Development and Evaluation of a Novel Fast Broad-Range ITS/LSU DNA PCR and Sequencing Assay (FBR-PCR/S) for Rapid Diagnosis of Invasive Fungal Diseases: Multi-Year Experience in a Large Canadian Healthcare Zone and a Literature Review

Abstract BackgroundThis study evaluated the performance of a novel fast broad range PCR and sequencing (FBR-PCR/S) assay for the improved diagnosis of invasive fungal disease (IFD) in high-risk patients in a large Canadian healthcare region.MethodsA total of 114 clinical specimens (CS) including bronchoalveolar lavages (BALs) were prospectively tested from 107 patients over a 2-year period. Contrived BALs (n=33) inoculated with known fungi pathogens were also tested to increase diversity. Patient characteristics, fungal stain and culture results were collected from the laboratory information system. Dual-priming oligonucleotide (DPO) primers targeted to the ITS (~350 bp) and LSU (~550 bp) gene regions were used to perform FBR-PCR/S assays on extracted BALs/CS. The performance of the molecular test was evaluated against results of fungal stains and culture, and where available, histopathology, and clinical review for the presence of IFD.ResultsThe 107 patients were predominantly male (67, 62.6%%) with a mean age of 59 yrs. (range = 0 to 85 yrs.): 74 (69.2%) patients had at least one underlying comorbidity: 19 (34.5%) had confirmed and 12 (21.8%) had probable IFD. Culture recovered 66 fungal isolates from 55 BALs/CS with Candida spp. and Aspergillus spp. being most common. For BALs, the molecular assay vs. fungal culture had sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV), and efficiency of 88.5% vs.100%, 100% vs. 61.1%, 100% vs. 88.5%, 61.1% vs. 100%, and 90.2% for both. For other CS, the molecular assay had similar performance to fungal culture with sensitivity, specificity, PPV, NPV and efficiency of 66.7%, 87.0%, 66.7%, 87.0% and 81.3% for both methods. Both methods also performed similarly, regardless of whether CS stain/microscopy showed yeast/fungal elements. FBR-PCR/S assays results were reported in ~8h compared to fungal cultures that took between 4 to 6 weeks.ConclusionsRapid molecular testing compared to culture has equivalent diagnostic efficiency but improves clinical utility by reporting a rapid species-level identification the same dayshift (~8h).

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2175. Rapid Detection of Carbapenemase Producing Organisms Directly from Blood Cultures Positive for Gram-Negative Bacilli

Open Forum Infectious Diseases ◽

10.1093/ofid/ofz360.1855 ◽

2019 ◽

Vol 6 (Supplement_2) ◽

pp. S738-S738

Author(s):

William Stokes ◽

Johann Pitout ◽

Lorraine Campbell ◽

Deirdre Church ◽

Dan Gregson

Keyword(s):

Predictive Value ◽

Rapid Detection ◽

Blood Cultures ◽

Gram Negative ◽

Carbapenem Resistant ◽

Direct Testing ◽

Appropriate Treatment ◽

Risk Patients ◽

Health Zone ◽

Sensitivity Specificity

Abstract Background The rapid detection of carbapenemase-producing organisms (CPOs) directly from blood cultures (BC) positive for Gram-negative bacilli (GNB) may accelerate the appropriate treatment of at-risk patients. Our objective was to evaluate the performance of two commercial assays in the rapid detection of CPOs directly from BC positive for GNB. Methods BC positive for GNB, taken from patients within the Calgary Health Zone over a 3 month period, were tested for the presence of CPOs with βCARBA® and NG-Test® CARBA 5. A subset of sterile BC samples was seeded with multi-drug-resistant (MDR) GNB. BC were incubated using the Bact-Alert™ system. Positive BC from clinical and seeded samples was tested directly with βCARBA and CARBA 5 from BC pellets processed for direct testing using an ammonium chloride lysis and wash method. Sensitivity, specificity, negative predictive value (NPV) and positive predictive value (PPV) were calculated with 95% confidence intervals for binomial proportions. Results 65 samples were tested (30 clinical, 35 seeded). Seeded samples included 1 GES, 4 IMP, 6 KPC, 1 co-producing KPC and NDM, 9 OXA, 4 VIM, 5 NDM, and 5 non-CPO carbapenem-resistant organisms. βCARBA had a sensitivity, specificity, NPV and PPV of 100% (88.4% - 100%), 65.7% (47.8–80.9%), 100%, and 71.4% (61.3%–79.8%), respectively. CARBA 5 had a sensitivity, specificity, NPV and PPV of 90.0% (73.5%–97.9%), 100% (90.0%–100%), 92.1% (80.0%–97.2%), and 100%. When excluding GES, which is known not to be detected by CARBA 5, sensitivity and NPV increased to 93.1% (77.2%–99.2%) and 93.1% (78.0%–98.1%), respectively. False negatives for βCARBA occurred with 1 VIM-1 and IMP-14. Conclusion This study demonstrates that the detection of CPOs directly from positive BC can be accurately achieved. βCARBA had excellent sensitivity but suffered from poor specificity. CARBA 5 had good sensitivity and specificity but is unable to detect certain CPOs. Testing positive BC directly using βCARBA and/or CARBA 5 may be useful in rapidly detecting CPOs. Results of direct testing from the CARBA5 assay would quickly identify patients amenable to treatment with avibactam combination compounds. Disclosures All authors: No reported disclosures.

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Molecular testing (strand displacement assay) for identification of urethral gonorrhoea in men: can it replace culture as the gold standard?

International Journal of STD & AIDS ◽

10.1258/0956462054094079 ◽

2005 ◽

Vol 16 (6) ◽

pp. 430-432 ◽

Cited By ~ 2

Author(s):

H L Wheeler ◽

C J Skinner ◽

A Khunda ◽

C Aitken ◽

D Perpanthan ◽

...

Keyword(s):

Predictive Value ◽

Diagnostic Yield ◽

Molecular Testing ◽

Strand Displacement ◽

Specific Test ◽

Strand Displacement Amplification ◽

Conventional Culture ◽

Study Population ◽

Displacement Assay ◽

Sensitivity Specificity

The objective was to evaluate the performance of Becton Dickinson's BD Probe TecTM (BDPT) strand displacement amplification (SDA) test for the detection of Neisseria gonorrhoeae on urethral specimens from men with urethritis compared with conventional culture and to show that SDA improves the diagnostic yield of gonorrhoea infections (GC). Anonymized retrospective testing of stored urethral swab samples from men attending genitourinary services in East London was performed using SDA. The prevalence of GC culture positive infections in this sample was 20/152 (13%). The sensitivity, specificity, positive predictive value and negative predictive value for the BDPT-SDA system compared with culture were 100%, 95%, 77% and 100%, respectively. In this study population, the BDPT-SDA assay was a highly sensitive and specific test for the diagnosis of N. gonorrhoeae from urethral swabs in men. Therefore, SDA can be used to complement culture in the diagnosis of N. gonorrhoeae infection. No ethics committee approval was obtained as all samples were anonymized.

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Validation of rapid antibody (IgG-IgM) test kit for SARS COV-2 infection in Qatar

Journal of Public Health Research ◽

10.4081/jphr.2021.2421 ◽

2021 ◽

Author(s):

Jesha Mundodan ◽

Samina Hasnain ◽

Hayat Khogali ◽

Soha Shawqi Al Bayat ◽

Dina Ali ◽

...

Keyword(s):

Predictive Value ◽

Local Population ◽

Rapid Test ◽

Antibody Test ◽

Molecular Testing ◽

Rt Pcr ◽

Test Kit ◽

Asymptomatic Individuals ◽

Sensitivity Specificity ◽

Rapid Antibody

Background: In response to the growing coronavirus disease 2019 (COVID-19) pandemic and the shortage of laboratory based molecular testing capacity and reagents, multiple diagnostic test manufacturers have developed rapid and easy to use devices to facilitate testing outside laboratory settings. These kits are either based on detection of proteins from SARS-CoV-2 virus or detection of antigen or human antibodies generated in response to the infection. However, it is important to understand their performance characteristics and they must be validated in the local population setting.Design and Methods: The objective is to assess the validity of the rapid test for IgG and IgM immunoglobulins compared to the current gold standard reverse transcription polymerase chain reaction (RT-PCR) test. A total of 16951 asymptomatic individuals were tested by the Ministry of Public Health track-and-trace team using both rapid immunodiagnostic test and RT-PCR as part of screening across various random settings with potential risk of community interaction prior to gradual lifting of restrictions in Qatar. Rapid test was considered to be posiive if both IgG and IgM are positive, while only IgG/IgM positive was considered as rapid test negative. Sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) were calculated.Results: The sensitivity of rapid test kit was found to be 0.9%, whereas the specificity was found to be 97.8%. the PPV was found to be 0.3% whereas the NPV was found to be 99.4%.Conclusion: Based on the outcome and results of the study, it appears that the sensitivity and PPV of the rapid antibody test are low. As such, this test is not recommended for use to assist in taking clinic-based decisions or decisions related to quarantine/isolation.

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Elastography for the Diagnosis of High-Suspicion Thyroid Nodules Based on the 2015 American Thyroid Association Guidelines: A Multicenter Study

10.21203/rs.2.17002/v5 ◽

2020 ◽

Author(s):

Hairu Li ◽

Yulan Peng ◽

Yan Wang ◽

Hong Ai ◽

Xiaodong Zhou ◽

...

Keyword(s):

Logistic Regression ◽

Regression Analysis ◽

Logistic Regression Analysis ◽

Predictive Value ◽

Thyroid Nodules ◽

Reference Method ◽

Final Analysis ◽

American Thyroid Association ◽

Diagnostic Efficiency ◽

Sensitivity Specificity

Abstract Background: An accurate diagnosis for high-suspicion nodules based on the 2015 American Thyroid Association (ATA) guidelines would reduce unnecessary invasive examinations. Elastography is a useful tool for discriminating benign and malignant thyroid nodules. The aim of this study is to investigate the diagnostic efficiency of elastography for high-suspicion thyroid nodules based on the 2015 ATA guidelines in the Chinese population.Methods: Thyroid nodules with high-suspicion characteristics based on the 2015 ATA guidelines were subjected to conventional ultrasound (US) and ultrasound strain elastography (USE) examinations at 12 hospitals from 4 geographic regions across China. Cytology/histology of thyroid nodules was used as a reference method. Receiver operating characteristic (ROC) curves were plotted to evaluate the diagnostic performance of the elasticity score (ES) and strain ratio (SR). Logistic regression analysis was used to determine the predictors of malignancy.Results: Overall, a total of 1445 thyroid nodules (834 malignant, 611 benign) from 12 centers were included in the final analysis. The areas under the curve of the ES and SR were 0.828 and 0.732, respectively. The sensitivity, specificity, accuracy, positive predictive value (PPV) and negative predictive value (NPV) of the ES were 92.4%, 60.7%, 79.0%, 76.3% and 85.5%, respectively, and those of the SR were 81.1%, 50.1%, 68.9%, 65.9% and 67.9%, respectively. The combination of the Thyroid Imaging Reporting and Data System (TI-RADS) and ES led to a significant increase in the sensitivity and NPV (97.1% and 91.9%, respectively) compared with the TI-RADS alone. Logistic regression analysis showed that microcalcifications (OR=5.290), taller than wide (OR=12.710), irregular margins (OR=10.117), extrathyroidal extension (ETE; OR=6.412), the ES (OR=3.741) and the SR (OR=1.083) were independent predictors of malignant thyroid nodules. The sensitivity, specificity, accuracy, PPV and NPV of the ES were all superior in nodules ≥1 cm than in those <1 cm (95.0% vs 90.4%, 68.8% vs 56.8%, 85.9% vs 74.4%, 85.2% vs 69.9%, and 87.8% vs 84.2%, respectively).Conclusions: Elastography combined with the ES is a valuable tool for the assessment of high-suspicion thyroid nodules based on the 2015 ATA guidelines, especially in nodules ≥1 cm.

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Elastography for the Diagnosis of High-Suspicion Thyroid Nodules Based on the 2015 American Thyroid Association Guidelines: A Multicenter Study

10.21203/rs.2.17002/v2 ◽

2020 ◽

Author(s):

Hairu Li ◽

Yulan Peng ◽

Yan Wang ◽

Hong Ai ◽

Xiaodong Zhou ◽

...

Keyword(s):

Logistic Regression ◽

Regression Analysis ◽

Logistic Regression Analysis ◽

Predictive Value ◽

Thyroid Nodules ◽

Reference Method ◽

Final Analysis ◽

American Thyroid Association ◽

Diagnostic Efficiency ◽

Sensitivity Specificity

Abstract Background: An accurate diagnosis for high-suspicion nodules based on the 2015 American Thyroid Association (ATA) guidelines would reduce unnecessary invasive examinations. Elastography is a useful tool for discriminating benign and malignant thyroid nodules.Aims: To investigate the diagnostic efficiency of elastography for high-suspicion thyroid nodules based on the 2015 ATA guidelines in the Chinese population.Materials and Methods: Thyroid nodules with high-suspicion characteristics based on the 2015 ATA guidelines were subjected to conventional ultrasound (US) and ultrasound strain elastography (USE) examinations at 12 hospitals from 4 geographic regions across China. Cytology/histology of thyroid nodules was used as a reference method. Receiver operating characteristic (ROC) curves were plotted to evaluate the diagnostic performance of the elasticity score (ES) and strain ratio (SR). Logistic regression analysis was used to determine the predictors of malignancy.Results: Overall, a total of 1445 thyroid nodules (834 malignant, 611 benign) from 12 centers were included in the final analysis. The areas under the curve of the ES and SR were 0.828 and 0.732, respectively. The sensitivity, specificity, accuracy, positive predictive value (PPV) and negative predictive value (NPV) of the ES were 92.4%, 60.7%, 79.0%, 76.3% and 85.5%, respectively, and those of the SR were 81.1%, 50.1%, 68.9%, 65.9% and 67.9%, respectively. The combination of the Thyroid Imaging Reporting and Data System (TI-RADS) and ES led to a significant increase in the sensitivity and NPV (97.1% and 91.9%, respectively) compared with the TI-RADS alone. Logistic regression analysis showed that microcalcifications (OR=5.290), taller than wide (OR=12.710), irregular margins (OR=10.117), extrathyroidal extension (ETE; OR=6.412), the ES (OR=3.741) and the SR (OR=1.083) were independent predictors of malignant thyroid nodules. The sensitivity, specificity, accuracy, PPV and NPV of the ES were all superior in nodules ≥1 cm than in those <1 cm (95.0% vs 90.4%, 68.8% vs 56.8%, 85.9% vs 74.4%, 85.2% vs 69.9%, and 87.8% vs 84.2%, respectively).Conclusions: Elastography combined with the ES is a valuable tool for the assessment of high-suspicion thyroid nodules based on the 2015 ATA guidelines, especially in nodules ≥1 cm.

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Could Negative Tc-99m-Methoxyisobutylisonitrile (MIBI) Scintigraphy Obviate the Need for Surgery for Bethesda III and IV Thyroid Nodules?

Surgeries ◽

10.3390/surgeries2030026 ◽

2021 ◽

Vol 2 (3) ◽

pp. 260-267

Author(s):

Stella Armefti ◽

Jasmin Mettler ◽

Matthias Schmidt ◽

Michael Faust ◽

Marianne Engels ◽

...

Keyword(s):

Negative Predictive Value ◽

Predictive Value ◽

Thyroid Nodules ◽

Needle Aspiration ◽

University Hospital ◽

Molecular Testing ◽

High Negative Predictive Value ◽

Indeterminate Cytology ◽

Sensitivity Specificity ◽

Mibi Scintigraphy

In about 20% of all cases, the fine needle aspiration cytology (FNAC) results are equivocal, delivering the two common categories of indeterminate cytology, Bethesda III and IV. The observed rates of malignancy vary widely among institutions, with the urgent need for a more precise risk stratification. 99mcTc methoxyisobutylisonitrile scintigraphy (MIBI) is less expensive than molecular testing and has been shown to have a high negative predictive value. For this reason, the results of MIBI scintigraphy in adult patients with indeterminate FNAC were collected, and correlated with the final pathology reports of surgical specimens. Patients receiving FNAC, MIBI scintigraphy and surgery for sonographic suspicious hypofunctional thyroid nodules between 2015 and 2019 at the University Hospital of Cologne, Germany were identified. Sensitivity, specificity, positive predictive and negative predictive value of MIBI scintigraphy were calculated. Seventy-eight patients with sonographic suspicious hypofunctional thyroid nodules underwent surgery after interdisciplinary case discussion of both FNAC and MIBI results. In 49 (62.5%) cases, FNAC consisted of Bethesda III and IV results. In 39 (79.6%) of these cases, MIBI scintigraphy resulted in mismatch and intermediary results, but in only 4 (10.2%) of these cases was a carcinoma diagnosed. The negative predictive value of MIBI scintigraphy was 90–100%, respectively. Relying on the negative predictive value of MIBI match results might have obviated the need for surgery in 20.4% cases; one papillary microcarcinoma, however, would have been missed. MIBI scintigraphy has an underused potential for improving the diagnostic precision of hypofunctional thyroid nodules.

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Comparative efficacy of admission cardiotocography in high risk and low risk pregnancies in predicting neonatal outcome

International Journal of Reproduction Contraception Obstetrics and Gynecology ◽

10.18203/2320-1770.ijrcog20213844 ◽

2021 ◽

Vol 10 (10) ◽

pp. 3823

Author(s):

Gurpreet Kaur Nandmer ◽

Shivangi Jaiswal ◽

Pooja Namdeo

Keyword(s):

High Risk ◽

Predictive Value ◽

Neonatal Outcome ◽

Low Risk ◽

Comparative Efficacy ◽

Risk Pregnancy ◽

Risk Patients ◽

Nicu Admission ◽

Fetal Wellbeing ◽

Sensitivity Specificity

Background: Admission cardiotocography (CTG) is a test of fetal wellbeing performed during labor. A normal CTG is for 20-30 minutes and ranges from 110-160 bpm with beat to beat variability, two accelerations and no decelerations with two contractions (as per NICE 2018 guidelines). To study comparative efficacy of admission CTG in predicting neonatal out in high risk, low risk and universally in all pregnancy.Methods: All high risk as well as low risk patients coming to labor room in labor were included in the study. CTG print was taken, and neonatal outcome as NICU admission were noted after taking written consent.Results: 189 cases were taken.138 were high risk cases, CTG was taken: 91were reassuring, 47were abnormal (non-reassuring +abnormal). In terms of NICU admission, 21 and 26 neonates were admitted. Out of 51 low risk cases, 33 had reassuring CTG, and18 had abnormal; 7and 6 was the number of NICU admission, respectively. When compared, highest sensitivity, specificity and positive predictive value of 55.31%, 77% and 55.3% was seen in high risk pregnancy, whereas negative predictive value (78.8%) was slightly higher in low risk cases.Conclusions: Admission CTG is a good predictor of neonatal outcome. Its predictive efficacy is more in high risk cases. It’s practicality in revealing poor neonatal outcome is more.

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The “Pink Pattern” Visualized in Magnifying Endoscopy with Narrow-Band Imaging is a New Feature of Early Gastric Differentiated Cancer——A Bridge Between Endoscopic Image and Histopathological Change

10.21203/rs.3.rs-596301/v1 ◽

2021 ◽

Author(s):

Shengsen Chen ◽

Jiangping Yu ◽

Rongwei Ruan ◽

Yali Tao ◽

Zhao Cui ◽

...

Keyword(s):

Gastric Cancer ◽

Epithelial Cells ◽

Predictive Value ◽

Color Change ◽

Narrow Band ◽

Narrow Band Imaging ◽

Magnifying Endoscopy ◽

Cosine Similarity ◽

Diagnostic Efficiency ◽

Sensitivity Specificity

Abstract Background A pink color change found occasionally by us under the magnifying endoscopy with narrow-band imaging (ME-NBI) may be a special feature of early gastric cancer (EGC), and it was named as “pink pattern”. The purposes of this study were to reveal the relationship between the “pink pattern” and the cytopathological changes of gastric cancer cells, and explore whether the pink pattern was useful for the diagnosis of EGC. Methods The color features of ME-NBI images and pathological images on gastric cancerous mucosal surface were extracted and quantized, and then the cosine similarity was calculated to evaluate the correlation between the pink pattern and the nucleus-to-plasm ratio of cancerous epithelial cells. Two diagnostic tests were performed by 12 endoscopists using stored ME-NBI images of 185 gastric lesions to investigate the diagnostic efficiency of “pink pattern” for EGC. The diagnostic values such as area under curve (AUC), accuracy, sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) between test 1 and test 2 were compared. Results The cosine similarity in 20 lesions between the color values of ME-NBI images and pathological images was at least 0.744. The median AUC, accuracy, sensitivity, specificity, PPV and NPV of test 2 were significantly improved compared with that of test 1 in all endoscopists, junior and experienced groups. Conclusions The “pink pattern” visualized in ME-NBI images is highly correlated with the nucleus-to-plasma ratio change of gastric epithelial cells, and it can be considered as a useful marker for the diagnosis of the differentiated EGC.

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Elastography for the Diagnosis of High-Suspicion Thyroid Nodules Based on the 2015 American Thyroid Association Guidelines: A Multicenter Study

10.21203/rs.2.17002/v4 ◽

2020 ◽

Author(s):

Hairu Li ◽

Yulan Peng ◽

Yan Wang ◽

Hong Ai ◽

Xiaodong Zhou ◽

...

Keyword(s):

Logistic Regression ◽

Regression Analysis ◽

Logistic Regression Analysis ◽

Predictive Value ◽

Thyroid Nodules ◽

Reference Method ◽

Final Analysis ◽

American Thyroid Association ◽

Diagnostic Efficiency ◽

Sensitivity Specificity

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Elastography for the Diagnosis of High-Suspicion Thyroid Nodules Based on the 2015 American Thyroid Association Guidelines: A Multicenter Study

10.21203/rs.2.17002/v3 ◽

2020 ◽

Author(s):

Hairu Li ◽

Yulan Peng ◽

Yan Wang ◽

Hong Ai ◽

Xiaodong Zhou ◽

...

Keyword(s):

Logistic Regression ◽

Regression Analysis ◽

Logistic Regression Analysis ◽

Predictive Value ◽

Thyroid Nodules ◽

Reference Method ◽

Final Analysis ◽

American Thyroid Association ◽

Diagnostic Efficiency ◽

Sensitivity Specificity

Abstract Background: An accurate diagnosis for high-suspicion nodules based on the 2015 American Thyroid Association (ATA) guidelines would reduce unnecessary invasive examinations. Elastography is a useful tool for discriminating benign and malignant thyroid nodules. Aims: To investigate the diagnostic efficiency of elastography for high-suspicion thyroid nodules based on the 2015 ATA guidelines in the Chinese population. Materials and Methods: Thyroid nodules with high-suspicion characteristics based on the 2015 ATA guidelines were subjected to conventional ultrasound (US) and ultrasound strain elastography (USE) examinations at 12 hospitals from 4 geographic regions across China. Cytology/histology of thyroid nodules was used as a reference method. Receiver operating characteristic (ROC) curves were plotted to evaluate the diagnostic performance of the elasticity score (ES) and strain ratio (SR). Logistic regression analysis was used to determine the predictors of malignancy. Results: Overall, a total of 1445 thyroid nodules (834 malignant, 611 benign) from 12 centers were included in the final analysis. The areas under the curve of the ES and SR were 0.828 and 0.732, respectively. The sensitivity, specificity, accuracy, positive predictive value (PPV) and negative predictive value (NPV) of the ES were 92.4%, 60.7%, 79.0%, 76.3% and 85.5% , respectively, and those of the SR were 81.1%, 50.1%, 68.9%, 65.9% and 67.9%, respectively. The combination of the Thyroid Imaging Reporting and Data System (TI-RADS) and ES led to a significant increase in the sensitivity and NPV (97.1% and 91.9%, respectively) compared with the TI-RADS alone. Logistic regression analysis showed that microcalcifications (OR=5.290), taller than wide (OR=12.710), irregular margins (OR=10.117), extrathyroidal extension (ETE; OR=6.412), the ES (OR=3.741) and the SR (OR=1.083) were independent predictors of malignant thyroid nodules. The sensitivity, specificity, accuracy, PPV and NPV of the ES were all superior in nodules ≥1 cm than in those <1 cm (95.0% vs 90.4%, 68.8% vs 56.8%, 85.9% vs 74.4%, 85.2% vs 69.9%, and 87.8% vs 84.2%, respectively). Conclusions: Elastography combined with the ES is a valuable tool for the assessment of high-suspicion thyroid nodules based on the 2015 ATA guidelines, especially in nodules ≥1 cm.

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