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 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 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 Predictors of Clostridioides difficile Infection-Related Complications and Treatment Patterns among Nucleic Acid Amplification Test-Positive/Toxin Enzyme Immunoassay-Negative Patients

2020 ◽  
Vol 58 (3) ◽  
Author(s):  
Ryan Miller ◽  
J. A. Morillas ◽  
Kyle D. Brizendine ◽  
Thomas G. Fraser
Keyword(s):  
Nucleic Acid ◽  
Enzyme Immunoassay ◽  
Severe Disease ◽  
Nucleic Acid Amplification ◽  
Clinical Failure ◽  
Fulminant Colitis ◽  
Related Complication ◽  
Content Type ◽  
Clostridioides Difficile ◽  
Complete Treatment

ABSTRACT The addition of toxin enzyme immunoassay (EIA) to nucleic acid amplification tests, including PCR, creates challenges in the diagnosis and management of Clostridioides difficile infection (CDI). There are limited data in large cohorts, with discordant results, that is, PCR-positive/EIA-negative (PCR+/EIA−) results. We conducted a retrospective cohort study on all PCR+/EIA− adult inpatients and assessed CDI-related complications and clinical failure. We identified 240 individuals. Twenty-three (9.6%) patients experienced a CDI-related complication, including 2 cases of megacolon, 1 colectomy, and 22 intensive care unit (ICU) admissions. In multivariable logistic regression analyses, baseline severe disease by Infectious Diseases Society of America (IDSA) criteria (odds ratio [OR], 5.84; 95% confidence interval [CI], 1.88 to 18.1; P = 0.002), baseline fulminant colitis (OR, 84.7; 95% CI, 14.3 to 500; P < 0.001), fever of >38.5°C (OR, 4.61; 95% CI, 1.42 to 15.0; P = 0.011), and proton pump inhibitor (PPI) use (OR, 3.50; 95% CI, 1.19 to 10.3; P = 0.023) were associated with increased odds of CDI-related complications. For 67 PCR+/EIA− patients who did not receive complete treatment, clinical failure was observed in 10 (15%) patients. A comparison of PCR+/EIA− patients who received complete treatment to all 112 PCR+/EIA+ patients showed no differences in CDI-related complications (11% and 13% for PCR+/EIA− and PCR+/EIA+ patients, respectively), 60-day all-cause mortality (17% and 18% for PCR+/EIA− and PCR+/EIA+ patients, respectively), or recurrent CDI (7% and 9% for PCR+/EIA− and PCR+/EIA+ patients, respectively). Predictors of CDI-attributable complications among PCR+/EIA− patients include baseline severe disease by IDSA criteria, baseline fulminant colitis, and fever of >38.5°C. Identifying the subgroup of PCR+/EIA− patients who could have true disease, and therefore allowing them to be targeted for treatment, is critical.

scholarly journals Nonconcordance of E, N, and RdRp Genes in SARS-Coronavirus-2 Nucleic Acid Amplification Test Among Patients Older than 60 Years

2020 ◽  
Vol 154 (Supplement_1) ◽  
pp. S126-S127
Author(s):  
H Caulkins ◽  
K Rand ◽  
N Harris ◽  
S Beal
Keyword(s):  
Nucleic Acid ◽  
Symptom Onset ◽  
Chart Review ◽  
Nucleic Acid Amplification ◽  
Onset Date ◽  
Sars Coronavirus ◽  
Future Directions ◽  
Systematic Processing ◽  
At Risk Populations ◽  
Processing Errors

Abstract Introduction/Objective During the COVID-19 pandemic, the FDA authorized emergency use of nucleic acid amplification (NAA) testing. Accurate and rapid testing identifies infected persons, especially among at-risk populations. In our institution, the InGenius platform detects three gene targets of SARS-Coronavirus-2: envelope (E), nucleocapsid (N), and RNA-dependent RNA polymerase (RdRp). Nonconcordance of these components present accuracy or precision errors or may correspond to varying expression of viral genes with disease progression. Methods We retrospectively analyzed the result components from 93 nasopharyngeal swabs from 50 patients older than 60 years and positive for SARS-Coronavirus-2 (SARS-CoV-2). The symptom onset date was determined by chart review. Results We found a significant 26% nonconcordance rate, with a predominant pattern demonstrating positive N with negative RdRp and E (χ2 = 27.25, P &lt; 0.0005). This nonconcordant pattern was more prevalent at longer symptom durations. In 7 patients with serial testing, the transition from concordant to nonconcordant results occurred 12 days (95% CI 3.5 – 20.3 days) after symptom onset. Conclusion This may be caused by several mechanisms. Possibilities include decreased expression of E and RdRp over time, inhibition of expression by treatments or host immune response, or lower viral titers by clearance or migration to the lower respiratory tract. Presence of a different viral strain or systematic processing errors are less likely causes of nonconcordance. Future directions of study would determine whether a similar decline in RdRp and E detection is seen in tracheal samples or if this correlates with changes in symptom severity.

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 Association of Cartridge Based Nucleic Acid Amplification Test (CBNAAT) Grading on the Basis of Cycle Threshold Value with Conventional Microbiological Diagnosis in Pediatric Tuberculosis

2021 ◽  
Vol 7 (2) ◽  
pp. 72-77
Author(s):  
Bineeta Kashyap ◽  
Neha Gupta ◽  
Pooja Dewan ◽  
NP Singh ◽  
Ashwani Khanna
Keyword(s):  
Nucleic Acid ◽  
Positive Association ◽  
Threshold Value ◽  
Nucleic Acid Amplification Test ◽  
Nucleic Acid Amplification ◽  
Microbiological Diagnosis ◽  
Significant Positive Association ◽  
Cycle Threshold ◽  
Culture Positivity ◽  
Pediatric Tuberculosis

Background: Microbiological confirmation of tuberculosis disease in children remains difficult due to paucibacillary disease and inability to obtain optimal samples. Recently introduced Cartridge based nucleic acid amplification test (CBNAAT) has improved microbiological diagnosis in pediatric tuberculosis. Objectives: We aimed to study association of CBNAAT grading based on cycle threshold value with conventional microbiological diagnosis. Methodology: This prospective study was conducted over a period from November 2016 to October 2017 in the Departments of Microbiology and Pediatrics, University College of Medical Sciences and Guru Teg Bahadur Hospital, Delhi. CBNAAT positive pediatric TB cases ≤12 years were recruited and subjected to Ziehl-Neelsen staining for acid fast bacilli (AFB) & culture on Lowenstein Jensen medium. CBNAAT positivity was graded based on cycle threshold value: very low, low, medium and high. Results: Smear and culture positivity was highest (100%) among specimens with high positive CBNAAT result based on CT value. Time to culture positivity was inversely related to CBNAAT grading (p=0.000). Conclusion: CBNAAT grading has significant positive association with smear and culture positivity. Bangladesh Journal of Infectious Diseases 2020;7(2):72-77

scholarly journals Comparative performance and cycle threshold values of 10 nucleic acid amplification tests for SARS-CoV-2 on clinical samples

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0252757
Author(s):  
Miyuki Mizoguchi ◽  
Sohei Harada ◽  
Koh Okamoto ◽  
Yoshimi Higurashi ◽  
Mahoko Ikeda ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Diagnostic Performance ◽  
Nucleic Acid Amplification ◽  
Clinical Samples ◽  
Nucleic Acid Amplification Tests ◽  
Cycle Threshold ◽  
E Gene ◽  
Viral Copy Number ◽  
Gene Test ◽  
Positive Results

Background A number of nucleic acid amplification tests (NAATs) for SARS-CoV-2 with different reagents have been approved for clinical use in Japan. These include research kits approved under emergency use authorization through simplified process to stabilize the supply of the reagents. Although these research kits have been increasingly used in clinical practice, limited data is available for the diagnostic performance in clinical settings. Methods We compared sensitivity, specificity, and cycle threshold (Ct) values obtained by NAATs using 10 kits approved in Japan including eight kits those receiving emergency use authorization using 69 frozen-stored clinical samples including 23 positive samples with various Ct values and 46 negative samples. Results Viral copy number of the frozen-stored samples determined with LightMix E-gene test ranged from 0.6 to 84521.1 copies/μL. While no false-positive results were obtained by any of these tests (specificity: 100% [95% CI, 88.9%-100%]), sensitivity of the nine tests ranged from 68.2% [95% CI, 45.1%-86.1%] to 95.5% [95% CI, 77.2%-99.9%] using LightMix E-gene test as the gold standard. All tests showed positive results for all samples with ≥100 copies/μL. Significant difference of Ct values even among tests amplifying the same genetic region (N1-CDC, N2) was also observed. Conclusion Difference in the diagnostic performance was observed among NAATs approved in Japan. Regarding diagnostic kits for emerging infectious diseases, a system is needed to ensure both rapidity of reagent supply and accuracy of diagnosis. Ct values, which are sometimes regarded as a marker of infectivity, are not interchangeable when obtained by different assays.

scholarly journals 2356. Increased Clinical Specificity with Ultrasensitive Detection of Clostridioides difficile Toxins: Reduction of Overdiagnosis Compared with Nucleic Acid Amplification Tests

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S811-S812 ◽  
Author(s):  
Johanna Sandlund ◽  
Joel Estis ◽  
Phoebe Katzenbach ◽  
Niamh Nolan ◽  
Kirstie Hinson ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Disease Severity ◽  
Single Molecule ◽  
Clinical Performance ◽  
Neutralization Assay ◽  
Nucleic Acid Amplification ◽  
Clostridioides Difficile ◽  
Percent Agreement ◽  
Clostridioides Difficile Infection ◽  
Healthcare Associated

Abstract Background Clostridioides difficile infection (CDI) is one of the most common healthcare-associated infections, resulting in significant morbidity, mortality, and economic burden. Diagnosis of CDI relies on the assessment of clinical presentation and laboratory tests. We have evaluated the clinical performance of ultrasensitive Single Molecule Counting technology for detection of C. difficile toxins A and B. Methods Stool specimens from 298 patients with suspected CDI were tested with nucleic acid amplification test (NAAT; BD MAX™ Cdiff assay or Xpert® C. difficile assay) and Singulex Clarity® C. difficile toxins A/B assay. Specimens with discordant results were tested with cell cytotoxicity neutralization assay (CCNA), and results were correlated with disease severity and outcome. Results 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 or overall death was more common in NAAT+/toxin+ patients than in NAAT+/toxin− and NAAT−/toxin− patients, and NAAT+/toxin+ patients were 3.7 times more likely to experience relapse or death (Figure 1). The clinical specificity of Clarity and NAAT was 97.4% and 89.0%, respectively, and overdiagnosis was over three times more common in NAAT+/toxin− than in NAAT+/toxin+ patients (Figure 2). Negative percent agreement between NAAT and Clarity was 98.3%, and positive percent agreement increased from 50.0% to effective 84.2% and 94.1% after CCNA testing and clinical assessment. Conclusion The Clarity assay was superior to NAATs in diagnosis of CDI, by reducing overdiagnosis and thereby increasing clinical specificity, and presence of toxins was associated with disease severity and outcome. Disclosures All authors: No reported disclosures.

scholarly journals PCR Cycle-Threshold-Derived Toxin Identifies Patients at Low-Risk for Complications of C. difficile Infection Who Do Not Require Treatment

2017 ◽  
Vol 4 (suppl_1) ◽  
pp. S395-S395 ◽  
Author(s):  
Matthew Hitchcock ◽  
Marisa Holubar ◽  
Lucy Tompkins ◽  
Niaz Banaei
Keyword(s):  
Treated Patient ◽  
Retrospective Chart Review ◽  
Patient Characteristics ◽  
Low Risk ◽  
Review Time ◽  
Cycle Threshold ◽  
Crude Mortality ◽  
Chi Squared ◽  
High Negative Predictive Value ◽  
The Impact

Abstract Background Literature suggests that toxin detection differentiates those who require treatment for C. difficile infection (CDI) from those who do not. In-house studies have shown that free toxin can be predicted with high negative predictive value at a predefined cycle threshold (CT) using Xpert tcdB PCR (Cepheid, Sunnyvale, CA). In October 2016, CT-toxin was added to the PCR result and a comment recommends against CDI therapy if CT-toxin is negative (CTtox-). Here we evaluate the effect of this reporting on treatment rates and outcomes of CTtox- patients. Methods Patients tested from October 2016 to Apr. 2017 with a positive Xpert PCR and CTtox- result were included. Clinical data were collected by retrospective chart review and analyzed with the Chi squared and Student t-tests using SPSS. Due to multiple comparisons, α=0.01. Results Of 1516 Xpert PCR tests, 248 (16.4%) were positive and 98 (39.5%) were CTtox-. Of these, 54 (55.7%) were treated. Patient characteristics and data at testing are shown below. There were no cases of CDI-related septic shock or toxic megacolon on review. Time to diarrhea resolution was significantly shorter in untreated patients and there was no difference in crude mortality or later onset of CTtox+ CDI. Conclusion This study demonstrates the impact of stand-alone PCR assay with toxin prediction on reducing CDI therapy rates and provides further evidence that PCR+/toxin- patients are at low risk for CDI-related complications and do not require treatment, though more data is needed in transplant populations. Disclosures N. Banaei, Cepheid: Collaborator, Research Contractor and Scientific Advisor, honorarium for advisory role and Research support

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.

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