Impact of rapid nucleic acid amplification tests for tuberculosis on patient outcomes

Most health care personnel (HCP) reporting symptoms consistent with COVID-19 illness are assessed by high-accuracy SARS-CoV-2 assays performed in clinical laboratories, but the results of such assays typically are not available until the following day. This is an observational study over 16 weeks of a rapid nucleic acid amplification test (NAAT) performed at point of contact. The benchmark for comparison was a simultaneously obtained specimen assayed by a routine NAAT assay performed in a clinical laboratory. There were 577 paired rapid and routine NAAT results. Rapid test positive predictive value was 90.0% (95% confidence interval = 88.8%-91.2%), and negative predictive value was 95.2% (95% confidence interval = 93.5%-96.9%). The rapid test avoided an estimated 160 to 184 lost work shifts over 4 months. A rapid NAAT test-based strategy proved effective in safely clearing symptomatic employees without infection for earlier return to work.

Comparison of rapid nucleic acid amplification tests and rapid antigen tests for influenza in the emergency department.

Rapid and accurate influenza diagnostics can improve patient care. To summarize and compare accuracy of traditional rapid influenza diagnostic tests (RIDTs), digital immunoassays (DIAs), and rapid nucleic acid amplification tests (NAATs) in children and adults with suspected influenza. 6 databases from their inception through May 2017. Studies in English, French, or Spanish comparing commercialized rapid tests (that is, providing results in <30 minutes) with reverse transcriptase polymerase chain reaction reference standard for influenza diagnosis. Data were extracted using a standardized form; quality was assessed using QUADAS-2 (Quality Assessment of Diagnostic Accuracy Studies 2) criteria. 162 studies were included (130 of RIDTs, 19 of DIAs, and 13 of NAATs). Pooled sensitivities for detecting influenza A from Bayesian bivariate random-effects models were 54.4% (95% credible interval [CrI], 48.9% to 59.8%) for RIDTs, 80.0% (CrI, 73.4% to 85.6%) for DIAs, and 91.6% (CrI, 84.9% to 95.9%) for NAATs. Those for detecting influenza B were 53.2% (CrI, 41.7% to 64.4%) for RIDTs, 76.8% (CrI, 65.4% to 85.4%) for DIAs, and 95.4% (CrI, 87.3% to 98.7%) for NAATs. Pooled specificities were uniformly high (>98%). Forty-six influenza A and 24 influenza B studies presented pediatric-specific data; 35 influenza A and 16 influenza B studies presented adult-specific data. Pooled sensitivities were higher in children by 12.1 to 31.8 percentage points, except for influenza A by rapid NAATs (2.7 percentage points). Pooled sensitivities favored industry-sponsored studies by 6.2 to 34.0 percentage points. Incomplete reporting frequently led to unclear risk of bias. Underreporting of clinical variables limited exploration of heterogeneity. Few NAAT studies reported adult-specific data, and none evaluated point-of-care testing. Many studies had unclear risk of bias. Novel DIAs and rapid NAATs had markedly higher sensitivities for influenza A and B in both children and adults than did traditional RIDTs, with equally high specificities. Québec Health Research Fund and BD Diagnostic Systems.

Development and Comparison of a Rapid Isothermal Nucleic Acid Amplification Test for Typing of Herpes Simplex Virus Types 1 and 2 on a Portable Fluorescence Detector

Our objective was to assess the cost-effectiveness of novel rapid diagnostic tests: rapid influenza diagnostic tests (RIDT), digital immunoassays (DIA), rapid nucleic acid amplification tests (NAAT), and other treatment algorithms for influenza in high-risk patients presenting to hospital with influenza-like illness (ILI). We developed a decision-analytic model to assess the cost-effectiveness of diagnostic test strategies (RIDT, DIA, NAAT, clinical judgement, batch polymerase chain reaction) preceding treatment; no diagnostic testing and treating everyone; and not treating anyone. We modeled high-risk 65-year old patients from a health payer perspective and accrued outcomes over a patient's lifetime. We reported health outcomes, quality-adjusted life years (QALYs), healthcare costs, and net health benefit (NHB) to measure cost-effectiveness per cohort of 100,000 patients. Treating everyone with no prior testing was the most cost-effective strategy, at a cost-effectiveness threshold of $50,000/QALY, in over 85% of simulations. This strategy yielded the highest NHB of 15.0344 QALYs, but inappropriately treats all patients without influenza. Of the novel rapid diagnostics, NAAT resulted in the highest NHB (15.0277 QALYs), and the least number of deaths (1,571 per 100,000). Sensitivity analyses determined that results were most impacted by the pretest probability of ILI being influenza, diagnostic test sensitivity, and treatment effectiveness. Based on our model, treating high-risk patients presenting to hospital with influenza-like illness, without performing a novel rapid diagnostic test, resulted in the highest NHB and was most cost-effective. However, consideration of whether treatment is appropriate in the absence of diagnostic confirmation should be taken into account for decision-making by clinicians and policymakers.

BackgroundOur objective was to assess the cost-effectiveness of novel rapid diagnostic tests: rapid influenza diagnostic tests (RIDT), digital immunoassays (DIA), rapid nucleic acid amplification tests (NAAT), and other treatment algorithms for influenza in high-risk patients presenting to hospital with influenza-like illness (ILI).MethodsWe developed a decision-analytic model to assess the cost-effectiveness of diagnostic test strategies (RIDT, DIA, NAAT, clinical judgement, batch polymerase chain reaction) preceding treatment; no diagnostic testing and treating everyone; and not treating anyone. We modeled high-risk 65-year old patients from a health payer perspective and accrued outcomes over a patient’s lifetime. We reported health outcomes, quality-adjusted life years (QALYs), healthcare costs, and net health benefit (NHB) to measure cost-effectiveness per cohort of 100,000 patients.ResultsTreating everyone with no prior testing was the most cost-effective strategy, at a cost-effectiveness threshold of $50,000/QALY, in over 85% of simulations. This strategy yielded the highest NHB of 15.0344 QALYs, but inappropriately treats all patients without influenza. Of the novel rapid diagnostics, NAAT resulted in the highest NHB (15.0277 QALYs), and the least number of deaths (1,571 per 100,000). Sensitivity analyses determined that results were most impacted by the pretest probability of ILI being influenza, diagnostic test sensitivity, and treatment effectiveness.ConclusionsBased on our model, treating high-risk patients presenting to hospital with influenza-like illness, without performing a novel rapid diagnostic test, resulted in the highest NHB and was most cost-effective. However, consideration of whether treatment is appropriate in the absence of diagnostic confirmation should be taken into account for decision-making by clinicians and policymakers.

Multiplexed technologies for sexually transmitted infections offer a convenient diagnostics option to screen, confirm, and treat multiple pathogens simultaneously. Due to scarce published real-world diagnostic performance data, we did a systematic review. Two reviewers searched major databases for data published between Jan 1, 2009, and April 20, 2020, and abstracted and analysed sensitivity and specificity data from 24 studies, which assessed 17 multiplex rapid nucleic acid amplification test platforms and seven multiplex immunochromatographic devices. Overall, these studies evaluated 19 sexually transmitted infections in 26 126 individuals. High sensitivity and specificity were shown for rapid nucleic acid amplification platform tests and immunochromatographic devices, with performance varying by pathogen, device, seropositivity, and subpopulation screened. As most devices yielded more than 95% sensitivity and specificity, immunochromatographic tests and rapid nucleic acid amplification test platforms can be advised for screening and confirmatory use. These highly accurate devices are appropriate for integrated, rapid screening initiatives for sexually transmitted infections to screen and treat many of these infections simultaneously, for antimicrobial stewardship, and for disease elimination programmes.

We evaluated the performance of new high-throughput digital lateral flow immunoassays (LFIAs) detecting influenza antigens and compared them with those of the widely used digital LFIA and the rapid nucleic acid amplification test (NAAT). We tested 199 clinical nasopharyngeal (nasal) swab samples using three LFIA tests (BD Veritor Plus, STANDARD F Influenza A/B FIA, and ichroma TRIAS) and the rapid NAAT (ID NOW Influenza A & B2). Agreements and clinical performances (sensitivity and specificity) were evaluated based on the results of reverse transcriptase-polymerase chain reaction (RT-PCR) and verification panel. The agreement of each test with RT-PCR was moderate to almost perfect. The sensitivity of ID NOW was significantly higher than that of LFIAs (P = .0005, .0044, and .0026 for influenza A and P = .0044, .0026, and .0044 for influenza B, respectively). The specificities were not significantly different between the four tests (P > .05). However, the reference panel suggests that ichroma TRIAS test is more sensitive than the other two LFIA tests. All three LFIA assays performed similarly with no false positives against influenza A. For influenza B, ichroma TRIAS had 2 of 166 false positives whereas there were no false positives for the other two LFIA tests. Influenza antigen digital LFIAs have advantages in terms of the workflow when simultaneous tests are required. Rapid NAAT has higher sensitivity, while new antigen LFIAs are efficient and high-throughput. It is recommended that users select appropriate methods and algorithms according to the number of specimens and laboratory conditions in each clinical laboratory.

A rapid, cost-effective diagnostic test for the detection of acute HIV-1 infection is highly desired. Isothermal amplification techniques, such as reverse-transcription loop-mediated isothermal amplification (RT-LAMP), exhibit characteristics that are ideal for the development of a rapid nucleic acid amplification test (NAAT) because they are quick, easy to perform and do not require complex, dedicated equipment and laboratory space. In this study, we assessed the ability of the HIV-1 RT-LAMP assay to detect acute HIV infection as compared to a representative rapid antibody test and several FDA-approved laboratory-based assays. The HIV-1 RT-LAMP assay detected seroconverting individuals one to three weeks earlier than a rapid HIV antibody test and up to two weeks earlier than a lab-based antigen/antibody (Ag/Ab) combo enzyme immunoassay (EIA). RT-LAMP was not as sensitive as a lab-based qualitative RNA assay, which could be attributed to the significantly smaller nucleic acid input volume. To our knowledge, this is the first demonstration of detecting acute HIV infection using the RT-LAMP assay. The availability of a rapid NAAT, such as the HIV-1 RT-LAMP assay, at the point of care (POC) or in laboratories that do not have access to large platform NAAT could increase the percentage of individuals who receive an acute HIV infection status or confirmation of their HIV status, while immediately linking them to counseling and medical care. In addition, early knowledge of HIV status could lead to reduced high-risk behavior at a time when individuals are at a higher risk for transmitting the virus.

Before 2020, we tested for CT/GC using a batched nucleic acid amplification test, with results available the following day. Starting in January 2020, we implemented rapid nucleic acid amplification test. Our primary outcome variables were undertreatment and overtreatment. We defined undertreatment as GC and/or CT-positive patients who did not receive appropriate treatment. We defined overtreatment as GC or CT-negative patients who received antibiotics. The balancing measure was the LOS. There were 758 patients evaluated in the preimplementation period (2019), 612 in the implementation period (2020), and 626 in the postimplementation period (2021). Postimplementation, overtreatment decreased from 18.4% to 8.1%. Undertreatment did not differ by period but was less common among those tested with rapid versus standard testing (12.7% versus 9.9%, P = 0.05). Median LOS increased from 166 minutes (preimplementation) to 187 minutes (implementation) and 202 minutes (postimplementation; P < 0.001). Rapid CT/GC testing reduced unnecessary antibiotic use but increased LOS due to patients waiting for the test results before being discharged. Given the rapid increases in CT/GC rates and antimicrobial resistance, health systems should consider implementing rapid testing to appropriately direct antimicrobials to patients most likely to benefit.

ObjectiveTo determine the prevalence and risk factors for Chlamydia trachomatis (CT) infection in pregnant women and the rate of transmission of CT to infants.MethodsPregnant women (≥28 weeks gestation) in Vellore, South India were approached for enrollment from April 2009 to January 2010. After informed consent was obtained, women completed a socio-demographic, prenatal, and sexual history questionnaire. Endocervical samples collected at delivery were examined for CT by a rapid enzyme test and nucleic acid amplification test (NAAT). Neonatal nasopharyngeal and conjunctival swabs were collected for NAAT testing.ResultsOverall, 1198 women were enrolled and 799 (67%) endocervical samples were collected at birth. Analyses were completed on 784 participants with available rapid and NAAT results. The mean age of women was 25.8 years (range 18–39 yrs) and 22% (95% CI: 19.7–24.4%) were primigravida. All women enrolled were married; one reported >one sexual partner; and six reported prior STI. We found 71 positive rapid CT tests and 1/784 (0.1%; 95% CI: 0–0.38%) true positive CT infection using NAAT.ConclusionsTo our knowledge, this is the largest study on CT prevalence amongst healthy pregnant mothers in southern India, and it documents a very low prevalence with NAAT. Many false positive results were noted using the rapid test. These data suggest that universal CT screening is not indicated in this population.

BackgroundThe World Health Organization has set ambitious targets for the global elimination of tuberculosis. However, these targets will not be achieved at the current rate of progress.MethodsWe performed a cluster-randomized, controlled trial in Ca Mau Province, Vietnam, to evaluate the effectiveness of active community-wide screening, as compared with standard passive case detection alone, for reducing the prevalence of tuberculosis. Persons 15 years of age or older who resided in 60 intervention clusters (subcommunes) were screened for pulmonary tuberculosis, regardless of symptoms, annually for 3 years, beginning in 2014, by means of rapid nucleic acid amplification testing of spontaneously expectorated sputum samples. Active screening was not performed in the 60 control clusters in the first 3 years. The primary outcome, measured in the fourth year, was the prevalence of microbiologically confirmed pulmonary tuberculosis among persons 15 years of age or older. The secondary outcome was the prevalence of tuberculosis infection, as assessed by an interferon gamma release assay in the fourth year, among children born in 2012.ResultsIn the fourth-year prevalence survey, we tested 42,150 participants in the intervention group and 41,680 participants in the control group. A total of 53 participants in the intervention group (126 per 100,000 population) and 94 participants in the control group (226 per 100,000) had pulmonary tuberculosis, as confirmed by a positive nucleic acid amplification test for Mycobacterium tuberculosis (prevalence ratio, 0.56; 95% confidence interval [CI], 0.40 to 0.78; P<0.001). The prevalence of tuberculosis infection in children born in 2012 was 3.3% in the intervention group and 2.6% in the control group (prevalence ratio, 1.29; 95% CI, 0.70 to 2.36; P=0.42).ConclusionsThree years of community-wide screening in persons 15 years of age or older who resided in Ca Mau Province, Vietnam, resulted in a lower prevalence of pulmonary tuberculosis in the fourth year than standard passive case detection alone. (Funded by the Australian National Health and Medical Research Council; ACT3 Australian New Zealand Clinical Trials Registry number, ACTRN12614000372684.)

Chapter 54 - Infectious diseases

Objective: The objective of the study is to compare three techniques, routinely used rapid diagnostic tests (lateral flow immune chromatography) versus nucleic acid amplification test (NAT) versus Paper-based microfluidics for DNA diagnostics of Malaria, in terms of their sensitivity and specificity as diagnostic tests in detecting malarial infection among febrile illnesses, suspected of malaria, as well as to compare their cost-effectiveness.&#x0D; Methodology: Three seventy febrile cases suspected of malaria with negative results with RDT will be screened by real-time PCR and DNA microfluidics techniques, sensitivity and specificity of these as screening tests will be compared. The number of extra positive cases detected by NAT gives us the yield. Cost-effectiveness analysis will be done by calculating the incremental cost-effectiveness ratio (ICER) and average cost-effectiveness ratio (ACER) for the tests.&#x0D; Statistical Analysis: Statistical analysis will be done using SPSS version 21. Sensitivity, specificity, Positive predictive values will be computed. Comparison of sensitivity and specificity of NAT, a paper microfluidic technique for DNA diagnostics and RDT will be carried out using McNemar’s test. Receiver operating curves will be generated separately to assess the utility of the NAT.&#x0D; Conclusion: The Implications of this study from the patient's perspective would mean early diagnosis which forms the tenet of control of the disease by increasing the yield. Early diagnosis at the community level would translate into the application of efficient prevention mechanisms to spread the infection. The cost-effectiveness analysis would provide a scientific basis for the adoption of the best test for the diagnosis, given the economic feasibility of the study.

The escalating threats to biodiversity, public health, and food security posed by emerging infectious diseases, wildlife trafficking, and invasive species expansions require novel approaches to biosurveillance. Modern genetic testing technology can detect many of these unseen threats, but existing genetic testing approaches are largely inaccessible to most people working in the field. The Nucleic Acid Barcode Identification Tool (NABIT) is a handheld, battery-powered device that enables rapid nucleic acid amplification tests to be performed at the point-of-contact by non-technical users, creating a critical bridge between centralized laboratories and the field by reducing barriers to accessible and routine genetic testing. In this work, we present initial performance data for the NABIT and lyophilized assays for nucleic acid amplification testing of two diverse applications to demonstrate the potential of the NABIT to serve as a platform for on-site biosurveillance and species detection. The results demonstrated that the NABIT COVID-19 test kit could detect SARS-CoV-2 at 0.93 NDU/µL. The NABIT sockeye test kit showed amplification between 13–22 minutes from filtered water samples from a salmon hatchery.