scholarly journals Successful Combination of Nucleic Acid Amplification Test Diagnostics and Targeted Deferred Neisseria gonorrhoeae Culture

2015 ◽  
Vol 53 (6) ◽  
pp. 1884-1890 ◽  
Author(s):  
Carolien M. Wind ◽  
Henry J. C. de Vries ◽  
Maarten F. Schim van der Loeff ◽  
Magnus Unemo ◽  
Alje P. van Dam
Keyword(s):  
Nucleic Acid ◽  
Antimicrobial Resistance ◽  
Confidence Interval ◽  
Sampling Site ◽  
Patient Characteristics ◽  
Nucleic Acid Amplification Test ◽  
Nucleic Acid Amplification ◽  
Content Type ◽  
Test Diagnostics ◽  
Storage Times

Nucleic acid amplification tests (NAATs) are recommended for the diagnosis ofN. gonorrhoeaeinfections because of their superior sensitivity. Increasing NAAT use causes a decline in crucial antimicrobial resistance (AMR) surveillance data, which rely on culture. We analyzed the suitability of the ESwab system for NAAT diagnostics and deferred targetedN. gonorrhoeaeculture to allow selective and efficient culture based on NAAT results. We included patients visiting the STI Clinic Amsterdam, The Netherlands, in 2013. Patient characteristics and urogenital and rectal samples for directN. gonorrhoeaeculture, standard NAAT, and ESwab were collected. Standard NAAT and NAAT on ESwab samples were performed using the Aptima Combo 2 assay forN. gonorrhoeaeandC. trachomatis. Two deferredN. gonorrhoeaecultures were performed on NAAT-positive ESwab samples after storage at 4°C for 1 to 3 days. We included 2,452 samples from 1,893 patients. In the standard NAAT, 107 samples wereN. gonorrhoeaepositive and 284 wereC. trachomatispositive. The sensitivities of NAAT on ESwab samples were 83% (95% confidence interval [CI], 75 to 90%) and 87% (95% CI, 82 to 90%), respectively. ESwab samples were available for 98 of the gonorrhea-positive samples. Of these, 82% were positive in direct culture and 69% and 56% were positive in the 1st and 2nd deferred cultures, respectively (median storage times, 27 and 48 h, respectively). Deferred culture was more often successful in urogenital samples or when the patient had symptoms at the sampling site. DeferredN. gonorrhoeaeculture of stored ESwab samples is feasible and enables AMR surveillance. To limit the loss in NAAT sensitivity, we recommend obtaining separate samples for NAAT and deferred culture.

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 Dual Reporting of Clostridioides difficile PCR and Predicted Toxin Result Based on PCR Cycle Threshold Reduces Treatment of Toxin-Negative Patients without Increases in Adverse Outcomes

2019 ◽  
Vol 57 (11) ◽  
Author(s):  
Matthew M. Hitchcock ◽  
Marisa Holubar ◽  
Catherine A. Hogan ◽  
Lucy S. Tompkins ◽  
Niaz Banaei
Keyword(s):  
Nucleic Acid ◽  
Chart Review ◽  
Patient Characteristics ◽  
Adverse Outcomes ◽  
Nucleic Acid Amplification ◽  
Content Type ◽  
Cycle Threshold ◽  
Clostridioides Difficile ◽  
All Cause Mortality ◽  
High Negative Predictive Value

ABSTRACT Nucleic acid amplification tests are commonly used to diagnose Clostridioides difficile infection (CDI). Two-step testing with a toxin enzyme immunoassay is recommended to discriminate between infection and colonization but requires additional resources. Prior studies showed that PCR cycle threshold (CT) can predict toxin positivity with high negative predictive value. Starting in October 2016, the predicted toxin result (CT-toxin) based on a validated cutoff was routinely reported at our facility. To evaluate the clinical efficacy of this reporting, all adult patients with positive GeneXpert PCR results from October 2016 through October 2017 underwent a chart review to measure the recurrence of or conversion to a CT-toxin+ result and 30-day all-cause mortality. There were 482 positive PCR tests in 430 unique patients, 282 CT-toxin+ and 200 CT-toxin−. Patient characteristics were similar at testing, though CT-toxin+ patients had higher white blood cell (WBC) counts (12.5 × 103 versus 9.3 × 103 cells/μl; P = 0.001). All cases (n = 21) of fulminant CDI had a CT-toxin+ result. Index CT-toxin+ patients were significantly more likely to have a CT-toxin+ result within 90 days than CT-toxin− patients (17.4% [n = 49] versus 8.0% [n = 16], respectively; P = 0.003). Thirty-day all-cause mortality was higher in CT-toxin− patients (11.1% versus 6.8%; P = 0.1), though no deaths in CT-toxin− patients were directly attributable to CDI. Of the 200 CT-toxin− patients, 51.5% (n = 103) were treated for CDI. The rates of conversion to a CT-toxin+ result (8.8% versus 7.2%; P = 0.8) and all-cause mortality (8.8% versus 13.4%; P = 0.3) were similar between treated and untreated CT-toxin− patients, respectively. CT-based toxin prediction may identify patients at higher risk for CDI-related complications and reduce treatment among CT-toxin− patients.

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 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 A Retrospective Cross-Sectional Study of the Utility of Cartridge-Based Nucleic Acid Amplification Test in Diagnosis of Pulmonary and Extrapulmonary Tuberculosis in People Living with HIV in Second Highest HIV Prevalent State in India

2021 ◽  
Author(s):  
Tade Bagbi ◽  
Ningthoukhongjam Reema ◽  
S. Bhagyabati Devi ◽  
Thangjam Gautam Singh ◽  
Mohammad Jaleel ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Cross Sectional Study ◽  
Nucleic Acid Amplification Test ◽  
Nucleic Acid Amplification ◽  
Rifampicin Resistance ◽  
Sputum Smear ◽  
Smear Microscopy ◽  
Sectional Study ◽  
Cross Sectional ◽  
Smear Negative

Abstract Introduction Tuberculosis (TB) in people living with human immunodeficiency virus (PLHIV) is difficult to diagnose due to fewer organisms in sputum and extrapulmonary samples. Sputum culture takes 4 to 8 weeks for growth of the mycobacteria. Delayed treatment for TB in PLHIV leads to increased mortality. This study evaluated cartridge-based nucleic acid amplification test (CBNAAT) as a diagnostic tool for diagnosis of pulmonary TB (PTB) and extrapulmonary TB (EPTB) in PLHIV in the second most HIV prevalent state in India and for comparing its efficacy between Ziehl–Neelsen (ZN) staining sputum smear–positive and sputum smear–negative TB. Methods This cross-sectional study was conducted in RIMS, Imphal, with 167 PLHIV patients, age 15 years or older, having signs and symptoms of TB. Appropriate samples for sputum microscopy and CBNAAT were sent. Conclusion The overall sensitivity of sputum smear for acid-fast bacillus (AFB) was found to be 30.71% and that of CBNAAT was 38.57%. Sensitivity of CBNAAT for sputum smear–positive and sputum smear–negative TB was 100 and 11.3%, respectively. Sensitivity of ZN smear for AFB of EPTB sample was 48.1% and that of CBNAAT was 59.25%. In both PTB and EPTB, CBNAAT showed an increase in diagnosis of microbiologically confirmed PTB cases by 7.8 and 11.1%, respectively, over and above the cases diagnosed by ZN smear microscopy. Rifampicin resistance was detected in five patients. We conclude that CBNAAT is a rapid test with better sensitivity in diagnosis of PTB and EPTB in PLHIV, compared with ZN smear microscopy. It detects rifampicin resistance for multidrug-resistant TB and helps in early treatment intervention.

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