scholarly journals Alternate Nucleic Acid Targets Can Be Used To Create a Composite Standard To Evaluate Clinical Performance of Nucleic Acid Amplification Tests

2019 ◽  
Vol 57 (8) ◽  
Author(s):  
Julius Schachter ◽  
Max Chernesky
Keyword(s):  
Nucleic Acid ◽  
Clinical Performance ◽  
Mycoplasma Genitalium ◽  
Nucleic Acid Amplification Test ◽  
Nucleic Acid Amplification ◽  
Reference Standard ◽  
New Paradigm ◽  
Content Type ◽  
Nucleic Acid Amplification Tests ◽  
Link Type

ABSTRACTEvaluating the clinical performance of a new nucleic acid amplification test (NAAT) forMycoplasma genitalium, B. Kirkconnell, B. Weinbaum, K. Santos, T. Le Nguyen, et al. (J Clin Microbiol 57:e00264-19, 2019,https://doi.org/10.1128/JCM.00264-19) created 3 alternate NAATs that detected other uniqueM. genitaliumgene targets. Lacking a reference standard, they used the consensus of results with those 3 NAATs as the comparator. This approach could be a new paradigm to evaluate new NAATs when there is no previously defined reference standard.

scholarly journals Design and Validation of Transcription-Mediated-Amplification Nucleic Acid Amplification Tests forMycoplasma genitalium

2019 ◽  
Vol 57 (8) ◽  
Author(s):  
Brett Kirkconnell ◽  
Barbara Weinbaum ◽  
Katherine Santos ◽  
Trisha Le Nguyen ◽  
Bryan Vinluan ◽  
...  
Keyword(s):  
Clinical Performance ◽  
Mycoplasma Genitalium ◽  
Vaginal Swab ◽  
Nucleic Acid Amplification ◽  
Clinical Validation ◽  
Analytical Sensitivity ◽  
Reference Standard ◽  
Content Type ◽  
Sensitivity Specificity

ABSTRACTMycoplasma genitaliumis a sexually transmitted bacterium linked to adverse sexual and reproductive health outcomes in women and men.M. genitaliumis difficult to culture, and in the absence of validated amplified molecular methods for diagnosis of infection, there is no reference standard available for use as a comparator for the validation of newM. genitaliumdiagnostic tests. We evaluated the analytical and clinical performance of three transcription-mediated amplification (TMA) tests forM. genitalium, each targeting unique rRNA sequences, for use as a composite comparator for clinical validation of the AptimaMycoplasma genitalium(AMG) assay, anin vitrodiagnostic (IVD) TMA test that targets 16 s rRNA ofM. genitalium. Analytical sensitivity, specificity, and strain inclusivity of all four TMA tests were determined using nine laboratory strains ofM. genitaliumand 56 nontarget bacteria, protozoa, and viruses. Analytical sensitivity of the tests forM. genitaliumranged from 0.017 to 0.040 genome equivalents/ml. None of the nontarget organisms evaluated cross-reacted with any test. A composite comparator reference standard consisting of the 3 alternate (Alt) TMA tests was used to evaluate the clinical performance of the AMG assay by testing residual vaginal swab, female urine, and male urine specimens obtained from 1,400 adult subjects from three U.S. clinical sites. Using this reference standard to establish infected specimen status, the sensitivity, specificity, and overall agreement of the AMG IVD assay were 100%, 99.9%, and 99.9%, respectively. These results demonstrate the utility of molecular composite reference standard methodology for the clinical validation of future IVD tests for this organism.

scholarly journals Nucleic Acid Amplification Test Quantitation as Predictor of Toxin Presence in Clostridium difficile Infection

2017 ◽  
Vol 56 (3) ◽  
Author(s):  
M. J. T. Crobach ◽  
N. Duszenko ◽  
E. M. Terveer ◽  
C. M. Verduin ◽  
E. J. Kuijper
Keyword(s):  
Nucleic Acid ◽  
Clostridium Difficile ◽  
Characteristic Curve ◽  
Nucleic Acid Amplification Test ◽  
Nucleic Acid Amplification ◽  
Toxin A ◽  
Toxin B ◽  
Content Type ◽  
Quantitative Results ◽  
Testing Algorithm

ABSTRACT Multistep algorithmic testing in which a sensitive nucleic acid amplification test (NAAT) is followed by a specific toxin A and toxin B enzyme immunoassay (EIA) is among the most accurate methods for Clostridium difficile infection (CDI) diagnosis. The obvious shortcoming of this approach is that multiple tests must be performed to establish a CDI diagnosis, which may delay treatment. Therefore, we sought to determine whether a preliminary diagnosis could be made on the basis of the quantitative results of the first test in algorithmic testing, which provide a measure of organism burden. To do so, we retrospectively analyzed two large collections of samples ( n = 2,669 and n = 1,718) that were submitted to the laboratories of two Dutch hospitals for CDI testing. Both hospitals apply a two-step testing algorithm in which a NAAT is followed by a toxin A/B EIA. Of all samples, 208 and 113 samples, respectively, tested positive by NAAT. Among these NAAT-positive samples, significantly lower mean quantification cycle ( C q ) values were found for patients whose stool eventually tested positive for toxin, compared with patients who tested negative for toxin (mean C q values of 24.4 versus 30.4 and 26.8 versus 32.2; P < 0.001 for both cohorts). Receiver operating characteristic curve analysis was performed to investigate the ability of C q values to predict toxin status and yielded areas under the curve of 0.826 and 0.854. Using the optimal C q cutoff values, prediction of the eventual toxin A/B EIA results was accurate for 78.9% and 80.5% of samples, respectively. In conclusion, C q values can serve as predictors of toxin status but, due to the suboptimal correlation between the two tests, additional toxin testing is still needed.

scholarly journals Increased Clinical Specificity with Ultrasensitive Detection of Clostridioides difficile Toxins: Reduction of Overdiagnosis Compared to Nucleic Acid Amplification Tests

2019 ◽  
Vol 57 (11) ◽  
Author(s):  
Johanna Sandlund ◽  
Joel Estis ◽  
Phoebe Katzenbach ◽  
Niamh Nolan ◽  
Kirstie Hinson ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Patient Outcomes ◽  
Single Molecule ◽  
Clinical Performance ◽  
Neutralization Assay ◽  
Nucleic Acid Amplification ◽  
Content Type ◽  
Clostridioides Difficile ◽  
Health Care Associated Infections ◽  
Stool Specimens

ABSTRACT Clostridioides difficile infection (CDI) is one of the most common health care-associated infections, resulting in significant morbidity, mortality, and economic burden. Diagnosis of CDI relies on the assessment of clinical presentation and laboratory tests. We evaluated the clinical performance of ultrasensitive single-molecule counting technology for detection of C. difficile toxins A and B. Stool specimens from 298 patients with suspected CDI were tested with the nucleic acid amplification test (NAAT; BD MAX Cdiff assay or Xpert C. difficile assay) and Singulex Clarity C. diff toxins A/B assay. Specimens with discordant results were tested with the cell cytotoxicity neutralization assay (CCNA), and the results were correlated with disease severity and outcome. There were 64 NAAT-positive and 234 NAAT-negative samples. Of the 32 NAAT+/Clarity− and 4 NAAT−/Clarity+ samples, there were 26 CCNA− and 4 CCNA− samples, respectively. CDI relapse was more common in NAAT+/toxin+ patients than in NAAT+/toxin− and NAAT−/toxin− patients. The clinical specificity of Clarity and NAAT was 97.4% and 89.0%, respectively, and overdiagnosis was more than three times more common in NAAT+/toxin− than in NAAT+/toxin+ patients. The Clarity assay was superior to NAATs for the diagnosis of CDI, by reducing overdiagnosis and thereby increasing clinical specificity, and the presence of toxins was associated with negative patient outcomes.

scholarly journals Supplementary Testing Is Not Required in the cobas 4800 CT/NG Test for Neisseria gonorrhoeae Weak-Positive Urogenital Samples

2014 ◽  
Vol 53 (1) ◽  
pp. 327-328 ◽  
Author(s):  
Collette Bromhead ◽  
Nadika Liyanarachchy ◽  
Julia Mayes ◽  
Arlo Upton ◽  
Michelle Balm
Keyword(s):  
Nucleic Acid ◽  
Neisseria Gonorrhoeae ◽  
Nucleic Acid Amplification Test ◽  
Pretest Probability ◽  
Nucleic Acid Amplification ◽  
Test Results ◽  
Content Type

Weak-positiveNeisseria gonorrhoeaenucleic acid amplification test results are difficult to interpret. We show that the frequency of unconfirmedN. gonorrhoeaeresults from the cobas 4800 test rises exponentially after 38.0 cycles, where the likelihood of an unconfirmed result exceeds 29%. Supplementary testing of such samples should be avoided; instead, treatment should be based on clinical pretest probability.

scholarly journals Pooled Nucleic Acid Amplification Test for Screening of Stool Specimens for Shiga Toxin-Producing Escherichia coli

2016 ◽  
Vol 54 (11) ◽  
pp. 2711-2715
Author(s):  
Agatha N. Jassem ◽  
Frank Y. Chou ◽  
Cathevine Yang ◽  
Matthew A. Croxen ◽  
Katarina D. M. Pintar ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Nucleic Acid ◽  
Shiga Toxin ◽  
Large Scale ◽  
Nucleic Acid Amplification Test ◽  
Nucleic Acid Amplification ◽  
Accurate Estimation ◽  
Content Type ◽  
Pooling Strategy ◽  
Stool Specimens

Shiga toxin-producingEscherichia coli(STEC)-associated enteric illness is attributed to O157 and non-O157 serotypes; however, traditional culture-based methods underdetect non-O157 STEC. Labor and cost of consumables are major barriers to implementation of the CDC recommendation to test all stools for both O157 and non-O157 serotypes. We evaluated the feasibility of a pooled nucleic acid amplification test (NAAT) as an approach for screening stool specimens for STEC. For retrospective evaluation, 300 stool specimens were used to create pools of 10 samples each. The sensitivity was 83% for the preenrichment pooling strategy and 100% for the postenrichment pooling strategy compared with those for individual NAAT results. The difference in cycle threshold (CT) between individual and pooled NAAT results for specimens was significantly lower and more consistent for postenrichment pooling (stx1mean = 3.90,stx2mean = 4.28) than those for preenrichment pooling (excluding undetected specimens;stx1mean = 9.34,stx2mean = 8.96) (P≤ 0.0013). Cost of consumables and labor time savings of 48 to 81% and 6 to 66%, respectively, were estimated for the testing of 90 specimens by the postenrichment pooled NAAT strategy on the basis of an expected 1 to 2% positivity rate. A 30-day prospective head-to-head clinical trial involving 512 specimens confirmed the sensitivity and labor savings associated with the postenrichment pooled NAAT strategy. The postenrichment pooled NAAT strategy described here is suitable for efficient large-scale surveillance of all STEC serotypes. Comprehensive detection of STEC will result in accurate estimation of STEC burden and, consequently, appropriate public health interventions.

scholarly journals Evaluation of the QiagenartusC. difficile QS-RGQ Kit for Detection of Clostridium difficile Toxins A and B in Clinical Stool Specimens

2015 ◽  
Vol 53 (6) ◽  
pp. 1942-1944 ◽  
Author(s):  
Nathalie Jazmati ◽  
Pia Wiegel ◽  
Božica Ličanin ◽  
Georg Plum
Keyword(s):  
Nucleic Acid ◽  
Clostridium Difficile ◽  
Positive Predictive Value ◽  
Negative Predictive Value ◽  
Predictive Value ◽  
Nucleic Acid Amplification Test ◽  
Nucleic Acid Amplification ◽  
Content Type ◽  
Stool Specimens ◽  
Sensitivity Specificity

We compared the QiagenartusC. difficile QS-RGQ kit, a new nucleic acid amplification test for the detection ofClostridium difficiletoxins in stool specimens, with the Cepheid XpertC. difficiletest. The sensitivity, specificity, positive predictive value, and negative predictive value for the QiagenartusC. difficile QS-RGQ test were 100%, 89.5%, 60.9%, and 100%, and those for the Cepheid XpertC. difficiletest were 100%, 90%, 62.2%, and 100%, respectively.

scholarly journals Evaluation of the Efficiency of the Sample Inactivation Reagent in the Abbott RealTime MTB Assay for Inactivation of Mycobacterium tuberculosis

2015 ◽  
Vol 53 (9) ◽  
pp. 3001-3002 ◽  
Author(s):  
Chao Qi ◽  
Carole Wallis ◽  
Vihanga Pahalawatta ◽  
Andrea Frank ◽  
Neeshan Ramdin ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Nucleic Acid ◽  
Nucleic Acid Amplification Test ◽  
Nucleic Acid Amplification ◽  
Content Type ◽  
Clinical Specimens ◽  
Reduced Viscosity

The Abbott RealTime MTB assay is a nucleic acid amplification test (NAAT) for the detection ofMycobacterium tuberculosiscomplex DNA. The sample inactivation procedure used in the assay, consisting of one part sample treated with 3 parts inactivation reagent for 60 min, effectively reduced viscosity and inactivatedM. tuberculosisin clinical specimens.

scholarly journals Advances Afoot in Microbiology

2017 ◽  
Vol 55 (7) ◽  
pp. 1984-1988 ◽  
Author(s):  
Robin Patel ◽  
Brad S. Karon
Keyword(s):  
Nucleic Acid ◽  
American Academy ◽  
Medical Care ◽  
Clinical Microbiology ◽  
Point Of Care ◽  
Nucleic Acid Amplification ◽  
Nucleic Acid Amplification Tests ◽  
Link Type ◽  
The Government

ABSTRACT In 2016, the American Academy of Microbiology convened a colloquium to examine point-of-care (POC) microbiology testing and to evaluate its effects on clinical microbiology. Colloquium participants included representatives from clinical microbiology laboratories, industry, and the government, who together made recommendations regarding the implementation, oversight, and evaluation of POC microbiology testing. The colloquium report is timely and well written (V. Dolen et al., Changing Diagnostic Paradigms for Microbiology , 2017, https://www.asm.org/index.php/colloquium-reports/item/6421-changing-diagnostic-paradigms-for-microbiology?utm_source=Commentary&utm_medium=referral&utm_campaign=diagnostics ). Emerging POC microbiology tests, especially nucleic acid amplification tests, have the potential to advance medical care.

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