Cepheid Xpert Research Articles

Evaluation of indeterminate SARS-CoV-2 results with repeat testing on an alternative platform

Introduction/ObjectiveAccurate SARS-CoV-2 results are crucial for patient management and infection prevention. Result confidence decreases with low viral load because near the assay’s limit of detection (LOD), test results may alternate between positive and negative, as characterized by Poisson distribution for target analytes at low density. Low positive results may indicate past infection, early infection, a vaccinated individual with low level viral shed, or a false-positive result. EUA methods provide guidance on test interpretation, but laboratories should assess clinical accuracy. The purpose of this study was to assess clinical accuracy of specimens with low positive results.Methods/Case ReportRespiratory specimens were tested by Cepheid Xpert® Xpress SARS-CoV-2 assay with positive results up to a Ct of 45. A low positive (defined as Ct ≥35), which could not be confirmed by Hologic Aptima® SARS-CoV-2 assay was reported as indeterminate and repeat testing recommended. Repeat testing occurred by Cepheid, Hologic, BioFire, Roche, or Quest assays. Retrospectively, final results were extracted from the LIS (Epic Beaker, Madison, WI, version May 2020) for 5-months (12/1/2020 to 5/31/2021), and chart review performed.Results (if a Case Study enter NA)A total of 19,969 tests were performed; 10.4% (n=2,083) were positive, 89% (n=17,728) negative, and 0.79% (n=158) indeterminate. Previous infection (up to 3 months prior) was documented in 18% (n=28) of indeterminate results and defined as true positive. Of remaining indeterminate results, 43% (n=68) had repeat testing as recommended by laboratory; 26% (n=18) were positive and 74% (n=50) were negative. The average number of days between indeterminate and negative result was 7.25 (range 1-38).ConclusionResult discordance occurred in < 1% of all samples, excellent agreement. For low positive samples, discordance was higher, as expected. It’s impossible to determine if negative results from the 50 repeat samples were false-positive by Cepheid or false-negative by other methods. In summary, 32% (50/158) of indeterminant samples did not repeat as positive. Overall concordance was high and results fluctuate when low virus is present. In absence of symptoms, we conclude repeat testing is not routinely recommended. Laboratories must recognize that normal variability occurs near assay LOD and must critically assess performance against other methods with similar LODs to fully assess performance of EUA methods.

Sequencing for COVID-19 in the Pandemic Era: What Does it Mean?

Abstract Introduction/Objective SARS-CoV-2 has been developing mutations over the course of the pandemic, leading to the rise of variants. The sequencing of these variants, however, has an unclear role for the medical center providing patient treatment. Methods/Case Report Patient specimens that were positive for the presence of SARS-CoV-2 with a cycle threshold &amp;lt;30 by reverse transcriptase polymerase chain reaction (RT-PCR) were sent for sequencing at the Veterans Health Administration Public Health Reference Laboratory (PHRL). Testing for SARS-CoV-2 was by RT-PCR was initially done by either the Abbott Alinity m SARS-CoV-2 assay (Chicago IL) or the Cepheid Xpert Xpress SARS-CoV- 2/Flu/RSV assay (Sunnyvale CA). All sent patient specimens had been selected by the clinical team for concern of the presence of a SARS-CoV-2 variant. Results (if a Case Study enter NA) There were a total of 8 patients (4 males and 4 females) that were sent for sequencing. The patient ages ranged from 38 to 80 years (average 58.8). The racial proportion of the 8 patients was 2 African Americans, 2 Caucasian Americans, and 4 unanswered. All were positive for SARS-CoV-2 by RT-PCR (4 Abbott assay and 4 Cepheid assay). Six of the sequenced samples showed the NextClade 20I/501Y.V1, Pango Lineage B.1.1.7, a variant first identified in the United Kingdom; four of these six patients had documentation of vaccination prior to the infection. One sequence was a NextClade 20C Pango Lineage B.1.526.1, a variant first identified in New York. The last sequence identified was a NextClade 20G, Pango Lineage B.1, a variant predominantly seen in the United States. Conclusion At the present time, sequencing of SARS-CoV-2 does not have a clear clinical role. However, from a public health and epidemiological point of view, sequencing has a role in SARS-CoV-2 variant tracing and detection. Vaccine protection against variant SARS-CoV-2 may not be complete as some infected patients had been vaccinated.

Performance of SARS-CoV-2 antigen testing in symptomatic and asymptomatic adults: a single-center evaluation

BackgroundAntigen testing offers rapid and inexpensive testing for SARS-CoV-2 but concerns regarding performance, especially sensitivity, remain. Limited data exists for use of antigen testing in asymptomatic patients; thus, performance and reliability of antigen testing remains unclear.Methods148 symptomatic and 144 asymptomatic adults were included. A nasal swab was collected for testing by Quidel Sofia SARS IFA (Sofia) as point of care. A nasopharyngeal swab was also collected and transported to the laboratory for testing by Cepheid Xpert Xpress SARS-CoV-2/Flu/RSV RT-PCR (Cepheid).ResultsOverall, Sofia had good agreement with Cepheid (> 95%) in adults, however was less sensitive. Sofia had a sensitivity of 87.8% and 33.3% for symptomatic and asymptomatic patients, respectively. Among symptomatic patients, testing > 5 days post symptom onset resulted in lower sensitivity (82%) when compared with testing within 5 days of symptom onset (90%). Of the four Sofia false-negative results in the asymptomatic cohort, 50% went on to develop COVID-19 disease within 5 days of testing. Specificity in both symptomatic and asymptomatic cohorts was 100%.ConclusionsSofia has acceptable performance in symptomatic adults when tested < 5 days of symptom onset. Caution should be taken when testing patients with ≥ 5 days of symptoms. The combination of low prevalence and reduced sensitivity results in relatively poor performance of in asymptomatic patients. NAAT-based diagnostic assays should be considered in when antigen testing is unreliable, particularly in symptomatic patients with > 5 days of symptom onset and asymptomatic patients.

Performance Analysis of Three Commercial Kits Designed for RNA Quantification of HIV-1 Group O Variants.

The genetic divergence of HIV-1 group O is high relative to pandemic group M, which could impact detection and quantification of plasma RNA. Recent commercial kits for RNA quantification seem to show good performances in HIV-1/O, but discrepancies are still observed. Here, we compare the performances of 3 commercial assays for the RNA quantification of HIV-1/O. We studied the RNA quantification of 117 clinical samples using Abbott RealTime HIV-1, Cepheid Xpert HIV-1 Viral Load, or Roche Cobas TaqMan HIV-1 v2. First, we conducted a qualitative description, and second, we focused on a quantitative analysis of the results above 40 cp/mL. The degree of agreement between methods and the strength of the correlation of viral load determination were estimated using Bland-Altman plot and Passing-Bablok regression with the Spearman coefficient, respectively. Our 2-by-2 analysis showed that the Abbott and Cepheid assays were very close in terms of correlation and dispersion of points, whereas Roche presented higher values in the highest range of quantification (>5 log10). The Cepheid assay combined better correlation with the consensus value and a lower dispersion of values, leading to an overall better performance of quantification. The quantification was still impacted by intragroup genetic diversity with, here, 1 strain (YBF26). Using a new approach to compare the performances of RNA quantification between more than 2 techniques, we demonstrated that Cepheid could be the most suitable assay for HIV-1/O quantification, although the results from all assays remained strain dependent.

Biobanking: Strengthening Uganda's Rapid Response to COVID-19 and Other Epidemics.

Introduction: SARS-CoV-2 is a fatal disease of global public health concern. Measures to reduce its spread critically depend on timely and accurate diagnosis of virus-infected individuals. Biobanks can have a pivotal role in elucidating disease etiology, translation, and advancing public health. In this article, we show how a biobank has been a critical resource in the rapid response to coronavirus disease of 2019 (COVID-19) in Uganda. Materials and Methods: The Integrated Biorepository of H3Africa Uganda established a COVID-19 biobank. Standard Operating Procedures for sample and data collection, sample processing, and storage were developed. An e-questionnaire data tool was used to collect sociodemographic factors. Samples were collected at 7-day intervals from patients, analyzed for key parameters, processed, annotated, characterized, and stored at appropriate temperatures. Results: Stored samples have been used in validation of 17 diagnostic kits, the Cepheid Xpert Xpress SARS-CoV-2 assay, as well as a sample pooling technique for mass screening and polymerase chain reaction assay validation. Kits that passed validation were deployed for mass screening boosting early detection, isolation, and treatment of COVID-19 cases. Also, 10 applications from researchers and biotech companies have been received and approved and 4 grants have been awarded Conclusion: The CoV-Bank has proven to be an invaluable resource in the fight against the COVID-19 pandemic in Uganda, as samples have been resources in the validation and development of COVID-19 diagnostic tools, which are important in tracing and isolation of infected cases to confront, delay, and stop the spread of the SARS-CoV-2 virus.

Misidentification of meticillin-resistant Staphylococcus aureus by the Cepheid Xpert MRSA NxG assay, the Netherlands, February to March 2021.

We describe two false-negative results in the detection of meticillin-resistant Staphylococcus aureus (MRSA) of sequence type 398 and spa type t011 using the Cepheid Xpert MRSA NxG assay. The isolates were recovered in late February and early March 2021 from two patients in different hospitals in the northern Netherlands. Variations between the two isolate genomes indicate that this MRSA strain might have been spreading for some time and could have disseminated to other regions of the Netherlands and other European countries.

Comparison of Cepheid Xpert HPV test and Hybrid capture 2 high risk HPV DNA test for detection of high risk HPV

Comparison of Cepheid Xpert HPV test and Hybrid capture 2 high risk HPV DNA test for detection of high risk HPV

CML-405: Treatment-Free Remission in Chronic Myeloid Leukemia: A Tunisian Experience

Context: Discontinuation of tyrosine kinase inhibitor (TKI) treatment for chronic phase (CP) chronic myeloid leukemia (CML) patients with a deep molecular response (DMR) has entered standard practice. Objective: In this study, we characterize the treatment-free remission in Tunisian CML patients. Design: This retrospective study collected data for CML patients who had discontinued TKI treatment as part of daily clinical practice in Sfax, Tunisia. Setting: Department of Medical Genetics in University Hospital. Patients or Other Participants: Patients with CML who discontinued their TKI were enrolled. Interventions: Quantitative assessment of the BCR-ABL transcript was performed using the Cepheid Xpert BCR-ABL ultra-assay. Main Outcome Measures: We investigated reasons for discontinuation, duration of TKI treatment before discontinuation, molecular response (MR) status at TKI discontinuation, and treatment-free remission (TFR) duration. Molecular recurrence is defined as the loss of major molecular response (MMR). Results: A total of 17 patients who discontinued treatment were enrolled in this study. Reasons for interruption were deep molecular response (n=13), adverse events (n = 1), and pregnancy (n = 3). TFR was maintained in 10 (64.7%) patients with a median follow-up of 26 months (8–127). The minimum treatment duration before discontinuation was 86 months. Five patients with sustained DMR (38.4%) had a molecular recurrence and re-initiated TKI. Conclusions: Our study highlights that TKI discontinuation was safe and effective in CML patients who are in sustained deep molecular response with longer TKI treatment duration. A larger study is mandatory for a comprehensive analysis of molecular recurrence in CML patients.

Accuracy of Xpert Carba-R Assay for the Diagnosis of Carbapenemase-Producing Organisms from Rectal Swabs and Clinical Isolates: A Meta-Analysis of Diagnostic Studies

The Cepheid Xpert Carba-R assay has demonstrated a promising value for the detection of carbapenemase-producing organisms, but its diagnostic performance remains unclear. Studies were retrieved from Cochrane Library, EMBASE, and PubMed databases according to predetermined selection criteria. The specificity, sensitivity, negative likelihood ratio, positive likelihood ratio, and area under the summary receiver operating characteristic curves of Xpert Carba-R were analyzed by STATA version 13.0. The quality of each study was examined by Quality Assessment of Diagnostic Accuracy Studies using RevMan version 5.2. In total, 17 unique studies involving 15,972 samples met the inclusion criteria. Nine studies performed Xpert Carba-R on rectal swabs. The pooled sensitivity, specificity, and area under the curve were as follows: 0.95 (95% CI, 0.91-0.97; I2=90.80%), 0.99 (95% CI, 0.97-0.99; I2=97.17%), and 0.99 (95% CI, 0.98-1.00), respectively. The sensitivity and specificity of Xpert Carba-R in high-risk populations were 0.99 (95% CI, 0.76-1.00; I2=78.51%) and 0.98 (95% CI, 0.97-0.99; I2=84.95%), respectively. The sensitivity and specificity in low-prevalence regions were 0.96 (95% CI, 0.88-0.99; I2=74.58%) and 0.99 (95% CI, 0.98-0.99; I2=77.66%), respectively. Eight studies performed Xpert Carba-R on clinical isolates. The pooled sensitivity and specificity were 1.00 (95% CI, 0.97-1.00; I2=97.43%) and 0.98 (95% CI, 0.97-0.99; I2=55.27%), respectively. This meta-analysis indicates that Xpert Carba-R assay has excellent diagnostic accuracy for diagnosing carbapenemase-producing organisms on rectal swabsand clinical isolates, especially for high-risk populations and low-prevalence regions.

Clinical evaluation of the molecular-based BD SARS-CoV-2/Flu for the BD MAX™ system.

BackgroundCOVID-19 and influenza (flu) share similar clinical symptoms. Therefore, differential detection of these viruses during the respiratory virus season will be an important component for proper patient triage, management, and treatment.ObjectivesEstablish the diagnostic performance related to SARS-CoV-2 and Flu A/B detection for the BD SARS-CoV-2/Flu for BD MAX™ System (“MAX SARS-CoV-2/Flu”) multiplex assay.Materials and methodsTwo hundred and thirty-five (235) retrospective nasopharyngeal specimens were obtained from external vendors. The BD BioGx SARS-CoV-2 Reagents for BD MAX™ System (“BioGx SARS-CoV-2″) and the Cepheid Xpert® Xpress Flu/RSV (“Xpert Flu/RSV”) were utilized as reference methods.ResultsBy reference methods, 52 specimens were SARS-CoV-2-positive, 59 were Flu A-positive, and 60 were Flu B-positive. MAX SARS-CoV-2/Flu had positive percent agreement (PPA) and negative percent agreement (NPA) values for SARS-CoV-2 detection of 96.2% ([95%CI]:87.0–98.9) and 100% [95%CI:88.7–100], respectively; PPA values for Flu A and Flu B of 100% [95%CI:93.9–100] and 98.3% [95%CI:91.1–99.7], respectively, and NPA values for Flu A and Flu B of 98.9% [95%CI:94.0–99.8] and 100% [95%CI:95.9–100], respectively.ConclusionsThe MAX SARS-CoV-2/Flu assay met FDA-EUA performance criteria for SARS-CoV-2 (≥95% for PPA and NPA) and FDA clearance criteria for Flu A/B (PPA ≥90%; lower bound of the 95%CI ≥80% and NPA ≥95%; lower bound of the 95%CI ≥90%).

Determination of carbapenemase genes in clinical isolates using Cepheid Xpert Carba-R

Detection of carbapenem resistance genes is a critical issue for hospitals due to possible recommendations for infection control and targeted therapy. The Cepheid Xpert instrument, a Carba-R test for the detection and differentiation of five common carbapenemase genes, was tested from September 2020 to February 2021. As part of the approbation, 20 tests were provided. This review presents the results of the approbation of a relatively regular sensitivity study on Siemens WalkAway‑96 plus. Cepheid Xpert Carba-R analysis has been shown to be an accurate and fast tool for detecting colonization by carbapenem-resistant gram-negative bacteria, which can help limit the spread of these organisms in hospitals.

Evaluating tests for diagnosing COVID-19 in the absence of a reliable reference standard: pitfalls and potential solutions

Evaluating tests for diagnosing COVID-19 in the absence of a reliable reference standard: pitfalls and potential solutions

Clinical Comparison of Three Sample-to-Answer Systems for Detecting SARS-CoV-2 in B.1.1.7 Lineage Emergence.

PurposeAccurate molecular diagnostic assays for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, are needed for epidemiology studies and to support infection-control measures. We evaluated the analytical sensitivity and clinical performance of three sample-to-answer molecular-diagnostics systems for detecting SARS-CoV-2 using 325 nasopharyngeal swab clinical samples from symptomatic patients.MethodsThe BioFire Respiratory Panel 2.1 (RP2.1), cobas Liat SARS-CoV-2 and Influenza A/B, and Cepheid Xpert Xpress SARS-CoV-2/Flu/RSV platforms, which have been granted emergency-use authorization by the US FDA, were tested and compared.ResultsThe positive percent agreement, negative percent agreement, and overall percent agreement among the three point of care testing systems were 98–100%, including for the wild-type SARS-CoV-2 (non-B.1.1.7) and a variant of concern (B.1.1.7). Notably, the BioFire RP2.1 may fail to detect the SARS-CoV-2 S gene in the B.1.1.7 lineage because of the spike protein mutation.ConclusionAll three point of care testing platforms provided highly sensitive, robust, and almost accurate results for rapidly detecting SARS-CoV-2. These automated molecular diagnostic assays can increase the effectiveness of control and prevention measures for infectious diseases.

Association of cycle threshold values of CBNAAT with severity and outcome in COVID-19

Determination of viral load through cycle threshold (Ct) values may act as a predictor of severity and outcomes in patients with corona virus disease 2019 (COVID-19). However, variable literature is available regarding this relationship. Our study attempted to explore this association and the effect of various socio-demographic and clinical parameters on severity and outcome of COVID-19. Retrospective analysis of records of 731 patients whose nasopharyngeal/ oropharyngeal swabs were subjected to cartridge based nucleic acid amplification (CBNAAT) on Cepheid Xpert Xpress SARS-Cov-2 was done. Cycle threshold (Ct) values of N2 and E genes were studied in relation to severity and outcome of COVID-19. The viral load as determined by Ct values was classified as high (&lt;25), medium (25.1-32) and low (&gt;32). Association of socio-demographic and clinical parameters with respect to severity and outcome was also studied. Severity and mortality were significantly more in elder individuals, those belonging to the rural background, those with symptoms &gt;7 days in duration before presentation and those with increasing number of co-morbidities (Severity: p&lt;0.001, mortality: p &lt;0.001, 0.005, 0.006 and &lt;0.001 respectively). The Ct values of gene N2 and E inversely correlated with severity and mortality from the disease (N2 gene: p=0.001 for both severity and mortality, E gene: severity: p&lt;0.001, mortality: p=0.016 respectively). The severity of the illness and chances of mortality were significantly lesser when the CT value of N2 gene was &gt;32, in comparison when it was upto 25, and when between 25.1 and 32 (severity: p=0.032 and 0.003 respectively, mortality: p=0.018 and &lt;0.001 respectively). Almost similar trends were seen with respect to E gene (severity: p&lt;0.001 and 0.067 respectively, mortality p=0.175 and 0.005 respectively). Viral load as determined by Ct values of N2 and E genes can act as surrogate markers for prediction of severity and disease outcomes in COVID-19.

SARS-CoV-2 N gene mutations impact detection by clinical molecular diagnostics: reports in two cities in the United States

Nasal and nasopharyngeal swab specimens tested by the Cepheid Xpert Xpress SARS-CoV-2 were analyzed by whole-genome sequencing based on impaired detection of the N2 target. Each viral genome had at least one mutation in the N gene, which likely arose independently in the New York City and Pittsburgh study sites.

Sociodemographic Factors, Cycle Threshold Values, and Clinical Outcomes of COVID-19

Background: The gold standard for diagnosis of COVID-19 has been SARS-CoV-2 detection by reverse-transcriptase-quantitative polymerase chain reaction (RT-qPCR), which provides a semiquantitative indicator of viral load (cycle threshold, Ct). Our research group previously described how African American race and poverty were associated with an increased likelihood of hospitalization due to COVID-19. We sought to characterize the relationship between Ct values and clinical outcomes while controlling for sociodemographic factors. Methods: We conducted a cross-sectional study of SARS-CoV-2–positive patients admitted to Froedtert Health between March 16 and June 1, 2020. Ct values were obtained by direct interrogation of either cobas SARS-CoV-2 or Cepheid Xpert Xpress platforms. Patient demographics, comorbidities, symptoms at admission, health insurance, and hospital course were collected using electronic medical records. A proxy for socioeconomic disadvantage, area-deprivation index (ADI), was assigned using ZIP codes. Multivariate models were performed to assess associations between Ct values and clinical outcomes while controlling for ADI, race, and type of insurance. Results: Overall, 302 patients were included. The mean age was 60.89 years (SD, 18.2); 161 (53%) were men, 177 (58%) were African Americans; and 156 (51%) had Medicaid or were uninsured. Of the 302 inpatients, 158 (52%) required admission to the ICU, 199 (65.9%) were discharged to home, 49 (16.2%) were discharged to a nursing home, and 54 (17.9%) died. Lower Ct values (higher viral load) were associated with Medicaid or lack of insurance (coefficient, −2.88, 95% confidence interval [CI], −4.96 to −0.79, P = .007) and age &gt;60 years old (coefficient, −2.98, 95% CI −4.87 to −1.08, P = .002). Contrary to what was expected, higher CT values (lower viral load) were associated with higher ADI scores (coefficient, 2.62, 95% CI, 0.52–4.85; P = .017). However, when patients were stratified into low, medium, and high ADI, those with Medicaid or no insurance had the lowest mean Ct values (23.3, 25.9, and 27.6, respectively) compared to Medicare or other insurance (Figure 1). Body mass index (odds ratio [OR], 1.04; 95% CI, 1.02–1.07; P = .001) and male sex (OR, 2.15; 95% CI, 1.28–3.60; P = .004) were independently associated with ICU admission. Every increase of a CT point (OR, 0.90; 95% CI, 0.85–0.95; p &lt;0.001) and age &gt;60 years old (OR 2.62, 95% CI; 1.14-6.04; p=0.023) was associated with death. Conclusions: In this cross-sectional study of adults tested for COVID-19 in a large midwestern academic health system, lower Ct values were independently associated with poverty and age &gt;60 years old.Funding: NoDisclosures: None

Characteristics of Inpatients with False-Negative SARS-CoV-2 PCR Test Results

Background: At our institution, the concern for false-negative nasopharyngeal testing for SARS-CoV-2 at the onset of illness led to a general policy of retesting inpatients at 48 hours. For such patients, 2 negative SARS-CoV-2 PCR test results were required prior to discontinuation of COVID-19 control precautions. To assess the utility of routine repeat testing We analyzed patients presenting to our hospital who initially tested negative for SARS-CoV-2 but were found to be positive on repeated testing. Methods: All inpatients with symptoms concerning for COVID-19 were tested via nasopharyngeal sample for SARS-CoV-2 by PCR on admission. Patients with continued symptoms and no alternative diagnosis were retested 48 hours later. Testing was performed using either the Roche cobas SARS-CoV-2 RT-PCR assay or the Cepheid Xpert Xpress SARS-CoV-2 test. Between March 17, 2020, and May 10, 2020, we retrospectively analyzed data from patients with false-negative SARS-CoV-2 PCR test results who were subsequently confirmed positive 48 hours later. We evaluated demographic information, days since symptom onset, symptomatology, chest imaging, vital sign trends, and the overall clinical course of each patient. Results: During the study period, 14,683 tests were performed, almost half (n = 7,124) were performed through the ED and in the inpatient setting. Of 2,283 patients who tested positive for SARS-CoV-2, only 19 (0.01%) initially tested negative. Patients with initial false-negative test results presented with symptoms that ranged from fever and dyspnea to fatigue and vomiting. Notably, few patients presented “early” in their disease (median, 6 days; range, 0–10 days). However, patients with initial false-negative PCR test results did seem to have consistent imaging findings, specifically bilateral bibasilar ground glass opacities on chest radiograph or computed tomography scan. Conclusions: Among inpatients with COVID-19, we found a very low rate of initial false-negative SARS-CoV-2 PCR test results, which were not consistently related to premature testing. We also identified common radiographic findings among patients with initially false-negative test results, which could be useful in triaging patients who may merit retesting. Based on these data, we revised our existing clearance criteria to allow for single-test removal of COVID-19 precautions. Evaluating subsequent reduction in unnecessary testing is difficult given changing community prevalence, increased census, and increased opening to elective procedures. However, given the significant percentage of ED and inpatient testing, removal of repeated testing has likely resulted in a reduction of several thousand unnecessary COVID-19 tests monthly.Funding: NoDisclosures: None

Does Every Patient with a Positive SARS-CoV-2 RT-PCR Test Require Isolation? A Prospective Analysis

Group Name: CDC Prevention Epicenters Program Background: Reverse-transcriptase polymerase chain reaction (RT-PCR) tests are the reference standard for diagnosing SARS-CoV-2 infection, but false positives can occur and viral RNA may persist for weeks-to-months following recovery. Isolating such patients increases pressure on limited hospital resources and may impede care. Therefore, we quantified the percentage of patients who tested positive by RT-PCR yet were unlikely to be infectious and could be released from isolation. Methods: We prospectively identified all adults hospitalized at Brigham and Women’s Hospital (Boston, MA) who tested positive for SARS-CoV-2 by RT-PCR (primarily Hologic Panther Fusion or Cepheid Xpert platforms) between December 24, 2020, and January 24, 2021. Each case was assessed by infection control staff for possible discontinuation of isolation using an algorithm that incorporated the patient’s prior history of COVID-19, current symptoms, RT-PCR cycle threshold (Ct) values, repeat RT-PCR testing at least 24 hours later, and SARS-CoV-2 serologies (Figure 1). Results: Overall, 246 hospitalized patients (median age, 66 years [interquartile range, 50–74]; 131 [53.3%] male) tested positive for SARS-CoV-2 by RT-PCR during the study period. Of these, 201 (81.7%) were deemed new diagnoses of active disease on the basis of low Ct values and/or progressive symptoms. Moreover, 44 patients (17.9%) were deemed noninfectious: 35 (14.2%) had prior known resolved infections (n = 21) or unknown prior infection but positive serology (n = 14), high Ct values on initial testing, and negative or stably high Ct values on repeat testing. Also, 5 (2.0%) had recent infection but &gt;10 days had passed since symptom onset and they were clinically improving. In addition, 4 (1.6%) results were deemed false positives based on lack of symptoms and at least 1 negative repeat RT-PCR test (Figure 2). One patient was asymptomatic with Ct value &lt;35 but was discharged before further testing could be obtained. Among the 44 noninfectious patients, isolation was discontinued a median of 3 days (IQR, 2–4) after the first positive test. We did not identify any healthcare worker infections attributable to early discontinuation of isolation in these patients. Conclusions: During the winter COVID-19 second surge in Massachusetts, nearly 1 in 5 hospitalized patients who tested positive for SARS-CoV-2 by RT-PCR were deemed noninfectious and eligible for discontinuation of precautions. Most of these cases were consistent with residual RNA from prior known or undiagnosed infections. Active assessments of SARS-CoV-2 RT-PCR tests by infection control practitioners using clinical data, Ct values, repeat tests, and serologies can safely validate the release many patients from isolation and thereby conserve resources and facilitate patient care.Funding: NoDisclosures: None

Comparative evaluation of the Thermo fisher TaqPath\u2122 COVID-19 combo kit with the Cepheid Xpert\xae Xpress SARS-CoV-2 assay for detecting SARS-CoV-2 in nasopharyngeal specimens

PurposeWith over 50 SARS-CoV-2 gene amplification assays that have been EUA cleared with minimal experimental validation performed, it is likely that not all of these assays are comparable in their ability to detect SARS-CoV-2 in clinical specimens. Thermo Fisher Scientific is a relatively new company in the molecular diagnostics field and the purpose of this study was to compare the performance of the Thermo Fisher TaqPath™ Combo Kit with an established test, the Cepheid Xpert® Xpress SARS-CoV-2 assay, for its ability to detect SARS-CoV-2 in nasopharyngeal specimens.MethodsA total of 300 randomly selected nasopharyngeal specimens were evaluated and tested by the TaqPath and GeneXpert assays. Discordant test specimens were arbitrated by performing an alternative PCR assay and Sanger sequencing.ResultsThe TaqPath assay had a 96.7 and 99.6% positive and negative agreement respectively when compared to the Xpert Xpress test. However, after test arbitration, the three discordant specimens were arbitrated in favor of the TaqPath assay producing a positive and negative percent agreement of 100% for the TaqPath Combo Kit while the Xpress SARS-CoV-2 assay had a positive and negative percent agreement of 98.3 and 99.2% respectively.ConclusionsThe TaqPath Combo Kit is a high complexity assay that compares favorably with the Xpert Xpress test and can be reliably used for the detection of SARS-CoV-2 in nasopharyngeal specimens.

Toxigenic Clostridium Difficile Colonization in Patients with Hematologic Malignancies Admitted to the Hospital for Chemotherapy or Hematopoietic Cell Transplantation

Background: Clostridium difficile (CD) is an important cause of infectious diarrhea in patients with hematologic malignancies (HM) admitted to the hospital for chemotherapy or hematopoietic cell transplantation (HM-HCT patients). These patients are at increased risk of developing Clostridium difficile infection (CDI) compared to non-oncology patients, and they are more likely to suffer adverse outcomes from the infection. Asymptomatic colonization of patients with CD is known to precede infection. However, the reported prevalence of asymptomatic colonization varies widely between studies. The primary objective of this study was to define the prevalence of toxigenic CD colonization in patients with hematologic malignancies who were admitted to the hospital for scheduled chemotherapy or hematopoietic cell transplantation (HCT). The secondary objective was to determine what microbiology tests are accurate in detecting CD colonization compared to the gold standard of toxigenic culture.Method: We performed a prospective cohort study of HM-HCT patients at our institution. Patients were included if they were age 18 years or older and scheduled for elective admission for chemotherapy or HCT (including both autologous and allogeneic HCT). Patients were excluded if they had diarrhea due to CDI in the past 30 days; if they had diarrhea of unknown etiology; if they were admitted on an unscheduled basis for treatment of acute illness; or if their anticipated length of stay was less than 72 hours. At the time of hospital admission for scheduled chemotherapy or HCT, a stool specimen was collected from each patient in a clean sterile collection vial. All samples were freshly collected and sent to the microbiology laboratory for processing. The stool samples were tested with six different methods: Simplexa™ C. difficile PCR Universal Direct Kit, Cepheid Xpert® PCR C.difficileCD/Epi (Xpert CD/Epi), C. diff Quik Chek Complete® GDH, C. diff Quik Chek Complete® Toxin A/B, LEUKO EZ VUE® ELISA test, and toxigenic culture. Toxigenic culture was used as the reference method. Baseline characteristics of those who tested positive versus negative were described using summary statistics, and univariable logistic regression analysis was used to identify risk factors for CD colonization. Sensitivity and specificity with 95% confidence interval for five tests were estimated.Results: A total of 114 patients were recruited for participation between April 2016 and November 2016. Thirteen patients either withdrew consent or did not provide a stool sample, so the final CD analysis included 101 patients. The demographic and clinical characteristics of the included patients are presented in Table 1. The prevalence of toxigenic CD colonization as determined by toxigenic culture was 13% (14/101, [95% CI: 8-22%]). The Cepheid Xpert PCR CD/Epi showed the highest sensitivity. The sensitivity and specificity of the different testing methods are shown in Table 2. The median (range) length of hospital stay was 13 (2-57) days. Among the 14 patients who tested positive by toxigenic culture, only 1 patient (7%) patient developed CDI during his hospitalization, and his stool tested positive by Cepheid Xpert PCR CD/Epi prior to the development of CDI. Univariable logistic regression analysis did not identify any risk factors for CD colonization including prior CDI, antibiotic use in the past 30 days, or treatment with proton pump inhibitors.Conclusions: Toxigenic CD colonization was high in our cohort of patients, but the majority of patients who were colonized with toxigenic CD did not develop CDI while hospitalized. There were no identifiable risk factors for CD colonization. The most sensitive test for identifying toxigenic CD colonization was the Cepheid Xpert PCR CD/Epi test. Our findings suggest that the Cepheid Xpert PCR CD/Epi test could be used to screen for toxigenic CD colonization in patients admitted for scheduled chemotherapy or HCT. However, the costs and benefits of such an approach warrant further investigation. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.