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The Indian Journal of Tuberculosis Jul 2020Tuberculosis (TB), which is caused by bacteria of the Mycobacterium tuberculosis complex, is one of the oldest diseases known to affect humans and a major cause of death... (Review)
Review
Tuberculosis (TB), which is caused by bacteria of the Mycobacterium tuberculosis complex, is one of the oldest diseases known to affect humans and a major cause of death worldwide. Tuberculosis continues to be a huge peril disease against the human population and according to WHO, tuberculosis is a major killer of the human population after HIV/AIDS. Tuberculosis is highly prevalent among the low socioeconomic section of the population and marginalized sections of the community. In India, National strategic plan (2017-2025) has a national goal of elimination of tuberculosis by 2025. It requires increased awareness and understanding of Tuberculosis. In this review article history, taxonomy, epidemiology, histology, immunology, pathogenesis and clinical features of both pulmonary tuberculosis (PTB) and extra-pulmonary tuberculosis (EPTB) has been discussed. A great length of detailed information regarding diagnostic modalities has been explained along with diagnostic algorithm for PTB and EPTB. Treatment regimen for sensitive, drug resistant and extensive drug resistant tuberculosis has been summarized along with newer drugs recommended for multi drug resistant tuberculosis. This review article has been written after extensive literature study in view of better understanding and to increase awareness regarding tuberculosis, as a sincere effort that will help eliminate tuberculosis off the face of the earth in near future.
Topics: Humans; Algorithms; Culture Techniques; Extensively Drug-Resistant Tuberculosis; History, 15th Century; History, 16th Century; History, 17th Century; History, 18th Century; History, 19th Century; History, 20th Century; History, Ancient; Interferon-gamma Release Tests; Mycobacterium tuberculosis; Nucleic Acid Amplification Techniques; Polymerase Chain Reaction; Tuberculin Test; Tuberculosis; Tuberculosis, Multidrug-Resistant; Tuberculosis, Pulmonary
PubMed: 32825856
DOI: 10.1016/j.ijtb.2020.02.005 -
International Journal of Public Health 2023We aimed to assess the association between rapid antigen detection tests and real-time reverse transcription-polymerase chain reaction assay for severe acute... (Meta-Analysis)
Meta-Analysis Review
Association Between Rapid Antigen Detection Tests and Real-Time Reverse Transcription-Polymerase Chain Reaction Assay for SARS-CoV-2: A Systematic Review and Meta-Analyses.
We aimed to assess the association between rapid antigen detection tests and real-time reverse transcription-polymerase chain reaction assay for severe acute respiratory syndrome coronavirus 2. We searched PubMed, Cochrane Library, EMBASE, and the Web of Science from their inception to 31 May 2023. A random-effects meta-analysis was used to estimate false positives in the RADTs group, relative to those in the RT-PCR group, and subgroup analyses were conducted based on the different Ct value cut-offs (<40 or ≥40). We performed this study in accordance with the guidelines outlined in the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). Fifty-one studies were included and considered to be of moderate quality. We found a satisfactory overall false positive rate (0.01, 95% CI: 0.00-0.01) for the RADTs compared to RT-PCR. In the stratified analysis, we also found that the false positive rates of the RADTs did not increase when Ct values of RT-PCR (Ct < 40, 0.01, 95% CI: 0.00-0.01; Ct ≥ 40, 0.01, 95% CI: 0.00-0.01). In conclusion, the best available evidence supports an association between RADTs and RT-PCR. When Ct-values were analyzed using cut-off <40 or ≥40, this resulted in an estimated false positive rate of only 1%.
Topics: Humans; Reverse Transcriptase Polymerase Chain Reaction; Reverse Transcription; SARS-CoV-2; COVID-19; COVID-19 Testing
PubMed: 37588042
DOI: 10.3389/ijph.2023.1605452 -
Reviews in Medical Virology Sep 2022The cornerstone of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection is reverse-transcription polymerase chain reaction (RT-PCR) of viral RNA. As a... (Meta-Analysis)
Meta-Analysis Review
The cornerstone of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection is reverse-transcription polymerase chain reaction (RT-PCR) of viral RNA. As a surrogate assay SARS-CoV-2 RNA detection does not necessarily imply infectivity. Only virus isolation in permissive cell culture systems can indicate infectivity. Here, we review the evidence on RT-PCR performance in detecting infectious SARS-CoV-2. We searched for any studies that used RT-PCR and cell culture to determine infectious SARS-CoV-2 in respiratory samples. We assessed (i) diagnostic accuracy of RT-PCR compared to cell culture as reference test, (ii) performed meta-analysis of positive predictive values (PPV) and (iii) determined the virus isolation probabilities depending on cycle threshold (Ct) or log genome copies/ml using logistic regression. We included 55 studies. There is substantial statistical and clinical heterogeneity. Seven studies were included for diagnostic accuracy. Sensitivity ranged from 90% to 99% and specificity from 29% to 92%. In meta-analysis, the PPVs varied across subgroups with different sampling times after symptom onset, with 1% (95% confidence interval [CI], 0%-7%) in sampling beyond 10 days and 27% (CI, 19%-36%) to 46% (CI, 33%-60%) in subgroups that also included earlier samples. Estimates of virus isolation probability varied between 6% (CI, 0%-100%) and 50% (CI, 0%-100%) at a Ct value of 30 and between 0% (CI, 0%-22%) and 63% (CI, 0%-100%) at 5 log genome copies/ml. Evidence on RT-PCR performance in detecting infectious SARS-CoV-2 in respiratory samples was limited. Major limitations were heterogeneity and poor reporting. RT-PCR and cell culture protocols need further standardisation.
Topics: COVID-19; COVID-19 Testing; Humans; RNA, Viral; SARS-CoV-2; Sensitivity and Specificity
PubMed: 35366033
DOI: 10.1002/rmv.2342 -
Clinical Microbiology and Infection :... Oct 2018To provide a summary of evidence for the diagnostic accuracies of three multiplex PCR systems (mPCRs)-BioFire FilmArray RP (FilmArray), Nanosphere Verigene RV+ test... (Meta-Analysis)
Meta-Analysis Review
OBJECTIVES
To provide a summary of evidence for the diagnostic accuracies of three multiplex PCR systems (mPCRs)-BioFire FilmArray RP (FilmArray), Nanosphere Verigene RV+ test (Verigene RV+) and Hologic Gen-Probe Prodesse assays-on the detection of viral respiratory infections.
METHODS
A comprehensive search up to 1 July 2017 was conducted on Medline and Embase for studies that utilized FilmArray, Verigene RV+ and Prodesse for diagnosis of viral respiratory infections. A summary of diagnostic accuracies for the following five viruses were calculated: influenza A virus (FluA), influenza B virus, respiratory syncytial virus, human metapneumovirus and adenovirus. Hierarchical summary receiver operating curves were used for estimating the viral detection performance per assay.
RESULTS
Twenty studies of 5510 patient samples were eligible for analysis. Multiplex PCRs demonstrated high diagnostic accuracy, with area under the receiver operating characteristic curve (AUROC) equal to or more than 0.98 for all the above viruses except for adenovirus (AUROC 0.89). FilmArray, Verigene RV+ and ProFlu+ (the only Prodesse assay with enough data) demonstrated a summary sensitivity for FluA of 0.911 (95% confidence interval, 0.848-0.949), 0.949 (95% confidence interval, 0.882-0.979) and 0.954 (95% confidence interval, 0.871-0.985), respectively. The three mPCRs were comparable in terms of detection of FluA.
CONCLUSIONS
Point estimates calculated from eligible studies showed that the three mPCRs (FilmArray, Verigene RV+ and ProFlu+) are highly accurate and may provide important diagnostic information for early identification of respiratory virus infections. In patients with low pretest probability for FluA, these three mPCRs can predict a low possibility of infection and may justify withholding empirical antiviral treatments.
Topics: Humans; Multiplex Polymerase Chain Reaction; Respiratory Tract Infections; Virus Diseases; Viruses
PubMed: 29208560
DOI: 10.1016/j.cmi.2017.11.018 -
Surgical Infections 2018We aim to update a meta-analysis to evaluate the efficiency of polymerase chain reaction (PCR) for diagnosis of periprosthetic joint infection (PJI) because different... (Meta-Analysis)
Meta-Analysis Review
BACKGROUND
We aim to update a meta-analysis to evaluate the efficiency of polymerase chain reaction (PCR) for diagnosis of periprosthetic joint infection (PJI) because different types of PCR assays have yielded variable diagnostic efficiency from 2013.
METHODS
We conducted our systematic review by searching for keywords in online databases from 2013 to May 2017. Studies were chosen based on inclusion and exclusion criteria and the quality of included studies was assessed. Pooled sensitivity and specificity were compared with other synovial fluid biomarkers. A total of 20 studies, comprising 2,526 participants were assessed.
RESULTS
The pooled sensitivity, specificity, and diagnostic odds ratio (DOR) were 0.76 (95% confidence interval [CI]: 0.65-0.85), 0.94 (95% CI: 0.92-0.95), and 0.94 (95% CI: 0.92-0.96), respectively. Meta-regression analysis indicated that use of specific genes, fresh samples, and more than one sample per patient may improve sensitivity.
CONCLUSIONS
Although novel PCR assays have been developed, the sensitivity of PCR for the diagnosis of PJI had decreased compared with the previous meta-analysis (0.86, 95% CI: 0.77-0.92), whereas the high specificity is reliable for excluding PJI. Novel synovial fluid biomarker such as α-defensin, which possesses pooled sensitivity between 0.96 and 1.00, might be more efficient than PCR in PJI diagnosis.
Topics: Biomarkers; Humans; Joint Prosthesis; Polymerase Chain Reaction; Prosthesis-Related Infections; Reproducibility of Results; Sensitivity and Specificity; Synovial Fluid
PubMed: 29920159
DOI: 10.1089/sur.2018.014 -
American Journal of Orthopedics (Belle... 2017Prosthetic joint infection (PJI) may be underreported because of difficulty in making a diagnosis, especially in infections with low-virulence organisms. Reports of PJI... (Review)
Review
Prosthetic joint infection (PJI) may be underreported because of difficulty in making a diagnosis, especially in infections with low-virulence organisms. Reports of PJI cases misdiagnosed as aseptic loosening suggest that current screening and diagnostic tools are not sensitive enough to detect all infections and that PJI likely is underdiagnosed. We reviewed the literature on recently developed novel synovial biomarkers and polymerase chain reaction (PCR) technologies, of which several have proved promising as highly sensitive and specific tools for detecting PJI. We followed the recommendations of PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses). Of 90 papers screened by title or abstract and then by full text, 15 met our inclusion criteria. Sensitivities reported in the included studies ranged from 63% to 100% for α-defensin, from 46.8% to 90.9% for interleukin 6, from 28.6% to 100% for leukocyte esterase, and from 67.10% to 95.7% for PCR. Specificities ranged from 95% to 100% for α-defensin, from 85.7% to 97.6% for interleukin 6, from 63.6% to 96.5% for leukocyte esterase, and from 12.3% to 97.8% for PCR. α-Defensin is a highly sensitive and specific screening tool that may help improve the accuracy of PJI detection, particularly in low-grade infections.
Topics: Biomarkers; Humans; Joint Prosthesis; Polymerase Chain Reaction; Prosthesis-Related Infections; Synovial Fluid; alpha-Defensins
PubMed: 28856346
DOI: No ID Found -
Journal of Medical Virology May 2016In this meta-analysis, we evaluated the diagnostic role of Epstein-Barr virus deoxyribonucleic acid detection and quantitation in the serum of pediatric and young adult... (Meta-Analysis)
Meta-Analysis Review
In this meta-analysis, we evaluated the diagnostic role of Epstein-Barr virus deoxyribonucleic acid detection and quantitation in the serum of pediatric and young adult patients with infectious mononucleosis. The primary outcome of this meta-analysis was the sensitivity and specificity of Epstein-Barr virus (EBV) deoxyribonucleic acid (DNA) detection and quantitation using polymerase chain reaction (PCR). A systematic review and meta-analysis was performed by searching for articles that were published through September 24, 2014 in the following databases: Medline, Cochrane, EMBASE, and Google Scholar. The following keywords were used for the search: "Epstein-Barr virus," "infectious mononucleosis," "children/young adults/infant/pediatric," and "polymerase chain reaction or PCR." Three were included in this analysis. We found that for detection by PCR, the pooled sensitivity for detecting EBV DNA was 77% (95%CI, 66-86%) and the pooled specificity for was 98% (95%CI, 93-100%). Our findings indicate that this PCR-based assay has high specificity and good sensitivity for detecting of EBV DNA, indicating it may useful for identifying patients with infectious mononucleosis. This assay may also be helpful to identify young athletic patients or highly physically active pediatric patients who are at risk for a splenic rupture due to acute infectious mononucleosis.
Topics: Adolescent; Adult; Child; Child, Preschool; DNA, Viral; Female; Herpesvirus 4, Human; Humans; Infant; Infectious Mononucleosis; Male; Molecular Diagnostic Techniques; Real-Time Polymerase Chain Reaction; Sensitivity and Specificity; Viral Load; Young Adult
PubMed: 26455510
DOI: 10.1002/jmv.24402 -
Memorias Do Instituto Oswaldo Cruz Apr 2015The diagnosis of mucocutaneous leishmaniasis (MCL) is hampered by the absence of a gold standard. An accurate diagnosis is essential because of the high toxicity of the... (Meta-Analysis)
Meta-Analysis Review
The diagnosis of mucocutaneous leishmaniasis (MCL) is hampered by the absence of a gold standard. An accurate diagnosis is essential because of the high toxicity of the medications for the disease. This study aimed to assess the ability of polymerase chain reaction (PCR) to identify MCL and to compare these results with clinical research recently published by the authors. A systematic literature review based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses: the PRISMA Statement was performed using comprehensive search criteria and communication with the authors. A meta-analysis considering the estimates of the univariate and bivariate models was performed. Specificity near 100% was common among the papers. The primary reason for accuracy differences was sensitivity. The meta-analysis, which was only possible for PCR samples of lesion fragments, revealed a sensitivity of 71% [95% confidence interval (CI) = 0.59; 0.81] and a specificity of 93% (95% CI = 0.83; 0.98) in the bivariate model. The search for measures that could increase the sensitivity of PCR should be encouraged. The quality of the collected material and the optimisation of the amplification of genetic material should be prioritised.
Topics: Biopsy; Clinical Trials as Topic; Confidence Intervals; DNA, Protozoan; Humans; Leishmaniasis, Mucocutaneous; Polymerase Chain Reaction; Qualitative Research; ROC Curve; Sensitivity and Specificity
PubMed: 25946238
DOI: 10.1590/0074-02760140280 -
Journal of Medical Virology Dec 2022Nucleic acid molecular diagnostic technology plays an important role in the detection of severe fever with thrombocytopenia syndrome (SFTS). However, no relevant reports... (Meta-Analysis)
Meta-Analysis
Accuracy of reverse-transcription polymerase chain reaction and loop-mediated isothermal amplification in diagnosing severe fever with thrombocytopenia syndrome: A systematic review and meta-analysis.
Nucleic acid molecular diagnostic technology plays an important role in the detection of severe fever with thrombocytopenia syndrome (SFTS). However, no relevant reports have been published on the accuracy of reverse-transcription polymerase chain reaction (RT-PCR) and reverse-transcription loop-mediated isothermal amplification (RT-LAMP) in the diagnosis of SFTS. Thus, we conducted a meta-analysis and systematic review to evaluate the accuracy of the two methods. On June 19, 2022, we comprehensively searched the PubMed, Embase, Cochrane Library, Web of Science, Scoups, Ovid, Proquest, China National Knowledge Infrastructure Database, Wan Fang Data, Traditional Chinese Medicine Database (Sinomed), VIP Database, and Reading Showing Database for articles on nucleic acid diagnostic techniques, such as RT-PCR and RT-LAMP, used to diagnose SFTS. Statistical analysis was performed using STATA 14.0 and Meta-Disc 1.4. Sixteen articles involving 2942 clinical blood samples were included in the analysis. RT-PCR and RT-LAMP were used as index tests, whereas RT-PCR or other detection methods were used as reference standards. The pooled values for the sensitivity, specificity, positive and negative likelihood ratios of the RT-PCR test were 0.97 (95% confidence interval [CI]: 0.92-0.99), 1.00 (95% CI: 0.98-1.00), 483.87 (95% CI: 58.04-4033.76), and 0.03 (95% CI:0.01-0.08), respectively. Those for the RT-LAMP test were 0.95 (95% CI: 0.91-0.97), 0.99 (95% CI: 0.93-1.00), 111.18 (95% CI: 13.96-885.27), and 0.05 (95% CI: 0.03-0.09), respectively. Both RT-PCR and RT-LAMP have high diagnostic value in SFTS and can be applied in different scenarios for laboratory confirmation or on-site screening.
Topics: Humans; Molecular Diagnostic Techniques; Nucleic Acid Amplification Techniques; Nucleic Acids; Reverse Transcriptase Polymerase Chain Reaction; Sensitivity and Specificity; Severe Fever with Thrombocytopenia Syndrome
PubMed: 35968756
DOI: 10.1002/jmv.28068 -
Systematic Reviews Oct 2021Rapid and accurate diagnosis of paediatric tuberculosis (TB) is key to manage the disease and to control and prevent its transmission. Collection of quality sputum... (Meta-Analysis)
Meta-Analysis
BACKGROUND
Rapid and accurate diagnosis of paediatric tuberculosis (TB) is key to manage the disease and to control and prevent its transmission. Collection of quality sputum samples without invasion methods from paediatrics (age < 16 years) with presumptive pulmonary tuberculosis (PTB) remains a challenge. Thus, the aim of this meta-analysis was to assess the overall accuracy of a real-time polymerase chain reaction (RT-PCR)-based assay, for routine diagnosis of MTB in different samples from paediatrics with active pulmonary and extra-pulmonary tuberculosis using mycobacterial culture as the gold standard in clinical microbiology laboratories.
METHODS
We conducted a systematic review and meta-analysis to examine the diagnostic test accuracy of RT-PCR based assay for the detection of MTB in paediatric clinical samples. A systematic literature search was performed for publications in any language. MEDLINE via PubMed, EMBASE, and Web of Science were among 9 bibliographic databases searched from August 2019 until November 2020. Bivariate random-effects model of meta-analysis were performed to generate pooled summary estimates (95% CIs) for overall accuracy of RT-PCR based assay compared to mycobacterial culture as the reference standard.
RESULTS
Of the 1592 candidate studies, twenty-one eligible studies met our inclusion criteria. In total, the review and meta-analysis included 5536 (3209 PTB and 2327 EPTB). Summary estimates for pulmonary TB (11 studies) were as follows: sensitivity 56 (95% CI 51-62), specificity 97 (95% CI 96-98) and summary estimates for extra-pulmonary TB (10 studies) were as follows: sensitivity 87 (95% CI 82-91)) specificity 100 (95% CI 99-100). There was significant heterogeneity in sensitivity and specificity among the enrolled studies (p < 0.001).
CONCLUSIONS
Our results suggested that the RT-PCR based assay could be a useful test for the diagnosis of paediatrics TB with high sensitivity and specificity in low-income/high-burden and upper medium income/low-burden settings. From the study, RT-PCR assay demonstrated a high degree of sensitivity for extra-pulmonary TB and good sensitivity for pulmonary TB which is an important factor in achieving effective global control and for patient management in terms of initiating early and appropriate anti-tubercular therapy.
SYSTEMATIC REVIEW REGISTRATION
PROSPERO CRD42018104052.
Topics: Adolescent; Child; Humans; Mycobacterium tuberculosis; Pediatrics; Real-Time Polymerase Chain Reaction; Sensitivity and Specificity; Tuberculosis; Tuberculosis, Pulmonary
PubMed: 34706779
DOI: 10.1186/s13643-021-01836-w