scholarly journals Evaluation of Copan FecalSwab as Specimen Type for Use in Xpert C. difficile Assay

2017 ◽  
Vol 55 (10) ◽  
pp. 3123-3129 ◽  
Author(s):  
Michael J. Mashock ◽  
Matthew L. Faron ◽  
Blake W. Buchan ◽  
Nathan A. Ledeboer
Keyword(s):  
Test Performance ◽  
Pcr Assay ◽  
Content Type ◽  
Molecular Assays ◽  
Specificity And Sensitivity ◽  
Collection Device ◽  
Stool Samples ◽  
Stool Specimens ◽  
Xpert Assay ◽  
Preservation Medium

ABSTRACT Liquid-based microbiology (LBM) devices incorporating flocked swabs and preservation medium ease transport of specimens and improve specimen yield compared to traditional fiber wound swabs; however, the performance of LBM collection devices has not been evaluated in many molecular assays. It is unclear how the differences in matrix and specimen loading with an LBM device will affect test performance compared to traditional collection devices. The purpose of this study was to evaluate the performance of specimens collected in FecalSwab transport medium (Copan Diagnostics, Murrieta, CA) compared to unpreserved stool using the Cepheid Xpert C. difficile assay (Cepheid, Sunnyvale, CA). Results equivalent to unpreserved stool samples were obtained when 400 μl of FecalSwab-preserved stool was employed in the Xpert assay. The positive and negative percent agreement of specimens inoculated with FecalSwab medium ( n = 281) was 97.0% (95% confidence interval [CI], 90.9 to 96.4%) and 99.4% (95% CI, 96.4 to 99.9%), respectively, compared to reference results obtained using unpreserved stool. Throughout this study, only four discrepant results occurred when comparing preserved specimens to unpreserved stool specimens in the Xpert C. difficile PCR assay. Post discrepant analysis, using the BD MAX Cdiff assay, the specificity and sensitivity both increased to 100%. The high positive and negative percent agreements observed in this study suggest that stool preserved in FecalSwab media yields equivalent results to using unpreserved stool when tested on the Xpert C. difficile assay, allowing laboratories to adopt this liquid-based microbiology collection device.

scholarly journals Quantitative Thresholds Enable Accurate Identification ofClostridium difficileInfection by the Luminex xTAG Gastrointestinal Pathogen Panel

2018 ◽  
Vol 56 (6) ◽  
Author(s):  
Sixto M. Leal ◽  
Elena B. Popowitch ◽  
Kara J. Levinson ◽  
Teny M. John ◽  
Bethany Lehman ◽  
...  
Keyword(s):  
Test Performance ◽  
Predictive Value ◽  
High Specificity ◽  
Clinical Suspicion ◽  
Performance Characteristics ◽  
Accurate Identification ◽  
Data Set ◽  
Content Type ◽  
Molecular Assays ◽  
Stool Samples

ABSTRACTClostridium difficilecolonizes the gastrointestinal (GI) tract, resulting in either asymptomatic carriage or a spectrum of diarrheal illness. If clinical suspicion forC. difficileis low, stool samples are often submitted for analysis by multiplex molecular assays capable of detecting multiple GI pathogens, and some institutions do not report this organism due to concerns for high false-positive rates. Since clinical disease correlates with organism burden and molecular assays yield quantitative data, we hypothesized that numerical cutoffs could be utilized to improve the specificity of the Luminex xTAG GI pathogen panel (GPP) forC. difficileinfection. Analysis of cotested liquid stool samples (n= 1,105) identified a GPP median fluorescence intensity (MFI) value cutoff of ≥1,200 to be predictive of two-step algorithm (2-SA; 96.4% concordance) and toxin enzyme immunoassay (EIA) positivity. Application of this cutoff to a second cotested data set (n= 1,428) yielded 96.5% concordance. To determine test performance characteristics, concordant results were deemed positive or negative, and discordant results were adjudicated via chart review. Test performance characteristics for the MFI cutoff of ≥150 (standard), MFI cutoff of ≥1,200, and 2-SA were as follows (respectively): concordance, 95, 96, and 97%; sensitivity, 93, 78, and 90%; specificity, 95, 98, and 98%; positive predictive value, 67, 82, and 81%;, and negative predictive value, 99, 98, and 99%. To capture the high sensitivity for organism detection (MFI of ≥150) and high specificity for active infection (MFI of ≥1,200), we developed and applied a reporting algorithm to interpret GPP data from patients (n= 563) with clinician orders only for syndromic panel testing, thus enabling accurate reporting ofC. difficilefor 95% of samples (514 negative and 5 true positives) irrespective of initial clinical suspicion and without the need for additional testing.

scholarly journals A New Highly Sensitive and Specific Real-Time PCR Assay Targeting the Malate Dehydrogenase Gene ofKingella kingaeand Application to 201 Pediatric Clinical Specimens

2018 ◽  
Vol 56 (8) ◽  
Author(s):  
Nawal El Houmami ◽  
Guillaume André Durand ◽  
Janek Bzdrenga ◽  
Anne Darmon ◽  
Philippe Minodier ◽  
...  
Keyword(s):  
Real Time ◽  
Malate Dehydrogenase ◽  
Real Time Pcr ◽  
Detection Sensitivity ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Content Type ◽  
Clinical Specimens ◽  
Specificity And Sensitivity ◽  
Pcr Assays

ABSTRACTKingella kingaeis a significant pediatric pathogen responsible for bone and joint infections, occult bacteremia, and endocarditis in early childhood. Past efforts to detect this bacterium using culture and broad-range 16S rRNA gene PCR assays from clinical specimens have proven unsatisfactory; therefore, by the late 2000s, these were gradually phased out to explore the benefits of specific real-time PCR tests targeting thegroELgene and the RTX locus ofK. kingae. However, recent studies showed that real-time PCR (RT-PCR) assays targeting theKingellasp. RTX locus that are currently available for the diagnosis ofK. kingaeinfection lack specificity because they could not distinguish betweenK. kingaeand the recently describedKingella negevensisspecies. Furthermore,in silicoanalysis of thegroELgene from a large collection of 45K. kingaestrains showed that primers and probes fromK. kingaegroEL-based RT-PCR assays display a few mismatches withK. kingae groELvariations that may result in decreased detection sensitivity, especially in paucibacillary clinical specimens. In order to provide an alternative togroEL- and RTX-targeting RT-PCR assays that may suffer from suboptimal specificity and sensitivity, aK. kingae-specific RT-PCR assay targeting the malate dehydrogenase (mdh) gene was developed for predicting no mismatch between primers and probe and 18 variants of theK. kingae mdhgene from 20 distinct sequence types ofK. kingae. This novelK. kingae-specific RT-PCR assay demonstrated high specificity and sensitivity and was successfully used to diagnoseK. kingaeinfections and carriage in 104 clinical specimens from children between 7 months and 7 years old.

scholarly journals Clinical Assessment of a Nocardia PCR-Based Assay for Diagnosis of Nocardiosis

2018 ◽  
Vol 56 (6) ◽  
Author(s):  
Claire Rouzaud ◽  
Véronica Rodriguez-Nava ◽  
Emilie Catherinot ◽  
Frédéric Méchaï ◽  
Emmanuelle Bergeron ◽  
...  
Keyword(s):  
Clinical Sample ◽  
Positive Control ◽  
Negative Control ◽  
Clinical Samples ◽  
Pcr Assay ◽  
Content Type ◽  
Underlying Condition ◽  
Alternative Diagnosis ◽  
Specificity And Sensitivity ◽  
Assay Result

ABSTRACT The diagnosis of nocardiosis, a severe opportunistic infection, is challenging. We assessed the specificity and sensitivity of a 16S rRNA Nocardia PCR-based assay performed on clinical samples. In this multicenter study (January 2014 to April 2015), patients who were admitted to three hospitals and had an underlying condition favoring nocardiosis, clinical and radiological signs consistent with nocardiosis, and a Nocardia PCR assay result for a clinical sample were included. Patients were classified as negative control (NC) (negative Nocardia culture results and proven alternative diagnosis or improvement at 6 months without anti- Nocardia treatment), positive control (PC) (positive Nocardia culture results), or probable nocardiosis (positive Nocardia PCR results, negative Nocardia culture results, and no alternative diagnosis). Sixty-eight patients were included; 47 were classified as NC, 8 as PC, and 13 as probable nocardiosis. PCR results were negative for 35/47 NC patients (74%). For the 12 NC patients with positive PCR results, the PCR assay had been performed with respiratory samples. These NC patients had chronic bronchopulmonary disease more frequently than did the NC patients with negative PCR results (8/12 patients [67%] versus 11/35 patients [31%]; P = 0.044). PCR results were positive for 7/8 PC patients (88%). There were 13 cases of probable nocardiosis, diagnosed solely using the PCR results; 9 of those patients (69%) had lung involvement (consolidation or nodule). Nocardia PCR testing had a specificity of 74% and a sensitivity of 88% for the diagnosis of nocardiosis. Nocardia PCR testing may be helpful for the diagnosis of nocardiosis in immunocompromised patients but interpretation of PCR results from respiratory samples is difficult, because the PCR assay may also detect colonization.

scholarly journals A Novel Stool PCR Test for Helicobacter pylori May Predict Clarithromycin Resistance and Eradication of Infection at a High Rate

2017 ◽  
Vol 55 (8) ◽  
pp. 2400-2405 ◽  
Author(s):  
Erin Beckman ◽  
Ilaria Saracino ◽  
Giulia Fiorini ◽  
Courtney Clark ◽  
Vladimir Slepnev ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Biopsy Sample ◽  
True Positive ◽  
Content Type ◽  
Clarithromycin Resistance ◽  
Urease Test ◽  
Eradication Of Infection ◽  
Stool Samples ◽  
Stool Specimens ◽  
H Pylori

ABSTRACTClarithromycin-based regimens are commonly used as a first-line therapy forHelicobacter pylori-positive patients; however, resistance to clarithromycin has led to treatment failures. The aim of this study was to evaluate the feasibility of using stool samples to detect the presence ofH. pyloriDNA while concurrently detecting mutations associated with resistance to clarithromycin. For this purpose, total DNA was extracted from 294 raw stool specimens fromH. pylori-positive and -negative patients. TaqMan real-time PCR amplification was used to detect the presence ofH. pylorias well as to predict the phenotype of the organism and the related outcome for patients treated with clarithromycin. Clarithromycin resistance was determined upon analysis of the PCR result. Patients were also tested by a urea breath test and were subjected to esophagogastroduodenoscopy, followed by histology, culture, and a rapid urease test, in order to obtain a consensus patient infection status. Of 294 total stool samples, 227 were deemed true positive. The sensitivity ofH. pyloridetection by PCR was 93.8%. Of 213 true-positive samples that were sequenced, 36.2% showed point mutations associated with clarithromycin resistance (A2142C, A2142G, A2143G). The final correlation of the mutant genotypes as determined by sequencing with the eradication of infection was 86%. We found thatHelicobacter pyloriDNA can be detected in human stool specimens with high sensitivity and can therefore be used to determine the presence of the bacterium without obtaining a biopsy sample. Moreover, genotypic resistance to clarithromycin can be predicted without obtaining a biopsy sample, facilitating the choice of the right therapeutic approach.

scholarly journals Comparative Clinical Evaluation of NeoPlex RB-8 with Seeplex PneumoBacter ACE for Simultaneous Detection of Eight Respiratory Bacterial Pathogens

2019 ◽  
Vol 58 (2) ◽  
Author(s):  
Jeong Woo Kim ◽  
Seong Soo Hong ◽  
In Seop Lee ◽  
Hyun Young Chi ◽  
Soo-Ok Kim ◽  
...  
Keyword(s):  
Sensitivity And Specificity ◽  
Legionella Pneumophila ◽  
Simultaneous Detection ◽  
Nasopharyngeal Swab ◽  
Pcr Assay ◽  
Content Type ◽  
Bordetella Parapertussis ◽  
Molecular Assays ◽  
Detection Assay ◽  
Higher Sensitivity

ABSTRACT There are several convenient and accurate molecular assays to detect respiratory bacterial infection. The NeoPlex RB-8 detection kit (NeoPlex RB-8) is a new multiplex real-time PCR assay that simultaneously detects Streptococcus pneumoniae, Mycoplasma pneumoniae, Chlamydophila pneumoniae, Legionella pneumophila, Haemophilus influenzae, Bordetella pertussis, Bordetella parapertussis, and Moraxella catarrhalis in a single test. This study compared the clinical concordance of NeoPlex RB-8 with another method, Seeplex PneumoBacter ACE detection assay (Seeplex PB ACE), which simultaneously detects S. pneumoniae, M. pneumoniae, C. pneumoniae, L. pneumophila, H. influenzae, and B. pertussis. We tested 2,137 nasopharyngeal swab and sputum specimens using both assays. For discordant Bordetella parapertussis and M. catarrhalis specimens, we also performed bidirectional sequencing. For S. pneumoniae, M. pneumoniae, C. pneumoniae, L. pneumophila, H. influenzae, and B. pertussis, which are detected by both NeoPlex RB-8 and Seeplex PB ACE, the positive and negative agreement between the two assays ranged from 91.7 to 100% (κ = 0.918 to 1). S. pneumoniae and H. influenzae were the most discordant targets and measured with higher sensitivity and specificity by NeoPlex RB-8 than Seeplex PB ACE. For Bordetella parapertussis and M. catarrhalis, which are not detected by Seeplex PB ACE, NeoPlex RB-8 sensitivity and specificity were >99%. Overall, NeoPlex RB-8 was highly comparable to Seeplex PB ACE, but NeoPlex RB-8 was more clinically accurate, with higher throughput and more convenience.

scholarly journals 749. A Nurse-Driven Protocol for Early Detection of Clostridiodes difficile Infections

2021 ◽  
Vol 8 (Supplement_1) ◽  
pp. S471-S472
Author(s):  
Shannon Beckman ◽  
Jonathan Chia ◽  
Bethany Stibbe ◽  
Monica Rykse ◽  
Michael S Wang
Keyword(s):  
Early Detection ◽  
Nursing Staff ◽  
Further Education ◽  
Pcr Assay ◽  
Inpatient Ward ◽  
Control Department ◽  
Stool Samples ◽  
Stool Specimens ◽  
Hospital Acquired ◽  
Community Onset

Abstract Background Clostridiodes difficile infections (CDI) are a significant cause of hospital acquired infections, resulting in significant morbidity and mortality. Early detection of CDI has been shown to reduce the spread of CDI within the hospital. As nurses are frequently at the patient’s bedside, we proposed to empower the nursing staff to assess, collect stool samples, and order C. difficile testing. Methods Rates of CDI were measured by our Infection Control Department. Hospital-onset CDI (HO-CDI) was defined as a positive C. difficile PCR assay after 3 days of admission, defined as a stay of at least 3 midnights. Community-onset CDI (CO-CDI) was defined as any case that was diagnosed in the Emergency Department or inpatient ward < 3 days of hospitalization based on stool testing as above. Nursing was instructed and empowered to assess, collect stool specimens, and place an order for C. difficile testing, based on the criteria of ≥3 loose or watery stools over 24 hours. Nursing was also educated to not order a test if patients had received stool softeners, enemas, or laxatives within 24 hours. The protocol was initiated in February 2019. Results Rates of HO-CDI increased during the intervention period, rising from 2.6 cases/10000 patient days and peaking at 17.7 cases/10000 patient days (average 6.7 vs. 12.1 monthly cases per 10,000 patient days. Rates of CO-CDI did not significantly change (12.4 vs. 11.5 monthly cases per 10000 patient days). Due to concerns of inappropriate testing, which included testing after laxatives, enemas, or sending specimens despite < 3 stools over 24 hours, the protocol was discontinued in June 2019. Although the HO-CDI rate remained elevated over the next month, the rate subsequently decreased over the next several months (12.1 vs. 8.0 cases per 10000 patient days). Overall testing also increased over the study period (148.3 vs. 169.9 cases/per 10000 patient days).Figure 1 - Clostridiodes difficile rates Figure 2 - CDI testing rates Conclusion A nursing driven protocol resulted in increased HO-CDI and overall CDI rates suggesting that the intervention may have been a factor in increasing the frequency of HO-CDI diagnoses, although the possibility of misdiagnosis of colonization for true CDI cannot be excluded. Further education of nursing staff may be a potential intervention in improving appropriate CDI testing. Disclosures All Authors: No reported disclosures

scholarly journals Semiquantitative Multiplexed Tandem PCR for Detection and Differentiation of Four Theileria orientalis Genotypes in Cattle

2014 ◽  
Vol 53 (1) ◽  
pp. 79-87 ◽  
Author(s):  
Piyumali K. Perera ◽  
Robin B. Gasser ◽  
Simon M. Firestone ◽  
Lee Smith ◽  
Florian Roeber ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Simultaneous Detection ◽  
Asia Pacific ◽  
Analytical Sensitivity ◽  
Pacific Region ◽  
Asia Pacific Region ◽  
Pcr Assay ◽  
Theileria Orientalis ◽  
Content Type ◽  
Specificity And Sensitivity

Oriental theileriosis is an emerging, tick-borne disease of bovines in the Asia-Pacific region and is caused by one or more genotypes of theTheileria orientaliscomplex. This study aimed to establish and validate a multiplexed tandem PCR (MT-PCR) assay using three distinct markers (major piroplasm surface protein, 23-kDa piroplasm membrane protein, and the first internal transcribed spacer of nuclear DNA), for the simultaneous detection and semiquantification of four genotypes (Buffeli, Chitose, Ikeda, and type 5) of theT. orientaliscomplex. Analytical specificity, analytical sensitivity, and repeatability of the established MT-PCR assay were assessed in a series of experiments. Subsequently, the assay was evaluated using 200 genomic DNA samples collected from cattle from farms on which oriental theileriosis outbreaks had occurred, and 110 samples from a region where no outbreaks had been reported. The results showed the MT-PCR assay specifically and reproducibly detected the expected genotypes (i.e., genotypes Buffeli, Chitose, Ikeda, and type 5) of theT. orientaliscomplex, reliably differentiated them, and was able to detect as little as 1 fg of genomic DNA from each genotype. The diagnostic specificity and sensitivity of the MT-PCR were estimated at 94.0% and 98.8%, respectively. The MT-PCR assay established here is a practical and effective diagnostic tool for the four main genotypes ofT. orientaliscomplex in Australia and should assist studies of the epidemiology and pathophysiology of oriental theileriosis in the Asia-Pacific region.

scholarly journals Usefulness of Adjunctive Fecal Calprotectin and Serum Procalcitonin in Individuals Positive for Clostridium difficile Toxin Gene by PCR Assay

2015 ◽  
Vol 53 (11) ◽  
pp. 3667-3669 ◽  
Author(s):  
Kristin Y. Popiel ◽  
Romina Gheorghe ◽  
Jennifer Eastmond ◽  
Mark A. Miller
Keyword(s):  
Clostridium Difficile ◽  
Fecal Calprotectin ◽  
Toxin Gene ◽  
Pcr Assay ◽  
Content Type ◽  
Nosocomial Diarrhea ◽  
Clostridium Difficile Toxin ◽  
Stool Samples

In 54/64 subjects with nosocomial diarrhea, fecal calprotectin levels correlated with the results of stool samples tested forClostridium difficiletoxin gene by PCR. Fecal calprotectin levels can be used as an adjunctive measure to PCR to support the diagnosis ofC. difficileinfection.

scholarly journals Development and Evaluation of a Molecular Hepatitis A Virus Assay for Serum and Stool Specimens

Viruses ◽  
2022 ◽  
Vol 14 (1) ◽  
pp. 159
Author(s):  
Robert A. Kozak ◽  
Candace Rutherford ◽  
Melissa Richard-Greenblatt ◽  
N. Y. Elizabeth Chau ◽  
Ana Cabrera ◽  
...  
Keyword(s):  
Clinical Utility ◽  
Hepatitis A ◽  
Hepatitis A Virus ◽  
Health Concern ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Treatment And Prevention ◽  
Virus Assay ◽  
Stool Samples ◽  
Stool Specimens

Hepatitis A virus (HAV) is an emerging public health concern and there is an urgent need for ways to rapidly identify cases so that outbreaks can be managed effectively. Conventional testing for HAV relies on anti-HAV IgM seropositivity. However, studies estimate that 10–30% of patients may not be diagnosed by serology. Molecular assays that can directly detect viral nucleic acids have the potential to improve diagnosis, which is key to prevent the spread of infections. In this study, we developed a real-time PCR (RT-PCR) assay to detect HAV RNA for the identification of acute HAV infection. Primers were designed to target the conserved 5′-untranslated region (5′-UTR) of HAV, and the assay was optimized on both the Qiagen Rotor-Gene and the BD MAX. We successfully detected HAV from patient serum and stool samples with moderate differences in sensitivity and specificity depending on the platform used. Our results highlight the clinical utility of using a molecular assay to detect HAV from various specimen types that can be implemented in hospitals to assist with diagnostics, treatment and prevention.

scholarly journals Pyrazinamide Susceptibility Testing in Mycobacterium tuberculosis: a Systematic Review with Meta-Analyses

2011 ◽  
Vol 55 (10) ◽  
pp. 4499-4505 ◽  
Author(s):  
Kwok Chiu Chang ◽  
Wing Wai Yew ◽  
Ying Zhang
Keyword(s):  
Systematic Review ◽  
Mycobacterium Tuberculosis ◽  
Dna Sequencing ◽  
Sensitivity And Specificity ◽  
Test Performance ◽  
Multidrug Resistant ◽  
Predictive Values ◽  
Content Type ◽  
Molecular Assays ◽  
Meta Analyses

ABSTRACTStandard culture-based testing of the susceptibility ofMycobacterium tuberculosisto pyrazinamide is difficult to perform. This systematic review with meta-analyses evaluated the roles of molecular assays targetingpncAand of pyrazinamidase assays. PubMed and Embase were searched for relevant publications in English. Sensitivity and specificity were estimated in bivariate random-effects models. Of 128 articles identified, 73 sets of data involving culture isolates were initially included in meta-analyses. Summary estimates of sensitivity and specificity, respectively, were 87% and 93% for PCR-DNA sequencing (n= 29), 75% and 95% for PCR-single-stranded conformation polymorphism (SSCP) (n= 5), 96% and 97% for a mixture of other molecular assays (n= 6), and 89% and 97% for pyrazinamidase assays using the Wayne method (n= 33). The median prevalence (range) of pyrazinamide resistance was 51% (31% to 89%) in multidrug-resistantM. tuberculosisisolates and 5% (0% to 9%) in non-multidrug-resistant isolates. Excluding studies with possibly considerable false resistance in the reference assay gave the following estimates of sensitivity and specificity, respectively: 92% and 93% for PCR-DNA sequencing (n= 20), 98% and 96% for other molecular assays (n= 5), and 91% and 97% for the Wayne assay (n= 27). The Wayne assay had significant funnel plot asymmetry, so the test performance might have been overestimated. Considering the prevalence of pyrazinamide resistance in different clinical settings, PCR-DNA sequencing, and possibly other molecular assays targetingpncA, can detect pyrazinamide resistance in multidrug-resistantM. tuberculosisisolates, with predictive values largely exceeding 90%, and rule out pyrazinamide resistance in non-multidrug-resistant isolates, with predictive values exceeding 99%. Molecular assays are probably the way forward for detecting pyrazinamide resistance.

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