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Sao Paulo Medical Journal = Revista... 2020A positive real-time reverse-transcriptase polymerase chain reaction (RT-PCR) for SARS CoV-2, from nasopharyngeal swabs, is the current gold standard diagnostic test for... (Comparative Study)
Comparative Study Meta-Analysis
Reverse-transcriptase polymerase chain reaction versus chest computed tomography for detecting early symptoms of COVID-19. A diagnostic accuracy systematic review and meta-analysis.
BACKGROUND
A positive real-time reverse-transcriptase polymerase chain reaction (RT-PCR) for SARS CoV-2, from nasopharyngeal swabs, is the current gold standard diagnostic test for this virus and has sensitivity of 60-70%. Some studies have demonstrated a significant number of false-negative RT-PCR tests while displaying significant tomographic findings, in the early days of symptoms of COVID-19.
OBJECTIVE
To compare accuracy between RT-PCR and computed tomography (CT) for detecting COVID-19 in the first week of its symptoms during the pandemic.
DESIGN AND SETTING
Systematic review of comparative studies of diagnostic accuracy within the Evidence-based Health Program of a federal university in São Paulo (SP), Brazil.
METHODS
A systematic search of the relevant literature was conducted in the PubMed, EMBASE, Cochrane Library, CINAHL and LILACS databases, for articles published up to June 6, 2020, relating to studies evaluating the diagnostic accuracy of RT-PCR and chest CT for COVID-19 diagnoses. The QUADAS 2 tool was used for methodological quality evaluation.
RESULTS
In total, 1204 patients with COVID-19 were evaluated; 1045 had tomographic findings while 755 showed positive RT-PCR for COVID-19. RT-PCR demonstrated 81.4% sensitivity, 100% specificity and 92.3% accuracy. Chest CT demonstrated 95.3% sensitivity, 43.8% specificity and 63.3% accuracy.
CONCLUSION
The high sensitivity and detection rates shown by CT demonstrate that this technique has a high degree of importance in the early stages of the disease. During an outbreak, the higher prevalence of the condition increases the positive predictive value of CT.
REGISTRATION NUMBER
DOI: 10.17605/OSF.IO/UNGHA in the Open Science Framework.
Topics: Betacoronavirus; Brazil; COVID-19; COVID-19 Testing; COVID-19 Vaccines; Clinical Laboratory Techniques; Coronavirus Infections; Humans; Pandemics; Pneumonia, Viral; Reverse Transcriptase Polymerase Chain Reaction; SARS-CoV-2; Sensitivity and Specificity; Tomography, X-Ray Computed
PubMed: 32844901
DOI: 10.1590/1516-3180.2020.034306072020 -
Clinical Infectious Diseases : An... Oct 2015Aspergillus polymerase chain reaction (PCR) was excluded from the European Organisation for the Research and Treatment of Cancer/Mycoses Study Group (EORTC/MSG)... (Comparative Study)
Comparative Study Review
BACKGROUND
Aspergillus polymerase chain reaction (PCR) was excluded from the European Organisation for the Research and Treatment of Cancer/Mycoses Study Group (EORTC/MSG) definitions of invasive fungal disease because of limited standardization and validation. The definitions are being revised.
METHODS
A systematic literature review was performed to identify analytical and clinical information available on inclusion of galactomannan enzyme immunoassay (GM-EIA) (2002) and β-d-glucan (2008), providing a minimal threshold when considering PCR. Categorical parameters and statistical performance were compared.
RESULTS
When incorporated, GM-EIA and β-d-glucan sensitivities and specificities for diagnosing invasive aspergillosis were 81.6% and 91.6%, and 76.9% and 89.4%, respectively. Aspergillus PCR has similar sensitivity and specificity (76.8%-88.0% and 75.0%-94.5%, respectively) and comparable utility. Methodological recommendations and commercial PCR assays assist standardization. Although all tests have limitations, currently, PCR is the only test with independent quality control.
CONCLUSIONS
We propose that there is sufficient evidence that is at least equivalent to that used to include GM-EIA and β-d-glucan testing, and that PCR is now mature enough for inclusion in the EORTC/MSG definitions.
Topics: Antigens, Fungal; Aspergillosis; Aspergillus; Galactose; Humans; Immunoenzyme Techniques; Mannans; Polymerase Chain Reaction; Quality Control; Sensitivity and Specificity; beta-Glucans
PubMed: 26113653
DOI: 10.1093/cid/civ507 -
The Lancet. Infectious Diseases Aug 2014Despite substantial decreases in recent decades, acute gastroenteritis causes the second greatest burden of all infectious diseases worldwide. Noroviruses are a leading... (Meta-Analysis)
Meta-Analysis Review
BACKGROUND
Despite substantial decreases in recent decades, acute gastroenteritis causes the second greatest burden of all infectious diseases worldwide. Noroviruses are a leading cause of sporadic cases and outbreaks of acute gastroenteritis across all age groups. We aimed to assess the role of norovirus as a cause of endemic acute gastroenteritis worldwide.
METHODS
We searched Embase, Medline, and Global Health databases from Jan 1, 2008, to March 8, 2014, for studies that used PCR diagnostics to assess the prevalence of norovirus in individuals with acute gastroenteritis. We included studies that were done continuously for 1 year or more from a specified catchment area (geographical area or group of people), enrolled patients who presented with symptoms of acute gastroenteritis, and used PCR-based diagnostics for norovirus on all stool specimens from patients with acute gastroenteritis. The primary outcome was prevalence of norovirus among all cases of gastroenteritis. We generated pooled estimates of prevalence by fitting linear mixed-effect meta-regression models.
FINDINGS
Of 175 articles included, the pooled prevalence of norovirus in 187 336 patients with acute gastroenteritis was 18% (95% CI 17-20). Norovirus prevalence tended to be higher in cases of acute gastroenteritis in community (24%, 18-30) and outpatient (20%, 16-24) settings compared with inpatient (17%, 15-19, p=0·066) settings. Prevalence was also higher in low-mortality developing (19%, 16-22) and developed countries (20%, 17-22) compared with high-mortality developing countries (14%, 11-16; p=0·058). Patient age and whether the study included years of novel strain emergence were not associated with norovirus prevalence.
INTERPRETATION
Norovirus is a key gastroenteritis pathogen associated with almost a fifth of all cases of acute gastroenteritis, and targeted intervention to reduce norovirus burden, such as vaccines, should be considered.
FUNDING
The Foodborne Disease Burden Epidemiology Reference Group (FERG) of WHO and the Government of the Netherlands on behalf of FERG.
Topics: Caliciviridae Infections; Developed Countries; Developing Countries; Endemic Diseases; Feces; Gastroenteritis; Global Health; Humans; Norovirus; Polymerase Chain Reaction; Prevalence
PubMed: 24981041
DOI: 10.1016/S1473-3099(14)70767-4 -
BMC Cancer Jan 2011The DNA repair protein O6-Methylguanine-DNA methyltransferase (MGMT) confers resistance to alkylating agents. Several methods have been applied to its analysis, with... (Meta-Analysis)
Meta-Analysis Review
O6-Methylguanine-DNA methyltransferase protein expression by immunohistochemistry in brain and non-brain systemic tumours: systematic review and meta-analysis of correlation with methylation-specific polymerase chain reaction.
BACKGROUND
The DNA repair protein O6-Methylguanine-DNA methyltransferase (MGMT) confers resistance to alkylating agents. Several methods have been applied to its analysis, with methylation-specific polymerase chain reaction (MSP) the most commonly used for promoter methylation study, while immunohistochemistry (IHC) has become the most frequently used for the detection of MGMT protein expression. Agreement on the best and most reliable technique for evaluating MGMT status remains unsettled. The aim of this study was to perform a systematic review and meta-analysis of the correlation between IHC and MSP.
METHODS
A computer-aided search of MEDLINE (1950-October 2009), EBSCO (1966-October 2009) and EMBASE (1974-October 2009) was performed for relevant publications. Studies meeting inclusion criteria were those comparing MGMT protein expression by IHC with MGMT promoter methylation by MSP in the same cohort of patients. Methodological quality was assessed by using the QUADAS and STARD instruments. Previously published guidelines were followed for meta-analysis performance.
RESULTS
Of 254 studies identified as eligible for full-text review, 52 (20.5%) met the inclusion criteria. The review showed that results of MGMT protein expression by IHC are not in close agreement with those obtained with MSP. Moreover, type of tumour (primary brain tumour vs others) was an independent covariate of accuracy estimates in the meta-regression analysis beyond the cut-off value.
CONCLUSIONS
Protein expression assessed by IHC alone fails to reflect the promoter methylation status of MGMT. Thus, in attempts at clinical diagnosis the two methods seem to select different groups of patients and should not be used interchangeably.
Topics: Brain Neoplasms; DNA Methylation; Humans; Immunohistochemistry; Neoplasms; O(6)-Methylguanine-DNA Methyltransferase; Polymerase Chain Reaction; Prognosis; Promoter Regions, Genetic
PubMed: 21269507
DOI: 10.1186/1471-2407-11-35 -
Clinical Infectious Diseases : An... Jun 2024This meta-analysis examines the comparative diagnostic performance of polymerase chain reaction (PCR) for the diagnosis of Pneumocystis pneumonia (PCP) on different...
BACKGROUND
This meta-analysis examines the comparative diagnostic performance of polymerase chain reaction (PCR) for the diagnosis of Pneumocystis pneumonia (PCP) on different respiratory tract samples, in both human immunodeficiency virus (HIV) and non-HIV populations.
METHODS
A total of 55 articles met inclusion criteria, including 11 434 PCR assays on respiratory specimens from 7835 patients at risk of PCP. QUADAS-2 tool indicated low risk of bias across all studies. Using a bivariate and random-effects meta-regression analysis, the diagnostic performance of PCR against the European Organisation for Research and Treatment of Cancer-Mycoses Study Group definition of proven PCP was examined.
RESULTS
Quantitative PCR (qPCR) on bronchoalveolar lavage fluid provided the highest pooled sensitivity of 98.7% (95% confidence interval [CI], 96.8%-99.5%), adequate specificity of 89.3% (95% CI, 84.4%-92.7%), negative likelihood ratio (LR-) of 0.014, and positive likelihood ratio (LR+) of 9.19. qPCR on induced sputum provided similarly high sensitivity of 99.0% (95% CI, 94.4%-99.3%) but a reduced specificity of 81.5% (95% CI, 72.1%-88.3%), LR- of 0.024, and LR+ of 5.30. qPCR on upper respiratory tract samples provided lower sensitivity of 89.2% (95% CI, 71.0%-96.5%), high specificity of 90.5% (95% CI, 80.9%-95.5%), LR- of 0.120, and LR+ of 9.34. There was no significant difference in sensitivity and specificity of PCR according to HIV status of patients.
CONCLUSIONS
On deeper respiratory tract specimens, PCR negativity can be used to confidently exclude PCP, but PCR positivity will likely require clinical interpretation to distinguish between colonization and active infection, partially dependent on the strength of the PCR signal (indicative of fungal burden), the specimen type, and patient population tested.
PubMed: 38860786
DOI: 10.1093/cid/ciae239 -
Diseases of the Colon and Rectum Nov 2019Few data are published on perianal tuberculosis.
BACKGROUND
Few data are published on perianal tuberculosis.
OBJECTIVE
This study aimed to determine the best method to diagnose tuberculosis in patients with fistula-in-ano and to conduct a systematic review to determine the incidence and characteristics of tuberculosis fistula-in-ano.
DATA SOURCES
The prospective study data and existing literature were derived from PubMed, Google scholar, and Scopus STUDY SELECTION:: Prospective analysis of patients with tuberculous fistula-in-ano treated between 2014 and 2018 was conducted, and a systematic review of studies describing ≥3 patients with tuberculosis fistula-in-ano was completed.
INTERVENTION
Testing of tuberculosis was performed by histopathology or polymerase chain reaction of tissue or pus from the fistula tract.
MAIN OUTCOME MEASURES
The primary outcomes measured were the detection rate of various tests to detect tuberculosis in fistula-in-ano and the prevalence rate of tuberculosis in simple versus complex fistulas.
RESULTS
In 637 samples (410 patients) tested, tuberculosis was detected in 49 samples (43 patients). Additional samples (n = 106) sent in patients with a high index of suspicion tested positive in 14 more patients. Thus, overall, 63 samples tested positive in 57 patients (total: 743 samples in 410 patients were tested). Tuberculosis was detected in 2 of 181 patients (1.1%) in tissue (histopathology), in 28 of 341 patients (8.2%) in tissue (polymerase chain reaction), and in 19 of 115 patients (16.5%) in pus (polymerase chain reaction) samples. To detect tuberculosis, tissue (polymerase chain reaction) was significantly better than tissue (histopathology) (28/341 vs 2/181, p < 0.00001) and pus (polymerase chain reaction) was significantly better than tissue (polymerase chain reaction) (19/115 vs 28/341, p < 0.0009). Tuberculosis was significantly more common in complex fistulas than in simple fistulas (20.3% vs 7.2%, p = 0.0002). The systematic review (n = 199) highlighted that tubercular fistulas are more common in recurrent and complex fistulas and in tuberculosis endemic regions.
LIMITATIONS
The true sensitivity and specificity of each testing modality could not be determined because not all patients with tuberculosis fistula-in-ano were tested by every diagnostic modality studied.
CONCLUSIONS
The tuberculosis detection rate of polymerase chain reaction was significantly higher than histopathology. Among polymerase chain reaction, pus had higher detection rate than tissue. Tuberculosis was associated with more complex and recurrent fistulas.
Topics: Aftercare; Antitubercular Agents; Bacteriological Techniques; Female; Fissure in Ano; Humans; Incidence; India; Magnetic Resonance Imaging; Male; Middle Aged; Mycobacterium tuberculosis; Outcome Assessment, Health Care; Polymerase Chain Reaction; Rectal Fistula; Recurrence; Reproducibility of Results; Streptomycin; Surgical Procedures, Operative; Tuberculosis, Gastrointestinal
PubMed: 31596764
DOI: 10.1097/DCR.0000000000001493 -
Scientific Reports Jul 2020Malaria rapid diagnostic tests (RDTs) are widely used to detect malaria parasites among patients who suspected malaria infections in malaria-endemic areas where... (Comparative Study)
Comparative Study Meta-Analysis
Summary of discordant results between rapid diagnosis tests, microscopy, and polymerase chain reaction for detecting Plasmodium mixed infection: a systematic review and meta-analysis.
Malaria rapid diagnostic tests (RDTs) are widely used to detect malaria parasites among patients who suspected malaria infections in malaria-endemic areas where microscopy is unavailable. Nevertheless, little is known about the performance of RDTs in detecting Plasmodium mixed infections. The present study aimed to evaluate the discordant results between RDTs and microscopy/polymerase chain reaction (PCR) in detecting Plasmodium mixed infections. The PubMed (MEDLINE), Web of Science, and Scopus databases were systematically reviewed to identify related studies that reported the performance of RDTs in detecting Plasmodium mixed infections. Studies were grouped according to the different RDT types including RDT type 2 (pf-HRP2/pan-aldolase), RDT type 3 (pf-HRP2/pan-pLDH), RDT type 4 (Pf-LDH/pan-pLDH), RDT type 5 (Pf/Pv-pLDH), and RDT type 6 (pf-HRP2/Pv-pLDH) for subgroup analysis. The estimates of the different proportions in each analysis group that were visually summarized in a forest plot showed the odds ratio (OR) and 95% confidence interval (CI). Plots were drawn using RevMan (version 5.3; Cochrane Community). Twenty-eight studies were included in the present study. Overall, the meta-analysis showed that RDTs could detect a significantly higher proportion of Plasmodium mixed infections than microscopy (p = 0.0007, OR = 3.33, 95% CI 1.66-6.68). Subgroup analysis demonstrated that only RDTs targeting Pf-specific histidine-rich protein 2 (HRP2)/pan-specific lactate dehydrogenase (LDH) could detect a significantly higher proportion of Plasmodium mixed infections than microscopy (p = 0.004, OR = 8.46, 95% CI 2.75-26.1). The subgroup analysis between RDTs and PCR methods demonstrated that RDTs targeting Pf-specific HRP2/Pv-specific LDH could detect a significantly lower proportion of Plasmodium mixed infections than PCR methods (p = 0.0005, OR = 0.42, 95% CI 0.26-0.68). This is the first study to summarize the discordant results between RDTs and microscopy/PCR in detecting Plasmodium mixed infections. Malaria RDTs targeting Pf-HRP2/pan-pLDH could detect a higher proportion of Plasmodium mixed infections than microscopy, while RDTs targeting Pf-HRP2/Pv-specific LDH could detect a lower proportion of Plasmodium mixed infections than PCR methods. The results of this study will support the selection and careful interpretations of RDTs for a better diagnosis of Plasmodium mixed-species infections and appropriate treatment of malaria patients in endemic and non-endemic settings.
Topics: Antigens, Protozoan; Cross-Sectional Studies; Diagnostic Tests, Routine; Humans; Malaria, Falciparum; Malaria, Vivax; Microscopy; Odds Ratio; Plasmodium falciparum; Plasmodium vivax; Polymerase Chain Reaction; Protozoan Proteins; Sensitivity and Specificity
PubMed: 32728145
DOI: 10.1038/s41598-020-69647-y -
PLoS Neglected Tropical Diseases Jan 2020Molecular diagnostic tests, notably polymerase chain reaction (PCR), are highly sensitive test for Leishmania detection, which is especially relevant in chronic... (Meta-Analysis)
Meta-Analysis
Test accuracy of polymerase chain reaction methods against conventional diagnostic techniques for Cutaneous Leishmaniasis (CL) in patients with clinical or epidemiological suspicion of CL: Systematic review and meta-analysis.
BACKGROUND
Molecular diagnostic tests, notably polymerase chain reaction (PCR), are highly sensitive test for Leishmania detection, which is especially relevant in chronic cutaneous lesion with lower parasite load. An accurate diagnosis is essential because of the high toxicity of the medications for the disease. Nevertheless, diagnosis of cutaneous leishmaniasis (CL) is hampered by the absence of a reference standard. Assuming that the PCR-based molecular tools are the most accurate diagnostic method, the objective of this systematic review was to assess the diagnostic accuracy of PCR-based molecular tools in a meta-analysis of the published literature.
METHODOLOGY/PRINCIPAL FINDINGS
A search of the published literature found 142 papers of which only 13 studies met the selection criteria, including conventional PCR, real-time PCR, Loop-mediated isothermal amplification (LAMP), recombinase polymerase amplification (RPA), polymorphism-specific PCR (PS-PCR). The sensitivities of the individual studies ranged from 61% to 100%, and specificities ranged from 11% to 100%. The pooled sensitivities of PCR in smears were 0.95 (95% CI, 0.90 to 0.98), and the specificity was 0.91(95% CI, 0.70 to 0.98). In general population, estimates were lower in aspirates, skin biopsies and swab samples with 0.90 (95% CI, 0.80 to 0.95) and 0.87 (95% CI, 0.76 to 0.94) for sensitivity and specificity, respectively. The specificity was lower in consecutive studies, at 0.88 (95% CI, 0.59 to 0.98) and its CI were wider.
CONCLUSIONS/SIGNIFICANCE
No statistically significant differences between the accuracy in smears, aspirate, skin biopsies or swabs samples were observed. Therefore, a simple smear sample run by PCR, instead more invasive samples, may be enough to obtain a positive diagnosis of CL. The results for PCR in all samples type confirm previous reports that consider PCR as the most accurate method for the diagnosis of CL.
Topics: Biopsy; Diagnostic Tests, Routine; Humans; Leishmania; Leishmaniasis, Cutaneous; Real-Time Polymerase Chain Reaction; Sensitivity and Specificity; Skin
PubMed: 31961871
DOI: 10.1371/journal.pntd.0007981 -
Interdisciplinary Perspectives on... 2021The current global pandemic of COVID-19 is considered a public health emergency. The diagnosis of COVID-19 depends on detection of the viral nucleic acid by real time...
BACKGROUND
The current global pandemic of COVID-19 is considered a public health emergency. The diagnosis of COVID-19 depends on detection of the viral nucleic acid by real time reverse transcription polymerase chain reaction (RT-PCR). However, false-negative RT-PCR tests are reported and could hinder the control of the pandemic. Chest computed tomography could achieve a more reliable diagnosis and represent a complementary diagnostic tool.
AIM
To perform a meta-analysis and systematic review to find out the role of chest computed tomography versus RT-PCR for precise diagnosis of COVID-19 infection.
METHODS
We searched three electronic databases (PubMed, ScienceDirect, and Scopus) from April 1 to April 20, 2020, to find out articles including the accuracy of chest computed tomography scan versus RT-PCR for diagnosis of SARS-CoV-2 infection. Observational studies, case series, and case reports were included.
RESULTS
A total of 238 articles were retrieved from the search strategy. Following screening, 39 articles were chosen for full text assessment and finally 35 articles were included for qualitative and quantitative analysis. Chest computed tomography showed a wide range of sensitivity varied from 12%-100%.
CONCLUSION
Chest computed tomography is playing a key role for diagnosis and detection of COVID-19 infection. Computed tomography image findings may precede the initially positive RT-PCR assay.
PubMed: 34194491
DOI: 10.1155/2021/8798575 -
Diagnostic Microbiology and Infectious... Jul 2021Loop-mediated isothermal amplification (LAMP) test is widely used in molecular diagnostics as a point-of-care technique alternative to traditional PCR especially in... (Meta-Analysis)
Meta-Analysis
Evaluation of diagnostic accuracy of loop-mediated isothermal amplification method (LAMP) compared with polymerase chain reaction (PCR) for Leptospira spp. in clinical samples: a systematic review and meta-analysis.
Loop-mediated isothermal amplification (LAMP) test is widely used in molecular diagnostics as a point-of-care technique alternative to traditional PCR especially in resource-limited countries. LAMP has been recently used to diagnose leptospirosis. Therefore, we undertook a systematic review and meta-analysis to compare the accuracy of LAMP with PCR in the diagnosis of leptospirosis. Sixty-one studies were extracted from three international databases and analyzed throughout using the PRISMA guideline. The pooled sensitivity of LAMP and PCR technique was 0.80 (95% CI: 0.58-0.90) and 0.54 (95% CI: 0.35-0.67) respectively indicating that LAMP is more sensitive than PCR. The Q* value of LAMP and PCR-based technique is 274.61 and 397.95, respectively. Among the analyzed studies, significant heterogeneity was observed where I is 90.90% for LAMP-based and 86.18% for PCR-based. Our study suggests that LAMP has better diagnostic accuracy than PCR. However, future work should be carried out to reduce heterogeneity as well as to improve and develop effective intervention strategies.
Topics: Humans; Leptospira; Leptospirosis; Molecular Diagnostic Techniques; Nucleic Acid Amplification Techniques; Polymerase Chain Reaction
PubMed: 33845305
DOI: 10.1016/j.diagmicrobio.2021.115369