EIA) were selected. HO CDI SIRs were calculated for facility-wide inpatient locations. We conducted the following analyses: (1) Among hospitals that did not switch their test type, we compared the distribution of HO incident rates and SIRs by those reporting NAAT vs EIA. (2) Among hospitals that switched their test type, we selected quarters with a stable switch pattern of 2 consecutive quarters of each of EIA and NAAT (categorized as pattern EIA-to-NAAT or NAAT-to-EIA). Pooled semiannual SIRs for EIA and NAAT were calculated, and a paired t test was used to evaluate the difference of SIRs by switch pattern. Results: Most hospitals did not switch test types (3,242, 89%), and 2,872 (89%) reported sufficient data to calculate SIRs, with 2,444 (85%) using NAAT. The crude pooled HO CDI incidence rates for hospitals using EIA clustered at the lower end of the histogram versus rates for NAAT (Fig. 1). The SIR distributions of both NAAT and EIA overlapped substantially and covered a similar range of SIR values (Fig. 1). Among hospitals with a switch pattern, hospitals were equally likely to have an increase or decrease in their SIR (Fig. 2). The mean SIR difference for the 42 hospitals switching from EIA to NAAT was 0.048 (95% CI, −0.189 to 0.284; P = .688). The mean SIR difference for the 26 hospitals switching from NAAT to EIA was 0.162 (95% CI, −0.048 to 0.371; P = .124). Conclusions: The pattern of SIR distributions of both NAAT and EIA substantiate the soundness of NHSN risk adjustment for CDI test types. Switching test type did not produce a consistent directional pattern in SIR that was statistically significant.Disclosures: NoneFunding: None

Analysis of National Healthcare Safety Network Clostridioides difficile Infection Standardized Infection Ratio by Test Type

Background: The National Healthcare Safety Network (NHSN) has used positive laboratory tests for surveillance of Clostridioides difficile infection (CDI) LabID events since 2009. Typically, CDIs are detected using enzyme immunoassays (EIAs), nucleic acid amplification tests (NAATs), or various test combinations. The NHSN uses a risk-adjusted, standardized infection ratio (SIR) to assess healthcare facility-onset (HO) CDI. Despite including test type in the risk adjustment, some hospital personnel and other stakeholders are concerned that NAAT use is associated with higher SIRs than EIA use. To investigate this issue, we analyzed NHSN data from acute-care hospitals for July 1, 2017, through June 30, 2018. Methods: Calendar quarters where CDI test type was reported as NAAT (includes NAAT, glutamate dehydrogenase (GDH)+NAAT and GDH+EIA followed by NAAT if discrepant) or EIA (includes EIA and GDH+EIA) were selected. HO-CDI SIRs were calculated for facility-wide inpatient locations. We conducted the following 2 analyses: (1) Among hospitals that did not switch their test type, we compared the distribution of HO incident rates and SIRs by those reporting NAAT versus EIA. (2) Among hospitals that switched their test type, we selected quarters with a stable switch pattern of 2 consecutive quarters of each of EIA and NAAT (categorized as EIA-to-NAAT or NAAT-to-EIA). Pooled semiannual SIRs for EIA and NAAT were calculated, and a paired t test was used to evaluate the difference in SIRs by switch pattern. Results: Most hospitals did not switch test types (3,242, 89%), and 2,872 (89%) reported sufficient data to calculate an SIR, with 2,444 (85%) using NAAT. The crude pooled HO CDI incidence rates for hospitals using EIAs clustered at the lower end of the histogram versus rates for NAATs (Fig. 1). The SIR distributions, both NAATs and EIAs, overlapped substantially and covered a similar range of SIR values (Fig. 1). Among hospitals with a switch pattern, hospitals were equally likely to have an increase or decrease in their SIRs (Fig. 2). The mean SIR difference for the 42 hospitals switching from EIA to NAAT was 0.048 (95% CI, −0.189 to 0.284; P = .688). The mean SIR difference for the 26 hospitals switching from NAAT to EIA was 0.162 (95% CI, −0.048 to 0.371; P = .124). Conclusions: The pattern of SIR distribution for both NAAT and EIA substantiate the soundness of the NHSN’s risk adjustment for CDI test types. Switching test type did not produce a consistent directional pattern in SIR that was statistically significant.Funding: NoneDisclosures: None

A Comparison of US Clinical Laboratory Chlamydia and Gonorrhea Testing Practices Before and After the 2014 Centers for Disease Control and Prevention Testing Recommendations.

Adherence to recommended laboratory testing practices is crucial for sexually transmitted infection prevention and control. The objective of this article is to compare Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) testing practices of US clinical laboratories in 2013 before the updated 2014 Centers for Disease Control and Prevention recommendations and in 2015 after the updated recommendations. A total of 236 clinical laboratories participated in surveys about their 2013 and 2015 CT and NG testing practices, including questions on specimen types collected and assays used. There was an increase of 5 laboratories offering CT nucleic acid amplification testing (NAAT) from 2013 to 2015 and an increase of 5 laboratories offering NG NAAT. There was a net increase of 3 laboratories accepting urine for CT and NG NAAT, the preferred specimen type for male individuals. There was not a net increase in the total number of laboratories accepting vaginal swabs for CT NAAT (n = 89 in 2013 and 2015), the preferred specimen type for female individuals, but there was an increase of 3 laboratories accepting vaginal swabs for NG NAAT. The number of laboratories performing NG susceptibility testing decreased from 100 in 2013 to 89 in 2015 (χ2 = 1.07, P > 0.10). There were no major changes in testing practices in the 2-year period from 2013 to 2015. However, there were some small shifts, including increases in the use of NAATs, acceptance of Centers for Disease Control and Prevention-preferred specimen types for CT/NG, and changes in usage of assays by manufacturer.

A fully automated centrifugal microfluidic system for sample-to-answer viral nucleic acid testing.

The outbreak of virus-induced infectious diseases poses a global public-health challenge. Nucleic acid amplification testing (NAAT) enables early detection of pandemic viruses and plays a vital role in preventing onward transmission. However, the requirement of skilled operators, expensive instrumentation, and biosafety laboratories has hindered the use of NAAT for screening and diagnosis of suspected patients. Here we report development of a fully automated centrifugal microfluidic system with sample-in-answer-out capability for sensitive, specific, and rapid viral nucleic acid testing. The release of nucleic acids and the subsequent reverse transcription loop-mediated isothermal amplification (RT-LAMP) were integrated into the reaction units of a microfluidic disc. The whole processing steps such as injection of reagents, fluid actuation by rotation, heating and temperature control, and detection of fluorescence signals were carried out automatically by a customized instrument. We validate the centrifugal microfluidic system using oropharyngeal swab samples spiked with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) armored RNA particles. The estimated limit of detection for armored RNA particles is 2 copies per reaction, the throughput is 21 reactions per disc, and the assay sample-to-answer time is approximately 70 min. This enclosed and automated microfluidic system efficiently avoids viral contamination of aerosol, and can be readily adapted for virus detection outside the diagnostic laboratory. Electronic Supplementary MaterialSupplementary material is available for this article at 10.1007/s11426-020-9800-6 and is accessible for authorized users.

Trends in U.S. Burden of Clostridioides difficile Infection and Outcomes

BackgroundEfforts to prevent Clostridioides difficile infection continue to expand across the health care spectrum in the United States. Whether these efforts are reducing the national burden of C. difficile infection is unclear.MethodsThe Emerging Infections Program identified cases of C. difficile infection (stool specimens positive for C. difficile in a person ≥1 year of age with no positive test in the previous 8 weeks) in 10 U.S. sites. We used case and census sampling weights to estimate the national burden of C. difficile infection, first recurrences, hospitalizations, and in-hospital deaths from 2011 through 2017. Health care–associated infections were defined as those with onset in a health care facility or associated with recent admission to a health care facility; all others were classified as community-associated infections. For trend analyses, we used weighted random-intercept models with negative binomial distribution and logistic-regression models to adjust for the higher sensitivity of nucleic acid amplification tests (NAATs) as compared with other test types.ResultsThe number of cases of C. difficile infection in the 10 U.S. sites was 15,461 in 2011 (10,177 health care–associated and 5284 community-associated cases) and 15,512 in 2017 (7973 health care–associated and 7539 community-associated cases). The estimated national burden of C. difficile infection was 476,400 cases (95% confidence interval [CI], 419,900 to 532,900) in 2011 and 462,100 cases (95% CI, 428,600 to 495,600) in 2017. With accounting for NAAT use, the adjusted estimate of the total burden of C. difficile infection decreased by 24% (95% CI, 6 to 36) from 2011 through 2017; the adjusted estimate of the national burden of health care–associated C. difficile infection decreased by 36% (95% CI, 24 to 54), whereas the adjusted estimate of the national burden of community-associated C. difficile infection was unchanged. The adjusted estimate of the burden of hospitalizations for C. difficile infection decreased by 24% (95% CI, 0 to 48), whereas the adjusted estimates of the burden of first recurrences and in-hospital deaths did not change significantly.ConclusionsThe estimated national burden of C. difficile infection and associated hospitalizations decreased from 2011 through 2017, owing to a decline in health care–associated infections. (Funded by the Centers for Disease Control and Prevention.)

Antenatal and intrapartum nucleic acid amplification test use for group B Streptococcus screening—United States, 2016

Perinatal group B Streptococcus (GBS) disease prevention guidelines in 2010 allowed for processing of screening specimens by nucleic acid amplification tests (NAATs); however, the extent of NAAT use is unknown. A 2016 laboratory survey sent to 10 surveillance sites found that 18.7% of responding laboratories offered NAAT for GBS screening (antenatal only: 7.3%; intrapartum only: 4.1%; both: 3.4%).

Sexual Assault and Sexually Transmitted Infections in Adults, Adolescents, and Children.

Survivors of sexual assault are at risk for acquiring sexually transmitted infections (STIs). We conducted literature reviews and invited experts to assist in updating the sexual assault section for the 2015 Centers for Disease Control and Prevention sexually transmitted diseases (STD) treatment guidelines. New recommendations for STI management among adult and adolescent sexual assault survivors include use of nucleic acid amplification tests (NAATs) for detection of Trichomonas vaginalis by vaginal swabs; NAATs for detection of Neisseria gonorrhoeae and Chlamydia trachomatis from pharyngeal and rectal specimens among patients with a history of exposure or suspected extragenital contact after sexual assault; empiric therapy for gonorrhea, chlamydia, and trichomoniasis based on updated treatment regimens; vaccinations for human papillomavirus (HPV) among previously unvaccinated patients aged 9-26 years; and consideration for human immunodeficiency virus (HIV) nonoccupational postexposure prophylaxis using an algorithm to assess the timing and characteristics of the exposure. For child sexual assault (CSA) survivors, recommendations include targeted diagnostic testing with increased use of NAATs when appropriate; routine follow-up visits within 6 months after the last known sexual abuse; and use of HPV vaccination in accordance with national immunization guidelines as a preventive measure in the post-sexual assault care setting. For CSA patients, NAATs are considered to be acceptable for identification of gonococcal and chlamydial infections from urine samples, but are not recommended for extragenital testing due to the potential detection of nongonococcal Neisseria species. Several research questions were identified regarding the prevalence, detection, and management of STI/HIV infections among adult, adolescent, and pediatric sexual assault survivors.

001.6 Exploring the benefits of molecular testing for gonorrhoea antibiotic resistance surveillance in remote settings

Background The latest nucleic acid amplification tests (NAAT) for gonorrhoea are convenient and accurate, and are often used in place of culture-based tests for diagnosis. However the increasing use of NAATs in remote settings in Australia has compromised surveillance for gonorrhoea antimicrobial resistance (AMR). A molecular resistance test that can make use of samples collected for NAAT diagnosis may provide a means to enhance surveillance in remote settings where the availability of samples suitable for culture-based AMR testing is declining. We used a mathematical model to assess the potential benefit of a molecular test in terms of the timeliness of detection of gonorrhoea AMR. Methods An individual-based mathematical model was developed to describe the transmission of gonorrhoea in a remote Indigenous population in Australia. We estimated the impact of the molecular test on the time delay between first importation and the first confirmation that the prevalence of gonorrhoea AMR has breached the WHO-recommended 5% threshold (when a change in antibiotic should occur). Results The model suggests that when culture is the only means of testing for AMR, the breach will only be detected when the actual prevalence of AMR in the population has already reached 8 – 18%. With the addition of a molecular AMR test and assuming AMR can be determined for all samples, the breach will be detected when the actual prevalence of AMR in the population has reached 6%, which only slightly exceeds the recommended notification threshold of 5%. Conclusion Molecular tests have the potential to provide more timely warning of the emergence of gonorrhoea AMR in remote settings where surveillance is compromised by the increased use of NAATs for diagnosis. This in turn will facilitate earlier treatment switching and more targeted treatment, which has the potential to reduce the population impact of gonorrhoea AMR. Disclosure of interest statement This work was supported by National Health and Medical Research Council Project Grants (APP1025517). The National Neisseria Network is funded by the Australian Government Department of Health. The Kirby Institute is funded by the Australian Government Department of Health and Ageing and is affiliated with the Faculty of Medicine, University of New South Wales. The views expressed in this publication do not necessarily represent the position of the Australian Government.

Management of the Potential Organ Donor in the ICU: Society of Critical Care Medicine/American College of Chest Physicians/Association of Organ Procurement Organizations Consensus Statement.

Management of the Potential Organ Donor in the ICU: Society of Critical Care Medicine/American College of Chest Physicians/Association of Organ Procurement Organizations Consensus Statement This consensus statement provides important guidelines for deceased donation to the transplant community. The document defines the standard of care for intensive care units regarding: (1) Definitions of death; (2) Timing and request for authorization; (3) Use of donors with malignancies and infections; (4) Testing for human immunodeficiency virus, hepatitis B and C; (5) Hemodynamic management; (6) Fluid resuscitation; (7) Vasoactive drugs; (8) Hemodynamic monitoring; (9) Endocrine dysfunction and hormone replacement; (10) Pediatric donor issues; (11) Specific organ management: heart, kidney, liver, lung and pancreas. The authors confirm the important impact that donation after circulatory determination of death (DCD) can make to increase the availability of organs. They highlight that liver and lungs can be used from selected DCD donors for transplantation. Clinicians must be prepared for potential DCD scenarios in which death does not occur within the established time after withdrawal of life-sustaining therapy: appropriate protocols should be in place to return the patient to a critical care setting for continuing care and to provide appropriate family support. The authors comment that intensive care unit caregivers and OPO representatives should provide all patients with equal opportunities for organ donation. One important recommendation is the early referral of potential donors to procurement agencies to increase the period available to evaluate a patient’s medical suitability for donation and to relay information to families in a manner that minimizes time pressure. The group recommends that OPO or designated coordinators with expertise should request authorization for organ donation in all institutions, using a collaborative approach with the rest of the healthcare team. There are several recommendations regarding malignancies and infections, but in general, risks of donor transmission must be weighed against risks for a potential recipient of not receiving the organ. Determinations about an individual donor’s medical suitability for organ donation should be made in conjunction with the local OPO and involved transplant centers. The authors recommend that patients with bacterial meningitis are suitable organ donors as long as they have received therapy directed against an identified or presumed pathogen while organ recipients get treated with a similar antibiotic regimen for 5 to 10 days. Organs should not be procured from patients with undiagnosed febrile illnesses, encephalitis, meningitis, or flaccid paralysis of unknown etiology. The use of nucleic acid amplification testing to detect the presence of human immunodeficiency virus RNA reduces the likelihood of unrecognized viremia by approximately half in all high-risk behavior categories; therefore, the use of nucleic-acid amplification testing was recommended for high-risk behavior groups. A frequent challenge for kidney and lung procurement is conflicting fluid requirements for the donor. Traditionally, aggressive fluid resuscitation and management were thought to result in improved procurement of kidneys, whereas a conservative fluid replacement strategy is thought to benefit the quality of lungs. The authors recommend a central venous catheter and/or pulmonary artery catheter to manage fluids: a combination of hormone replacement therapy and CVP-targeted fluid resuscitation should be the gold standard. Specific variables include a mean arterial pressure of 60 to 70 mm Hg, urinary output of 1 to 3 mL/kg per hour, a decrease in dose of vasoactive agents (dopamine ≤ 10 μg/kg per minute), and a left ventricular ejection fraction of at least 45%. Isotonic crystalloids and lactated Ringer are recommended as first line fluid management. Dopamine and arginine vasopressin replacement should be considered when hypotension persists despite adequate volume resuscitation. High-dose corticosteroid administration reduces the potential deleterious effects of the inflammatory cascade set in place subsequent to brain death. Ideally, steroids should be administered after blood has been collected for tissue typing as the expression of human leukocyte antigen may be suppressed. Thyroid replacement therapy—either alone or as part of a combination hormone therapy with intravenous arginine vasopressin, corticosteroids, and insulin—should be considered for hemodynamically unstable donors or for potential cardiac donors with abnormal (<45%) left ventricular ejection fraction. Specific aspects of death declaration for pediatric donors, including management goals are detailed in this report and differ from adult donors. Furthermore, organ-specific considerations are discussed in great detail—an extremely helpful tool in donor management and procurement.

How do changes in the population tested for chlamydia over time affect observed trends in chlamydia positivity? Analysis of routinely collected data from young women tested for chlamydia in family planning clinics in the Pacific Northwest (USA), between 2003 and 2010.

Background The proportion of chlamydia tests that are positive (positivity) is dependent on the population tested and the test technology used. The way in which changes in these variables might affect trends in positivity over time is investigated. Data from 15- to 24-year-old women tested for chlamydia in family planning clinics participating in the Infertility Prevention Project in the Pacific Northwest, United States (USA Public Health Service Region X) during 2003-2010 (n=590557) were analysed. Trends in positivity and in test, demographic and sexual behaviour variables were identified. Unadjusted and adjusted trends in chlamydia positivity were calculated using logistic regression. The proportion of tests carried out using nucleic acid amplification tests (NAATs) increased dramatically during the analysis period in two states. Smaller changes in demographic and behavioural characteristics were seen. Controlling for test technology used had the largest effect on the trend in testing positive per year, leading to a fall in the calculated odds ratio of testing positive from 1.06 to 1.02 in Oregon, and from 1.07 to 1.02 in Idaho. Controlling for other variables had minimal effect on chlamydia positivity trends. Changes in NAAT use had a large effect on observed trends in chlamydia positivity over time in the two states where NAATs were introduced during the analysis period. While trends in chlamydia positivity may be a useful metric for monitoring chlamydia burden, it is important to consider changes in test type when interpreting these data.

Can newly developed, rapid immunochromatographic antigen detection tests be reliably used for the laboratory diagnosis of influenza virus infections?

Five years ago, the Point-Counterpoint series was launched. The initial article asked about the role of rapid immunochromatographic antigen testing in the diagnosis of influenza A virus 2009 H1N1 infection (D. F. Welch and C. C. Ginocchio, J Clin Microbiol 48:22-25, 2010, http://dx.doi.org/10.1128/JCM.02268-09). Since that article, not only have major changes been made in immunochromatographic antigen detection (IAD) testing for the influenza viruses, but there has also been rapid development of commercially available nucleic acid amplification tests (NAATs) for influenza virus detection. Further, a novel variant of influenza A, H7N9, has emerged in Asia, and H5N1 is also reemergent. In that initial article, the editor of this series, Peter Gilligan, identified two issues that required further consideration. One was how well IAD tests worked in clinical settings, especially in times of antigen drift and shift. The other was the role of future iterations of influenza NAATs and whether this testing would be available in a community hospital setting. James Dunn, who is Director of Medical Microbiology and Virology at Texas Children's Hospital, has extensive experience using IAD tests for diagnosing influenza. He will discuss the application and value of these tests in influenza diagnosis. Christine Ginocchio, who recently retired as the Senior Medical Director, Division of Infectious Disease Diagnostics, North Shore-LIJ Health System, and now is Vice President for Global Microbiology Affairs at bioMérieux, Durham, NC, wrote the initial counterpoint in this series, where she advocated the use of NAATs for influenza diagnosis. She will update us on the commercially available NAAT systems and explain what their role should be in the diagnosis of influenza infection.

Chlamydia Infections in Children and Adolescents

1. Lorena M. Siqueira, MD, MSPH* 1. *Division of Adolescent Medicine, Miami Children’s Hospital, Miami, FL. * Abbreviations: CDC: : Centers for Disease Control and Prevention FDA: : Food and Drug Administration HIV: : human immunodeficiency virus LGV: : lymphogranuloma venereum MIF: : microimmunofluorescent MSM: : men who have sex with men NAAT: : nucleic acid amplification tests PID: : pelvic inflammatory disease STI: : sexually transmitted infection 1. The need for annual screening for chlamydia in sexually active adolescents and young adults is underrecognized because this infection is asymptomatic in most females (75%) and males (50%). 2. Difficulty in diagnosis arises from the range of possible symptoms at presentation of symptomatic infections and the type of testing that can be used in each situation. After completing this article the reader should be able to: 1. Recognize the spectrum of clinical manifestations of chlamydia infection in neonates, children, and adolescents. 2. Discuss the appropriate use of culture and nonculture diagnostic tests for chlamydia infections in various age groups. 3. List the current recommendations for screening and treatment of chlamydia infections. A 17-year-old girl presents with prolonged menstrual bleeding associated with severe menstrual cramping pain. Her menarche was at age 13 years. Subsequent menstrual cycles were monthly, lasting 5 days, with average flow associated with mild to moderate pain relieved by over-the-counter pain medications. The current cycle began a month ago and is associated with severe lower abdominal pain. She admits to sexual activity with one partner and uses condoms intermittently. On examination she is afebrile and in discomfort, with a heart rate of 120 beats per minute. She does not appear anemic and has good capillary refill. She has diffuse abdominal pain with significant tenderness in both the right lower and upper quadrants. Chlamydiae are small obligate, gram-negative, intracellular bacteria that contain both DNA and RNA and were formerly considered to be viruses. There are 3 species that are pathogenic to humans: Chlamydia trachomatis , Chlamydophilia pneumoniae, and Chlamydophilia psittaci . They fall within 2 genera in the family Chlamydiaceae . C trachomatis is in …

S02.3 Extra-Genital CT/GC Testing by NAATS: Use in Screening and Prevalence of Infection in MSM, Issues in Validation

Most Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (GC) infections in men who have sex with men (MSM) are not in the urethra. This has been confirmed often since it was...

The effect on Neisseria gonorrhoeae screening rates in an integrated clinic following the introduction of dual nucleic acid amplification tests

Sirs: We read with interest the findings of Killick et al. 1 and agree that Neisseria gonorrhoeae (GC) nucleic acid amplification testing (NAAT) can provide a valuable addition to culture for identifying GC in low prevalence settings. Following the introduction of GC NAAT into our integrated family planning (FP) and genitourinary (GU) medicine service, we evaluated whether the use of NAAT increased the rates of GC screening and of GC detection. 2 Prior to the introduction of GC NAAT, prevalence of diagnosed GC within the clinic as assessed by culture alone was 0.87%. We sought to investigate concordance between NAAT and culture when both were carried out, within this low prevalence population. Dual-testing for GC and chlamydia (CT) using Aptima Combo 2 (AC2; Gen-Probe Inc., San Diego, CA, USA) was per- formed using self-taken vaginal swabs for asymptomatic women and urine for asymptomatic men. Those patients with clinical symptoms or signs, or contacts of GC underwent GC culture in addition to NAAT. When using AC2, all positive GC results were confirmed according to the manufacturer's instructions using the single analyte NAAT targeting a different RNA sequence: Aptima GC (Gen-Probe). All patients attending the clinic and undergoing GC screen- ing during a four-month period prior to, and following GC NAAT introduction were identified using laboratory databases; data were collected retrospectively. Follow-up attendances within an episode were excluded from analysis. Individuals diagnosed with GC were identified and case-notes were reviewed. We found that in the four months prior to the introduction of NAAT, 2307 symptomatic and asymptomatic patients were screened using GC culture alone, of which 20 (0.87%) were positive. Following the introduction of GC NAAT during a similar four-month period, a significant increase in screening was observed, with 3444 symptomatic and asymptomatic patients being screened with AC2. Of these, 43 (1.25%) were confirmed positive for GC. GC culture was also performed in 217 of the symptomatic individuals; of these 18 (8.3%) were culture posi- tive for GC. GC culture and NAAT showed concordance of positivity in 20/43 (46.5%) of cases. Eleven patients were NAAT positive, culture negative; 10/11 of these individuals had symptoms, signs or were high risk for GC. One of 11 cul- tured Neisseria meningitidis although subsequent GC NAAT testing using a different platform was also positive at the Sexually Transmitted Bacteria Reference Laboratory in Colindale, making it unlikely this was a false-positive. Twelve patients who were AC2 positive had no culture performed. Similarly to the findings by Killick et al., all patients with posi- tive GC cultures were also GC NAAT positive. In conclusion, following the introduction of GC NAAT we observed increased rates of screening and a doubling in the number of GC diagnoses during a similar time period. While it is possible there was an actual rise in the local GC incidence, the increase in diagnoses might also be attributable to a more sensitive test, acceptability of self-screening and a less time- consuming approach for the clinicians. The use of GC NAAT identified more infections than if culture alone had been used. Despite concern over the positive predictive value of GC NAAT in low prevalence settings, of those patients with posi- tive NAAT/negative cultures all had documented risk factors or symptoms of GC. We believe both these studies provide reassuring evidence for the use of GC NAAT in this setting, provided a confirmatory strategy is in place.

Performance of Clostridium difficile Toxin Enzyme Immunoassay and Nucleic Acid Amplification Tests Stratified by Patient Disease Severity

Many clinical laboratories in the United States are transitioning from toxin enzyme immunoassays (EIA) to nucleic acid amplification tests (NAATs) as the primary diagnostic test for Clostridium difficile infection (CDI). While it is known that the analytical sensitivity of the toxin EIA is poor, there are limited clinical data on the performance of these assays for patients with mild or severe CDI. Two hundred ninety-six hospital inpatients with diarrhea and clinical suspicion for CDI were tested prospectively by toxin EIA, by C. difficile NAAT, and with a reference standard toxigenic culture. Following completion of laboratory testing, retrospective chart reviews were performed to stratify patients into mild and severe disease groups based on clinical criteria using a standard point-based system. One hundred forty-three patients with CDI confirmed by toxigenic culture were evaluated in this study. Among the patients with mild CDI, 49% tested positive by toxin EIA and 98% tested positive by NAAT. Among patients with severe CDI, 58% tested positive by toxin EIA and 98% tested positive by NAAT. Increased CDI disease severity was not associated with an increased sensitivity of EIA (P = 0.31). These data demonstrate that toxin EIA performs poorly both for patients with severe CDI and for those with mild CDI and support the routine use of NAAT for the diagnosis of CDI. The presence of stool toxin measured by EIA does not correlate with disease severity.

Clinical impact of switching conventional enzyme immunoassay with nucleic acid amplification test for suspected Clostridium difficile-associated diarrhea

The impact of a new Clostridium difficile nucleic acid amplification test (NAAT) on antibiotic utilization in patients with suspected C difficile infection was assessed. This single-center, cross-sectional study of 270 patients demonstrated that the use of NAAT decreased antibiotic expenditure by reducing prolonged empiric days of therapy in these patients.

Evaluation of anopagene-based nucleic acid amplification test for detection ofNeisseria gonorrhoeaein urogenital samples in North India

Due to the poor positive predictive value of nucleic acid amplification tests (NAATs) for gonorrhoea when applied to a low-prevalence setting, current guidelines recommend the use of supplementary polymerase chain reaction (PCR) targeting a different gene for confirmation of true positives in urogenital specimens. This study sought to standardize and evaluate performance of an in-house opa gene-based PCR assay for gonorrhoea compared to assays targeting the porA pseudogene and 16S rRNA gene. Four hundred samples (300 endocervical, 100 urethral swabs) from patients attending STD clinics in New Delhi, India were used. The sensitivity, specificity, positive predictive value and negative predictive value of the opa-based PCR were 100%, 97·9%, 89·5% and 100%, respectively. In females, the use of NAATs provided enhanced diagnosis of gonorrhoea.

Testing Men Who Have Sex With Men for Urethral Infection With Chlamydia trachomatis and Neisseria gonorrhoeae Is Only Half the Job, and We Need the Right Tools

Standard operating procedure in STD clinics commonly has been to test urethral specimens when evaluating males, whether they are heterosexual or men who have sex with men (MSM). Rectal or oropharyngeal specimens may be tested in MSM with symptoms, or in some clinics as screening tests if individuals report sexual practices that would indicate risk of infection at these sites. In a report in this issue of Sexually Transmitted Diseases, Marcus and colleagues studied the prevalence of infection with Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (GC) in the urethra, the oropharynx, and rectum in asymptomatic MSM visiting the San Francisco STD clinic.1 A retrospective analysis of 3398 patient visits found CT or GC at 549 (16.2%) of those visits. The prevalence of infections among these asymptomatic men ranged from a high of 7.8% for rectal CT to a low of 0.4% for urethral GC. Strikingly, 83.8% of CT and GC infections would have been missed if only urethral screening was performed. What was found in the Marcus study, and in others, as well, is that the majority of infections with CT/GC in MSM are not in the urethra. The first major study to make this point was performed by Kent and colleagues, in 2 clinics in San Francisco, where they found that 50% of chlamydial and gonococcal infections were extraurethral.2 That finding has been confirmed by a number of approaches, including retrospective chart reviews and prospectively designed studies (Table 1). While these studies have focused on rectal and pharyngeal CT/GC infections in MSM, it must be noted that such infections are far from rare in women.12,13 In many clinical settings, the infections in women will be seen more often than those in men. These extragenital infections should not be ignored now, and we need more research to better define their potential consequences. Both CT and GC are recognized as causes of proctitis, and even asymptomatic infections have been associated with HIV transmission. 14 Current CDC recommendations call for routine screening of the oropharynx and rectum in MSM who may be exposed to GC or CT at those sites. It is not clear whether pharyngeal infections have a major direct impact on health. But evidence is emerging that infection can be transmitted from the oropharynx to the urethra of sex partners, thus continuing chains of infection.15 All of the cited studies have been made possible by the introduction and application of highly sensitive and specific nucleic acid amplification tests (NAATs) for the diagnosis of CT and GC infections. NAATs are recommended for routine diagnosis of CT/GC infections.15 Where direct comparisons have been done, it has been shown that the increment in sensitivity for NAATs as compared to culture is greater with pharyngeal and rectal specimens than it is with cervical and urethral specimens. An approximate doubling of the number of infections detected has been obtained with NAATs. 4,11 Alas, there remains a gap wherein the best tests are not readily available to the patients and providers who need them. Several NAATs are commercially available and have received FDA clearance for male and female urine specimens, urethral swabs from men, and cervical and vaginal swabs from women. Unfortunately, none have been cleared by the FDA for pharyngeal or rectal specimens. But the CDC, recognizing the superior performance of these tests used on these specimens, has taken an unusual step and recommended the use of NAATs for diagnosis of CT/GC in oropharyngeal and rectal specimens, even though such use has not received FDA clearance. 16 The