Rapid Nucleic Acid Amplification Tests Research Articles

Review: Diagnostic Potential for Collaborative Pharyngitis Biomarkers.

Pharyngitis is an inflammatory condition of the pharynx and/or tonsils commonly seen in both children and adults. Viruses and bacteria represent the most common encountered etiologic agents-yeast/fungi and parasites are infrequently implicated. Some of these are predominantly observed in unique populations (eg, immunocompromised or unvaccinated individuals). This manuscript (part 3 of 3) summarizes the current state of biomarker diagnostic testing and highlights the expanding role they will likely play in the expedited diagnosis and management of patients with acute pharyngitis. Biomarkers, in conjunction with rapid antigen and/or nucleic acid amplification testing, will likely become the standard of care to accurately diagnose the etiologic agent(s) of pharyngitis. This novel testing paradigm has the potential to guide appropriate patient management and antibiotic stewardship by accurately determining if the cause of pharyngitis is due to a viral or bacterial etiology.

A-296 Streck Urine Preserve Provides Sample Stability for Cepheid Xpert CT/NG test

Abstract Background Sexually transmitted infections (STIs) are one of the most common communicable diseases worldwide and are associated with significant morbidity and mortality. Data indicates that the four curable STIs - chlamydia, gonorrhea, trichomoniasis, and syphilis - cause over 375 million infections annually. Further, the infection rate for gonorrhea has increased by 63% in the United States and the emergence of resistant gonorrhea is an urgent global public health concern. To prevent transmission of gonorrhea and other curable STIs and minimize the escalation of untreated infections, early and effective prevention and control strategies are paramount. Rapid diagnostic testing and nucleic acid amplification tests (NAATs) have become the gold standard for STI detection. However, limited global access to these technologies often requires that samples be shipped to central laboratories for analysis. Current protocols recommend that neat urine be analyzed within 24 hours of collection if stored at 2 °C to 8 °C or within four days if frozen, as prolonged storage and exposure to freeze-thaws can induce cell lysis and release of nucleases, leading to degradation of DNA and false negative test results. Without sample stabilization, laboratories are left with a small window for accurate analysis. Here, we demonstrate that Streck Urine Preserve (SUP) maintains target and donor DNA concentrations during prolonged storage and that these stabilized samples are compatible with Cepheid’s automated GeneXpert System and associated Xpert CT/NG test. Methods Fresh human urine, with or without SUP, was tested neat or spiked with Neisseria gonorrhoeae (N. gonorrhoeae). Samples were stored at room temperature for up to 18 days before being analyzed on the Cepheid GeneXpert System using the Xpert CT/NG test per manufacturer’s instructions. Differences in average Ct values were compared for the sample processing control, sample adequacy control, and N. gonorrhoeae targets. DNA stability was assessed by comparing the changes between fresh and SUP-treated samples throughout the study period. Results Following prolonged storage, Ct values for neat, untreated urine increased by 3-7 cycles, correlating to a 10- to 100-fold decrease in detectable copies of N. gonorrhoeae and the sample adequacy control compared to urine samples stabilized with SUP. The average Ct value for samples stabilized with SUP did not change by more than 1.5 cycles throughout the study period. Additionally, Ct values for the sample processing control remained constant throughout the testing period, indicating that SUP did not impact sample processing. Conclusions When limited point-of-care testing options require storage and shipping of samples to central laboratories, urine stabilizers are imperative to obtain results representative of the patient sample at the time of collection. SUP effectively stabilized N. gonorrhoeae DNA and donor DNA prior to analysis with the Cepheid Xpert CT/NG test. This contrasts with the marked decrease in DNA copy number in non-stabilized urine over the study duration, which may lead to false negative results for low-positive urine samples. Taken together, SUP provides clinical researchers and assay developers with added flexibility when handling, shipping, and processing urine specimens and supports compatibility with automated NAAT systems and tests.

Evaluation of a nucleic acid amplification system, GENECUBE, for rapid detection of staphylococcal nuc and mecA in blood culture samples

ObjectiveThis study determined whether the GENECUBE rapid nucleic acid amplification test could directly detect nuc and mecA genes in clinical blood culture samples of Staphylococcus and various other pathogens. MethodsBetween September 2020 and December 2021, 537 blood culture samples from 192 patients with suspected bacteremia were tested using conventional assays (MicroScan WalkAway96 or VITEK 2 systems) and GENECUBE nuc and mecA assays. Isolates from samples with discrepant results between the conventional and GENECUBE assays were further evaluated using MALDI-TOF mass spectrometry, disk diffusion testing using cefoxitin, broth microdilution testing using oxacillin, and sequencing for mecA. Bacterial solutions containing a mixture of methicillin-susceptible Staphylococcus aureus (MSSA) and methicillin-resistant Staphylococcus epidermidis (MRSE) were prepared to evaluate the limit of detection (LOD) of mecA. ResultsUsing conventional assays as the reference, the sensitivity, specificity, and positive and negative predictive values (95 % confidence interval) of GENECUBE were 100 % (96.8–100 %), 100 % (99.1–100 %), 100 % (96.8–100 %), and 100 % (99.1–100 %), respectively, for nuc detection and 100 % (96.1–100 %), 98.9 % (97.4–99.6 %), 94.9 % (88.5–98.3 %), and 100 % (99.2–100 %), respectively, for mecA detection. Sequencing analysis of five samples identified as methicillin-sensitive staphylococci using conventional assays and methicillin-resistant staphylococci using GENECUBE revealed the presence of methicillin-resistant isolates in all samples. The estimated LOD of mecA was 104 colony-forming units (CFU)/mL of MRSE with GENECUBE, compared with 105 CFU/mL with conventional assays. ConclusionThe GENECUBE assay accurately detected mecA in positive blood culture samples and had higher sensitivity than conventional assays.

SYPHILIS IN THE 21ST CENTURY: CHALLENGES AND ADVANCES IN DIAGNOSIS AND TREATMENT

The article titled Syphilis in the 21st Century: Challenges and Advances in Diagnosis and Treatment aimed to analyze the main challenges and significant advances in the diagnosis and treatment of syphilis throughout the 21st century. The research focused on understanding how new technologies and public health strategies have contributed to the improvement of disease management, as well as identifying the existing barriers. A bibliographic review was conducted to compile and synthesize relevant data from previous studies, providing a comprehensive overview of the topic. The explanatory methodology used allowed for a theoretical deepening of the issues involved in the detection and treatment of syphilis. The technical procedures included the analysis of scientific articles, health organization reports, and systematic reviews that addressed both technological advances and the challenges faced by health professionals. Among the main advances discussed were rapid tests and nucleic acid amplification tests (NAATs), which have significantly improved the ability to diagnose the infection early and accurately. Improvements in public awareness and prevention programs were also addressed. Despite the advances, the article also highlighted persistent challenges such as antibiotic resistance and difficulties in accessing effective treatments, especially in less developed regions. Benzathine penicillin G was reaffirmed as the treatment of choice, but distribution logistics and adherence to treatment remain important obstacles. The bibliographic review concluded that, for effective control of syphilis, integrated strategies that combine education, prevention, early diagnosis, and adequate treatment are necessary, as indicated in the reviewed literature.

METODE DIAGNOSIS INFEKSI TRICHOMONAS VAGINALIS TERKINI

Recent advances in tests for the sexually transmitted protozoan parasite Trichomonas vaginalis have increased opportunities for diagnosis and treatment of this important sexually transmitted infection. This review summarizes current available tests, highlighting their performance characteristics, advantages, and limitations. The recent development of molecular tests for the detection of T vaginalis, including rapid antigen detection and nucleic acid amplification tests, has significantly improved the quality of diagnostics for trichomoniasis, particularly in women. In light of the expanded menu of testing options now available, improved recognition and better control of trichomoniasis are in sight, which should enable the eventual reduction of adverse reproductive consequences associated with T vaginalis infection.

Comparative analysis of CBNAAT (GeneXpert) and Ziehl-Nielsen staining test as diagnostic modalities of tuberculosis.

As centuries and millennia passed, tuberculosis remains the major health threat for millions of people. Due to this resurgence of tuberculosis, scientists around the globe have intensified their research efforts to curb down the transmission of this disease and that is the reason which led to the development of new and efficient diagnostic tools, one such being the rapid cartridge-based nucleic acid amplification test which can give the real-time results and that too in a short period of time. These diagnostic tools which are based on the latest technologies help in paving the way to eliminate tuberculosis by early detection method and further prevent the transmission. In this study, we did a comparative analysis of the effectiveness of CBNAAT technique in the early detection of Mycobacterium tuberculosis over the conventional method of Ziehl-Nielsen microscopy as diagnostic modalities. Comparative analysis of CBNAAT (GeneXpert) and Ziehl-Nielsen staining test was done as diagnostic modalities using standard protocols. Out of total 300 samples, 153 were female, 146 were male, while one was transgender. For all these samples, the positivity rates were 48% for the CBNAAT technique and 21.3% for ZN staining method, respectively. For extrapulmonary samples, positivity rates were 49.1% and 11.86% for CBNAAT and ZN microscopy, respectively, while the same for pulmonary samples was 47.7% and 23.6%, respectively. ZN microscopy and CBNAAT are both initial tests for the detection of Mycobacterium tuberculosis, but the introduction of CBNAAT is a boon for peripheral sites. The higher positivity rate of CBNAAT over ZN staining is the icing on the cake with the ability to detect even those cases that could be missed by the latter.

EE188 A Retrospective Cohort Comparing the Tuberculosis Diagnosis Related Costs and Health Resource Use (HRU) Using a Rapid Nucleic Acid Amplification (NAA) Test Vs. Conventional Tests in China, Followed By a Budget Impact Model

EE188 A Retrospective Cohort Comparing the Tuberculosis Diagnosis Related Costs and Health Resource Use (HRU) Using a Rapid Nucleic Acid Amplification (NAA) Test Vs. Conventional Tests in China, Followed By a Budget Impact Model

Scanning Electron Microscopy and EDX Spectroscopy of Commercial Swabs Used for COVID-19 Lateral Flow Testing.

The chemical composition of COVID test swabs has not been examined beyond the manufacturer's datasheets. The unprecedented demand for swabs to conduct rapid lateral flow tests and nucleic acid amplification tests led to mass production, including 3D printing platforms. Manufacturing impurities could be present in the swabs and, if so, could pose a risk to human health. We used scanning electron microscopy and energy dispersive X-ray (EDX) spectroscopy to examine the ultrastructure of seven assorted brands of COVID test swabs and to identify and quantify their chemical elements. We detected eight unexpected elements, including transition metals, such as titanium and zirconium, the metalloid silicon, as well as post-transition metals aluminium and gallium, and the non-metal elements sulphur and fluorine. Some of the elements were detected as trace amounts, but for others, the amount was close to reported toxicological thresholds for inhalation routes. Experimental studies have shown that the detrimental effects of unexpected chemical elements include moderate to severe inflammatory states in the exposed epithelium as well as proliferative changes. Given the massive testing still being used in the context of the COVID pandemic, we urge caution in continuing to recommend repeated and frequent testing, particularly of healthy, non-symptomatic, individuals.

Comparison of an ID NOW COVID-19 Assay Used at the Point of Care to Laboratory-Based Nucleic Acid Amplification Tests.

The emergence of a novel coronavirus, namely, SARS-CoV-2, necessitated the use of rapid, accurate diagnostics to quickly diagnose COVID-19. This need has increased with the emergence of new variants and continued waves of COVID-19 cases. The ID NOW COVID-19 assay is a rapid nucleic acid amplification test (NAAT) that is used by hospitals, urgent care facilities, medical clinics, and public health laboratories for rapid molecular SARS-CoV-2 testing at the point of care. The District of Columbia Department of Forensic Sciences Public Health Laboratory Division (DC DFS PHL) implemented ID NOW COVID-19 testing in nontraditional laboratory settings, including a mobile testing unit, health clinic, and emergency department, to assist with rapid identification and isolation for populations at high risk of SARS-CoV-2 transmission in the District of Columbia. The DC DFS PHL provided these nontraditional laboratories with safety risk assessment, assay training, competency assessment, and quality control monitoring as parts of a comprehensive quality management system (QMS). We assessed the accuracy of the ID NOW COVID-19 assay when operated in the context of these trainings and systems. This was done by comparing results from 9,518 paired tests, and strong agreement (κ = 0.88, OPA = 98.3%) was found between the ID NOW COVID-19 assay and laboratory-based NAATs. These findings indicate that the ID NOW COVID-19 assay can be used to detect SARS-CoV-2 in nontraditional laboratory settings when used within the context of a comprehensive QMS.

Gene Xpert MTB/RIF assay in patients with clinical suspicion of tuberculous meningitis

Early diagnosis and treatment of tubercular meningitis (TBM) is one of the best predictors of survival. The smear testing of the cerebrospinal fluid (CSF) has a low sensitivity and cultures, though having higher sensitivity, take a long time in TBM diagnosis. The present study was done to evaluate the proportion of positive Gene Xpert test, a rapid nucleic acid amplification test, in clinically suspected patients with TBM. The results of Gene Xpert tests were then compared with the culture results. One hundred and fifty prospective patients with a clinical suspicion of TBM were classified as probable or possible TBM and underwent CSF examination for culture and Gene Xpert assay. Out of 124 patients available for statistical evaluation, 52 were in the probable and 72 in possible TBM group. The proportion of patients with Gene Xpert positivity were significantly more in probable compared to possible TBM (63.15% vs 36.85%, p<0.001). Twenty-eight patients had a positive culture result. The sensitivity of Gene Xpert relative to culture testing was 68.42%, specificity of 97.61%, a positive predictive value of 92.85% and a negative predictive value of 87.23%. Gene Xpert testing provided a rapid diagnosis in patients suspected with TBM. The high sensitivity and specificity of this test relative to culture testing is a strong indication that it should be included as one of the gold standard tests in patients with suspected TBM.

Improving Management of Suspected Chlamydia and Gonorrhea in Adolescents with a Rapid Diagnostic Test.

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.

EUS-guided through-the-needle microforceps biopsy for diagnosis of tubercular lymphadenitis mimicking pancreatic cystic lesion (with video).

A 40-year-old male presented with upper abdominal discomfort and ultrasound abdomen revealed a cystic lesion in the uncinate process. Contrast-enhanced computed tomography revealed a thick-walled cystic lesion measuring 4.2 cm in the uncinate process [Figure 1]. Positron emission computed tomography revealed flouro-deoxyglucose avidity in the wall of this cystic lesion [Figure 2]. EUS-guided fine-needle biopsy from the cystic lesion done elsewhere was inconclusive on two separate occasions. EUS done at our center revealed a complex cystic lesion posterior to the head of the pancreas and closely abutting the inferior vena cava with normal uncinate process [Figure 3; arrows]. Contrast-enhanced harmonic EUS using Sonovue (Bracco, Milan, Italy) at low mechanical index of 0.12 revealed nonhomogenous enhancement of the cystic lesion with solid areas showing enhancement [arrows; Figure 4] and anechoic areas not enhancing. EUS-guided fine-needle biopsy form the solid as well as liquid areas was inconclusive and revealed necrosis only. Thereafter, tissue sampling was done from the solid area of the lesion under EUS guidance using through the needle forceps device (Moray Micro Forceps, US Endoscopy, United States) [Figure 5 and Video 1]. To improve the visualization of opening of forceps in the lesion, biopsy was performed using both B mode and harmonic EUS [Video 1]. The use of harmonic EUS led on to better visualization of the tip of Microforceps. Two passes were taken and crush smear was prepared with one specimen and the other specimen was sent in formalin vial. The cytopathological examination revealed lymphoid tissue with the presence of loose collection of epitheloid cells and necrosis [Figure 6]. No acid fast bacilli could be detected. The rapid nucleic acid amplification test (Xpert MTB/RIF; Cepheid, Sunnyvale, CA, USA) performed on the aspirated specimen was negative. The Mantoux test was positive (induration of 16 mm), C-reactive protein was elevated (16 mg/L), and the patient was started on anti-tubercular therapy (ATT). The patient responded to ATT and the abdominal discomfort subsided after 1 month of initiating ATT. Serum CRP normalized at 2 months and ultrasound of the abdomen done three months after initiation of ATT revealed reduction in size of the lesion (2.3 cm).Figure 1: Contrast enhanced computed tomography: thick walled cystic lesion in the uncinate process of pancreasFigure 2: Positron emission computed tomography: flouro-deoxyglucose avidity in the wall of cystic lesionFigure 3: EUS: Complex cystic lesion (arrows) posterior to the head of pancreas and closely abutting the inferior vena cava with normal uncinate processFigure 4: Contrast-enhanced harmonic EUS: Nonhomogenous enhancement of the cystic lesion with solid areas showing enhancement (arrows) and anechoic areas not enhancingFigure 5: EUS-guided biopsy using through the needle forceps deviceFigure 6: Microphotograph of microbiopsy specimen: a loose collection of epithelioid cells (arrows) with necrosis in the background (H and E, ×40)To improve the diagnostic yield of EUS-guided tissue sampling, through-the-needle micro-forceps device has been introduced and studies have reported high diagnostic yield in pancreatic cystic lesions.[1,2] It can also be used for tissue diagnosis in difficult to diagnose lesions as in the index case. Declaration of patient consent The authors certify that they have obtained all appropriate patient consent forms. In the form, the patient has given his consent for his images and other clinical information to be reported in the journal. The patient understands that his name and initials will not be published and due efforts will be made to conceal his identity, but anonymity cannot be guaranteed. Financial support and sponsorship Nil. Conflicts of interest Surinder Singh Rana is an Editorial Board Member of the journal. This article was subject to the journal’s standard procedures, with peer review handled independently of this editor and his research group.

2167. Use and Timing of Antiviral Therapy for Influenza in Hospitalized U.S. Children, 2016–2020

Abstract Background According to the 2018 Infectious Diseases Society of America (IDSA) clinical practice guidelines and Centers for Disease Control and Prevention (CDC) guidance, clinicians should start antiviral treatment as soon as possible for children who are hospitalized with suspected or confirmed influenza. We assessed the use of influenza-specific antiviral therapy in children hospitalized with symptoms of acute respiratory illness and laboratory-confirmed influenza. Methods We conducted active, population-based surveillance of children hospitalized with fever and/or respiratory symptoms (12/01/2016–02/28/2020) at the seven U.S. medical centers that comprise the CDC New Vaccine Surveillance Network. We excluded children who did not undergo clinical testing (by rapid antigen testing or nucleic acid amplification test [NAAT]) or research testing (by NAAT) for influenza, those who presented out of influenza season (site- and season-specific), and those whose date of antiviral therapy or whether antiviral therapy was given was unknown. We assessed the use of influenza-specific antiviral therapy in this cohort and defined timely antiviral therapy as administration within 2 days of hospitalization. Results Of 11,275 eligible children, 1,149 (10.2%) tested positive for influenza by clinical and/or research assays (Table 1). Overall, 154 influenza cases (13.4%) were detected by clinical testing only, 428 (37.2%) by research testing only, and 567 (49.3%) by both. During their influenza-associated hospitalization, 620 children (54.0%) received influenza-specific antivirals, and therapy was timely in 572 cases (92.3%). Of those who tested positive clinically, 445/721 (61.7%) received timely antiviral therapy, 38 (5.3%) received delayed antiviral therapy, and 238 (33.0%) received no antiviral therapy. Oseltamivir was the antiviral used in all treated cases. The distribution of antiviral-treated cases varied by race and Hispanic origin and study site, but not by age at presentation or influenza season (Figure 1). Table 1 Demographic characteristics of 1,149 children with influenza enrolled in the New Vaccine Surveillance Network over four influenza seasons between December 1, 2016, and February 28, 2020. Figure 1Proportions of children with influenza enrolled in the New Vaccine Surveillance Network who received timely, delayed, or no antiviral therapy by age at presentation, race and Hispanic origin, study site, and influenza season (N=1,149). Conclusion Although antiviral therapy is recommended for all influenza-associated hospitalizations in children, antiviral prescribing remains suboptimal. Further studies would help identify and address barriers to antiviral therapy in children with influenza. Disclosures John Williams, MD, GlaxoSmithKline: Advisor/Consultant|Quidel: Advisor/Consultant Janet A. Englund, MD, AstraZeneca: Advisor/Consultant|AstraZeneca: Grant/Research Support|GlaxoSmithKline: Grant/Research Support|Meissa Vaccines: Advisor/Consultant|Merck: Grant/Research Support|Pfizer: Grant/Research Support|Sanofi Pasteur: Advisor/Consultant Rangaraj Selvarangan, BVSc, PhD, D(ABMM), FIDSA, F(AAM), BioFire: Grant/Research Support|Luminex: Grant/Research Support Mary A. Staat, MD, MPH, Centers for Disease Control and Prevention: Grant/Research Support|Cepheid: Grant/Research Support|National Institute of Health: Grant/Research Support|Uptodate: Royalties Geoffrey A. Weinberg, MD, Merck &amp; Co.: Honoraria|Merck &amp; Co.: Honoraria for composing and reviewing textbook chapters, Merck Manual of Therapeutics Flor M. Munoz, MD, MSc, Gilead: Grant/Research Support|Moderna: DSMB|Pfizer: DSMB Christopher J Harrison, MD, Astellas: Grant/Research Support|GSK: Grant/Research Support|Merck: Grant/Research Support|Pediatric news: Honoraria|Pfizer: Grant/Research Support Natasha B. Halasa, MD, Quidel: Grant/Research Support|Quidel: equipment donation|Sanofi: Grant/Research Support|Sanofi: HAI testing and vaccine donation.

Comparative analysis of three multiplex platforms for the detection of respiratory viral pathogens.

Acute viral respiratory infections are a major health burden in children worldwide. In recent years, rapid and sensitive multiplex nucleic acid amplification tests (NAATs) have replaced conventional methods for routine virus detection in the clinical laboratory. We compared BioFire® FilmArray® Respiratory Panel (FilmArray V1.7), Luminex NxTag® Respiratory Pathogen Panel (NxTag RPP) and Applied Biosystems TaqMan Array Card (TAC) for the detection of eight viruses in pediatric respiratory specimens. Results from the three platforms were analyzed with a single-plex real-time RT-PCR (rRT-PCR) assay for each virus. Of the 170/210 single-plex virus-positive samples, FilmArray detected a virus in 166 (97.6%), TAC in 163 (95.8%) and NxTag RPP in 160 (94.1%) samples. The Positive Percent Agreement (PPA) of FilmArray, NxTag RPP and TAC was highest for influenza B (100%, 100% and 95.2% respectively) and lowest for seasonal coronaviruses on both FilmArray (90.2%) and NxTag RPP (81.8%), and for parainfluenza viruses 1- 4 on TAC (84%). The Negative Percent Agreement (NPA) was lowest for rhinovirus/enterovirus (92.9%, 96.7% and 97.3%) on FilmArray, NxTag RPP and TAC respectively. NPA for all three platforms was highest (100%) for both parainfluenza viruses 1- 4 and influenza A and B, and 100% for human metapneumovirus with TAC as well. All three multiplex platforms displayed high overall agreement (&gt;90%) and high NPA (&gt;90%), while PPA was pathogen dependent and varied among platforms; high PPA (&gt;90%) was observed for FilmArray for all eight viruses, TAC for six viruses and NxTag RPP for 4 viruses.

Diagnostic test property of transcription-reverse transcription concerted reaction reagent TRCReady® SARS-CoV-2 i using nasopharyngeal swab samples

TRCReady® SARS-CoV-2 i is a reagent for transcription-reverse transcription concerted reaction (TRC) to detect SARS-CoV-2 N2 gene, used with the automated rapid isothermal nucleic acid amplification test (NAAT) analyzer TRCReady®-80. Sensitivity and specificity of TRCReady® SARS-CoV-2 i was assessed by comparison with the results of real-time reverse transcription-polymerase chain reaction (RT-PCR) using nasopharyngeal swab samples. From November 2020 to March 2021, a total of 441 nasopharyngeal swabs were obtained and analyzed both with TRCReady® SARS-CoV-2 i and RT-PCR. Sensitivity and specificity of TRCReady® SARS-CoV-2 i were 94.6% (53/56) and 99.2% (382/385), respectively. Reaction time to positivity of TRCReady® SARS-CoV-2 i ranged from 1.166 to 9.805 (median: 2.887) min, and minimum detection sensitivity of TRCReady® SARS-CoV-2 i was 9 copies per test, with reaction time as 5.014 min. Detection of SARS-CoV-2 gene from nasopharyngeal swab sample using TRCReady® SARS-CoV-2 i shows comparative diagnostic test accuracy with RT-PCR, and can be used as a useful test to diagnose SARS-CoV-2 infection.

Sensitivity of Various Case Detection Algorithms for Community-based Tuberculosis Screening.

Using data from 388 people diagnosed with tuberculosis through a community-based screening program in Lima, Peru, we estimated that cough screening followed by sputum smear microscopy would have detected only 23% of cases found using an algorithm of radiographic screening followed by rapid nucleic acid amplification testing and clinical evaluation.

Xpert MTB/XDR for detection of pulmonary tuberculosis and resistance to isoniazid, fluoroquinolones, ethionamide, and amikacin.

Xpert MTB/XDR for detection of pulmonary tuberculosis and resistance to isoniazid, fluoroquinolones, ethionamide, and amikacin.

Comparative study of rapid antigen testing and two nucleic acid amplification tests for influenza virus detection

IntroductionThis study aimed to evaluate rapid antigen detection (RAD) and rapid nucleic acid amplification tests (NAATs) to detect influenza virus (IV). MethodsThe conventional RAD test (Quick Chaser Flu A, B: QC), using silver amplified immunochromatography (Quick Chaser Auto Flu A, B: QCA), as well as two NAATs (Xpert Xpress Flu/RSV: Xpert, cobas Influenza A/B & RSV: cobas) were evaluated using nasopharyngeal swabs from suspected cases of influenza. A reference method was performed using real-time reverse transcription polymerase chain reaction according to the manual of the Japanese National Institute of Infectious Disease (NIID). ResultsFrom a total of 177 samples, 51 were positive according to the NIID assay. The kappa (κ) coefficient in Xpert and cobas for influenza A virus (IAV)/influenza B virus (IBV) was 1.00, which was the highest among the four detection assays. However, the κ coefficients in QC and QCA for IAV/IBV were 0.71–0.77 and 0.87–0.89, respectively. The sensitivities of the RAD tests were 41.7% in QC and 50.0% in QCA at < 6 h after onset, and 100.0% in both QC and QCA at 24–48 h after onset. The cycle threshold (Ct) values were significantly lower in the group in which all detection assays were positive for IAV. ConclusionsXpert and cobas have comparable analytical performances and are highly useful as influenza virus detection assays. QC and QCA could show false negatives frequently in the early stage of infection and when viral load is low.

Turnaround times for molecular testing of pediatric viral cerebrospinal fluid samples in United Kingdom laboratories.

BACKGROUNDRapid molecular testing has revolutionized the management of suspected viral meningitis and encephalitis by providing an etiological diagnosis in < 90 min with potential to improve outcomes and shorten inpatient stays. However, use of molecular assays can vary widely.AIMTo evaluate current practice for molecular testing of pediatric cerebrospinal fluid (CSF) samples across the United Kingdom using a structured questionnaire.METHODSA structured telephone questionnaire survey was conducted between July and August 2020. Data was collected on the availability of viral CSF nucleic acid amplification testing (NAAT), criteria used for testing and turnaround times including the impact of the coronavirus disease 2019 pandemic.RESULTSOf 196/212 (92%) microbiology laboratories responded; 63/196 (32%) were excluded from final analysis as they had no on-site microbiology laboratory and outsourced their samples. Of 133 Laboratories included in the study, 47/133 (35%) had onsite facilities for viral CSF NAAT. Hospitals currently undertaking onsite NAAT (n = 47) had much faster turnaround times with 39 centers (83%) providing results in ≤ 24 h as compared to those referring samples to neighboring laboratories (5/86; 6%).CONCLUSIONOnsite/near-patient rapid NAAT (including polymerase chain reaction) is recommended wherever possible to optimize patient management in the acute setting.

ESCMID COVID-19 guidelines: diagnostic testing for SARS-CoV-2

ScopeThe objective of these guidelines is to identify the most appropriate diagnostic test and/or diagnostic approach for SARS-CoV-2. The recommendations are intended to provide guidance to clinicians, clinical microbiologists, other health care personnel, and decision makers. MethodsAn ESCMID COVID-19 guidelines task force was established by the ESCMID Executive Committee. A small group was established, half appointed by the chair and the remaining selected with an open call. Each panel met virtually once a week. For all decisions, a simple majority vote was used. A list of clinical questions using the PICO (population, intervention, comparison, outcome) format was developed at the beginning of the process. For each PICO, two panel members performed a literature search focusing on systematic reviews, with a third panellist involved in case of inconsistent results. Quality of evidence assessment was based on the GRADE-ADOLOPMENT (Grading of Recommendations Assessment, Development and Evaluation - adoption, adaptation, and de novo development of recommendations) approach. RecommendationsA total of 43 PICO questions were selected that involve the following types of populations: (a) patients with signs and symptoms of COVID-19; (b) travellers, healthcare workers, and other individuals at risk for exposure to SARS-CoV-2; (c) asymptomatic individuals, and (d) close contacts of patients infected with SARS-CoV-2. The type of diagnostic test (commercial rapid nucleic acid amplification tests and rapid antigen detection), biomaterial, time since onset of symptoms/contact with an infectious case, age, disease severity, and risk of developing severe disease are also taken into consideration.