scholarly journals Prediction of Clostridium difficile infection in patients with polymerase chain reaction using a classification and regression tree

2020 ◽  
Author(s):  
Diana Martínez-Ruíz ◽  
Luis Gabriel Parra-Lara ◽  
Fernando Rosso
Keyword(s):  
Polymerase Chain Reaction ◽  
Clostridium Difficile ◽  
Negative Predictive Value ◽  
Predictive Value ◽  
Regression Tree ◽  
Antifungal Drugs ◽  
Classification And Regression Tree ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Classification And Regression

Abstract BackgroundClostridium difficile infection (CDI) is commonly diagnosed with the polymerase chain reaction (PCR), but this test finds a high percentage of false positives, so their use and interpretation in CDI is a challenge in the clinical practice. That is why it is necessary to define an algorithm to optimize the use of PCR that considers clinical characteristics to classify patients with diarrhea as CDI or without CDI. ObjectiveTo identify a predictive algorithm with the clinical features that best classify patients with CDI vs. without CDI, to help physicians in making decisions to request PCR. Materials and methodsA case-control study was conducted at Fundación Valle del Lili. The population was inpatients between 2012 and 2016, with 18 or more years, and diarrhea, abdominal pain, or other nonspecific gastrointestinal symptoms who underwent PCR. Cases were defined as patients with positive PCR for C. difficile and as controls patients with negative PCR for C. difficile. Predictive algorithms to classify patients was constructed using a classification tree, classification and regression tree (CART). ResultsA total of 149 patients were included (48 cases with positive PCR and 99 controls with negative PCR). The CART has a high capacity to classify patients with a negative PCR correctly. It includes variables about the history of antibiotics use, the use of proton-pump inhibitor, the use of ranitidine, and the use of antifungal drugs. The CART showed sensitivity 64.6%, specificity 85.8%, positive predictive value 68.8%, negative predictive value 83.3%. and AUC 79.7%.DiscussionCART had good specificity and a high negative predictive value; it could be considered as an algorithm to identify conditions that indicate when it is not necessary to perform a PCR test in a patient symptom of CDI.

scholarly journals Evaluation of Nested Polymerase Chain Reaction targeting hsp65 of Mycobacterium tuberculosis for the Detection of Organism in the Sputum Samples

2016 ◽  
Vol 20 (1) ◽  
pp. 28-33
Author(s):  
Yogaraje GC Varadaiah ◽  
Raghu K Chinnappa ◽  
Rakshitha M Nagaraj ◽  
Thejashwini NA ◽  
Robinson K Samuel ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Mycobacterium Tuberculosis ◽  
Negative Predictive Value ◽  
Nested Pcr ◽  
Predictive Value ◽  
Healthy Controls ◽  
Chain Reaction ◽  
Nested Polymerase Chain Reaction ◽  
Gene Target ◽  
Polymerase Chain

ABSTRACT Introduction The poor sensitivity of conventional smear microscopy and the delay in obtaining Mycobacterium culture results prevent the early diagnosis of Myobacterium tuberculosis (MTB). By using nucleic acid amplification techniques like polymerase chain reaction (PCR), one may be able to diagnose the disease on the day of arrival of specimen in the laboratory. The present study aimed to evaluate the applicability of the nested-PCR (nPCR) technique as a rapid and direct molecular method for the diagnosis of M. tuberculosis in sputum specimens of patients whose sputum smear was acid-fast bacilli (AFB) negative using heat shock protein (hsp65) as the gene target. Materials and methods Early morning sputum samples were collected in sterile containers respectively from about 40 suspected patients of pulmonary tuberculosis, attending the outpatient units of JSS Medical College and PKTB Hospital, Mysore and from 20 age and sex-matched healthy controls. Sputum samples were decontaminated by modified Petroff's method and DNA was isolated using QIAGEN DNA extraction kit. The nPCR was carried out for the detection of MTB using the target gene hsp65. Results Nested-PCR showed specific amplification (165bp) of M. tuberculosis in 18 out of 20 sputum AFB positive samples and 9 out of 20 AFB negative samples. None of the healthy controls showed any amplification with nPCR. The nPCR when compared to that of Ziehl-Neelsen staining had a sensitivity of 90%, specificity of 77.5%, positive predictive value (PPV) of 66.6%, and negative predictive value (NPV) of 93.9%. The percentage of false positive was 33.3% and percentage of false negative was 6.1%. Conclusion The detection of M. tuberculosis with nPCR in smear negative patients provides the bacteriological data 4 to 8 weeks earlier. A molecular approach, based on the amplification of hsp65 gene by nPCR, showed that there is high probability of the disease being absent when the test is negative because of the high negative predictive value (NPV). How to cite this article Varadaiah YGC, Prashant A, Chinnappa RK, Nagaraj RM, Thejashwini, Samuel RK, Devegowda D, Vishwanath P. Evaluation of Nested Polymerase Chain Reaction targeting hsp65 of Mycobacterium tuberculosis for the Detection of Organism in the Sputum Samples. Indian J Med Biochem 2016;1(1):28-33.

scholarly journals A Comparison of Ligase Chain Reaction to Polymerase Chain Reaction in the Detection ofChlamydia trachomatisEndocervical Infections

1998 ◽  
Vol 6 (2) ◽  
pp. 57-60 ◽  
Author(s):  
J. D. Davis ◽  
P. K. Riley ◽  
C. W. Peters ◽  
K. H. Rand
Keyword(s):  
Polymerase Chain Reaction ◽  
Positive Predictive Value ◽  
Negative Predictive Value ◽  
Predictive Value ◽  
Gold Standard ◽  
Chain Reaction ◽  
True Negative ◽  
Predictive Values ◽  
Ligase Chain Reaction ◽  
Polymerase Chain

Objective:To compare the reliability of ligase chain reaction (LCR) to polymerase chain reaction (PCR) in detectingChlamydia trachomatisendocervical infections.Methods:We conducted a prospective study of 486 patients at risk for chlamydial infection of the endocervix. We obtained two endocervical specimens from each patient and used LCR and PCR to detectC. trachomatis. Discrepant results between the two techniques were resolved by repeat testing and by testing for the major outer membrane protein (MOMP) gene, if necessary. We determined the sensitivity, specificity, positive predictive value, and negative predictive value for each test, using concordant results or MOMP gene results as the “gold standard”.Results:Of the 486 patients, 42 (8.6%) had evidence ofC. trachomatisinfection after resolution of discrepant results. Of the 42 true positive specimens, 41 were positive by initial LCR and 38 were positive by initial PCR. Of the 444 true negative specimens, none had a positive initial LCR result, while 2 had a positive initial PCR test. Therefore, compared to the gold standard, LCR had a sensitivity of 97.6% and specificity of 100%, while PCR had a sensitivity of 90% and a specificity of 99.5%. The positive and negative predictive values of LCR were 100% and 99.8%, respectively. PCR had a positive predictive value of 95% and a negative predictive value of 99.1%. The difference in sensitivity of LCR versus PCR was not statistically significant (P= .125).Conclusion:LCR and PCR perform equally well in detectingC. trachomatisendocervical infections.

scholarly journals A meta-analysis of accuracy and sensitivity of chest CT and RT-PCR in COVID-19 diagnosis

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Fatemeh Khatami ◽  
Mohammad Saatchi ◽  
Seyed Saeed Tamehri Zadeh ◽  
Zahra Sadat Aghamir ◽  
Alireza Namazi Shabestari ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Reverse Transcriptase ◽  
Ct Scan ◽  
Predictive Value ◽  
Meta Analysis ◽  
Chest Ct ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Chest Ct Scan

AbstractNowadays there is an ongoing acute respiratory outbreak caused by the novel highly contagious coronavirus (COVID-19). The diagnostic protocol is based on quantitative reverse-transcription polymerase chain reaction (RT-PCR) and chests CT scan, with uncertain accuracy. This meta-analysis study determines the diagnostic value of an initial chest CT scan in patients with COVID-19 infection in comparison with RT-PCR. Three main databases; PubMed (MEDLINE), Scopus, and EMBASE were systematically searched for all published literature from January 1st, 2019, to the 21st May 2020 with the keywords "COVID19 virus", "2019 novel coronavirus", "Wuhan coronavirus", "2019-nCoV", "X-Ray Computed Tomography", "Polymerase Chain Reaction", "Reverse Transcriptase PCR", and "PCR Reverse Transcriptase". All relevant case-series, cross-sectional, and cohort studies were selected. Data extraction and analysis were performed using STATA v.14.0SE (College Station, TX, USA) and RevMan 5. Among 1022 articles, 60 studies were eligible for totalizing 5744 patients. The overall sensitivity, specificity, positive predictive value, and negative predictive value of chest CT scan compared to RT-PCR were 87% (95% CI 85–90%), 46% (95% CI 29–63%), 69% (95% CI 56–72%), and 89% (95% CI 82–96%), respectively. It is important to rely on the repeated RT-PCR three times to give 99% accuracy, especially in negative samples. Regarding the overall diagnostic sensitivity of 87% for chest CT, the RT-PCR testing is essential and should be repeated to escape misdiagnosis.

scholarly journals EXPRESS: Clinical performance of the Elecsys® Anti-SARS-CoV-2 combined in an algorithm with two specific anti-IgG immunoassays for the evaluation of the serological response of patients with COVID-19 in a population with a high prevalence of infection

2021 ◽  
pp. 000456322110380
Author(s):  
Xavier Gabaldó-Barrios ◽  
Simona Iftimie ◽  
Anna Hernández-Aguilera ◽  
Isabel Pujol ◽  
Frederic Ballester ◽  
...  
Keyword(s):  
Immune Response ◽  
Polymerase Chain Reaction ◽  
Predictive Value ◽  
Clinical Performance ◽  
Polymerase Chain Reaction Test ◽  
Serological Response ◽  
Chain Reaction ◽  
Automated Assay ◽  
High Prevalence ◽  
Polymerase Chain

Background: Anti-SARS-CoV-2 antibodies have been used in the study of the immune response in infected patients. However, differences in sensitivity and specificity have been reported, depending on the method of analysis. The aim of the present study was to evaluate the diagnostic accuracy of an algorithm in which a high-throughput automated assay for total antibodies was used for screening and two semi-automated IgG-specific methods were used to confirm the results, and also to correlate the analytical results with the clinical data and the time elapsed since infection. Methods: We studied 306 patients, some hospitalized and some outpatients, belonging to a population with a high prevalence of COVID-19. One-hundred and ten patients were classified as SARS-CoV-2 negative and 196 as positive by polymerase chain reaction. Results: The algorithm and automated assay alone had a specificity and a positive predictive value of 100%, although the sensitivity and negative predictive value of the algorithm was higher. Both methods showed a good sensitivity from day 11 of the onset of symptoms in asymptomatic and symptomatic patients. The absorbance of the total antibodies was significantly higher in severely symptomatic than in asymptomatic or mildly symptomatic patients, which suggests the antibody level was higher. We found 15 patients that did not present seroconversion at 12 days from the onset of symptoms or the first polymerase chain reaction test. Conclusion: This study highlights the proper functioning of algorithms in the diagnosis of the immune response to COVID-19, which can help to define testing strategies against this disease.

scholarly journals Peripheral Blood Leukocytes and Serum Nested Polymerase Chain Reaction Are Complementary Methods for Monitoring Active Cytomegalovirus Infection in Transplant Patients

2013 ◽  
Vol 24 (3) ◽  
pp. e69-e74 ◽  
Author(s):  
PD Andrade ◽  
MT Fioravanti ◽  
EBV Anjos ◽  
C De Oliveira ◽  
DM Albuquerque ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Positive Predictive Value ◽  
Predictive Value ◽  
Cytomegalovirus Infection ◽  
Clinical Symptoms ◽  
Peripheral Blood Leukocytes ◽  
Active Infection ◽  
Chain Reaction ◽  
Blood Leukocytes ◽  
Polymerase Chain

BACKGROUND: Human cytomegalovirus is an important cause of morbidity and mortality in immunocompromised patients. Qualitative polymerase chain reaction (PCR) has proven to be a sensitive and effective technique in defining active cytomegalovirus infection, in addition to having low cost and being a useful test for situations in which there is no need for quantification. Real-time PCR has the advantage of quantification; however, the high cost of this methodology makes it impractical for routine use.OBJECTIVE: To apply a nested PCR assay to serum (sPCR) and to evaluate its efficiency to diagnose active cytomegalovirus infection compared with PCR of peripheral blood leukocytes (L-PCR).METHODS: Samples of 37 patients were prospectively evaluated. An internal control was created and applied to sPCR to exclude false-negative results.RESULTS: In total, 21 patients (57%) developed active cytomegalovirus infection. After analyzing the two methods for the diagnosis of active infection, higher sensitivity and negative predictive value of the L-PCR versus sPCR (100% versus 62%), and higher specificity and positive predictive value of sPCR versus L-PCR (81% versus 50% and 72%, respectively) were observed. Discordant results were observed in 11 patients who were L-PCR-positive but sPCR-negative for active cytomegalovirus infection, five of whom developed clinical symptoms of cytomegalovirus. Clinical symptoms were observed in 14 patients, 12 of whom were diagnosed with active infection by nested L-PCR (P=0.007) and seven by nested sPCR (P=0.02). Higher specificity and a positive predictive value for sPCR were observed.CONCLUSION: Nested L-PCR and sPCR were considered to be complementary methods for the diagnosis and management of symptomatic cytomegalovirus infection.

scholarly journals Performance of the Innova SARS-CoV-2 antigen rapid lateral flow test in the Liverpool asymptomatic testing pilot: population based cohort study

BMJ ◽  
2021 ◽  
pp. n1637 ◽  
Author(s):  
Marta García-Fiñana ◽  
David M Hughes ◽  
Christopher P Cheyne ◽  
Girvan Burnside ◽  
Mark Stockbridge ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Viral Load ◽  
Predictive Value ◽  
High Viral Load ◽  
Test Results ◽  
Chain Reaction ◽  
Viral Loads ◽  
Flow Test ◽  
Polymerase Chain ◽  
Lateral Flow Test

Abstract Objective To assess the performance of the SARS-CoV-2 antigen rapid lateral flow test (LFT) versus polymerase chain reaction testing in the asymptomatic general population attending testing centres. Design Observational cohort study. Setting Community LFT pilot at covid-19 testing sites in Liverpool, UK. Participants 5869 asymptomatic adults (≥18 years) voluntarily attending one of 48 testing sites during 6-29 November 2020. Interventions Participants were tested using both an Innova LFT and a quantitative reverse-transcriptase polymerase chain reaction (RT-qPCR) test based on supervised self-administered swabbing at testing sites. Main outcome measures Sensitivity, specificity, and predictive values of LFT compared with RT-qPCR in an epidemic steady state of covid-19 among adults with no classic symptoms of the disease. Results Of 5869 test results, 22 (0.4%) LFT results and 343 (5.8%) RT-qPCR results were void (that is, when the control line fails to appear within 30 minutes). Excluding the void results, the LFT versus RT-qPCR showed a sensitivity of 40.0% (95% confidence interval 28.5% to 52.4%; 28/70), specificity of 99.9% (99.8% to 99.99%; 5431/5434), positive predictive value of 90.3% (74.2% to 98.0%; 28/31), and negative predictive value of 99.2% (99.0% to 99.4%; 5431/5473). When the void samples were assumed to be negative, a sensitivity was observed for LFT of 37.8% (26.8% to 49.9%; 28/74), specificity of 99.6% (99.4% to 99.8%; 5431/5452), positive predictive value of 84.8% (68.1% to 94.9%; 28/33), and negative predictive value of 93.4% (92.7% to 94.0%; 5431/5814). The sensitivity in participants with an RT-qPCR cycle threshold (Ct) of <18.3 (approximate viral loads >10 6 RNA copies/mL) was 90.9% (58.7% to 99.8%; 10/11), a Ct of <24.4 (>10 4 RNA copies/mL) was 69.4% (51.9% to 83.7%; 25/36), and a Ct of >24.4 (<10 4 RNA copies/mL) was 9.7% (1.9% to 23.7%; 3/34). LFT is likely to detect at least three fifths and at most 998 in every 1000 people with a positive RT-qPCR test result with high viral load. Conclusions The Innova LFT can be useful for identifying infections among adults who report no symptoms of covid-19, particularly those with high viral load who are more likely to infect others. The number of asymptomatic adults with lower Ct (indicating higher viral load) missed by LFT, although small, should be considered when using single LFT in high consequence settings. Clear and accurate communication with the public about how to interpret test results is important, given the chance of missing some cases, even at high viral loads. Further research is needed to understand how infectiousness is reflected in the viral antigen shedding detected by LFT versus the viral loads approximated by RT-qPCR.

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