scholarly journals A Laboratory Medicine Best Practices Systematic Review and Meta-analysis of Nucleic Acid Amplification Tests (NAATs) and Algorithms Including NAATs for the Diagnosis of Clostridioides (Clostridium) difficile in Adults

2019 ◽  
Vol 32 (3) ◽  
Author(s):  
Colleen S. Kraft ◽  
J. Scott Parrott ◽  
Nancy E. Cornish ◽  
Matthew L. Rubinstein ◽  
Alice S. Weissfeld ◽  
...  
Keyword(s):  
Systematic Review ◽  
Nucleic Acid ◽  
Best Practices ◽  
Diagnostic Accuracy ◽  
Meta Analysis ◽  
Laboratory Medicine ◽  
Nucleic Acid Amplification ◽  
Content Type ◽  
Repeat Testing ◽  
Testing Algorithms

SUMMARY The evidence base for the optimal laboratory diagnosis of Clostridioides (Clostridium) difficile in adults is currently unresolved due to the uncertain performance characteristics and various combinations of tests. This systematic review evaluates the diagnostic accuracy of laboratory testing algorithms that include nucleic acid amplification tests (NAATs) to detect the presence of C. difficile. The systematic review and meta-analysis included eligible studies (those that had PICO [population, intervention, comparison, outcome] elements) that assessed the diagnostic accuracy of NAAT alone or following glutamate dehydrogenase (GDH) enzyme immunoassays (EIAs) or GDH EIAs plus C. difficile toxin EIAs (toxin). The diagnostic yield of NAAT for repeat testing after an initial negative result was also assessed. Two hundred thirty-eight studies met inclusion criteria. Seventy-two of these studies had sufficient data for meta-analysis. The strength of evidence ranged from high to insufficient. The uses of NAAT only, GDH-positive EIA followed by NAAT, and GDH-positive/toxin-negative EIA followed by NAAT are all recommended as American Society for Microbiology (ASM) best practices for the detection of the C. difficile toxin gene or organism. Meta-analysis of published evidence supports the use of testing algorithms that use NAAT alone or in combination with GDH or GDH plus toxin EIA to detect the presence of C. difficile in adults. There is insufficient evidence to recommend against repeat testing of the sample using NAAT after an initial negative result due to a lack of evidence of harm (i.e., financial, length of stay, or delay of treatment) as specified by the Laboratory Medicine Best Practices (LMBP) systematic review method in making such an assessment. Findings from this systematic review provide clarity to diagnostic testing strategies and highlight gaps, such as low numbers of GDH/toxin/PCR studies, in existing evidence on diagnostic performance, which can be used to guide future clinical research studies.

scholarly journals A Systematic Review and Meta-analysis of the Diagnostic Accuracy of Nucleic Acid Amplification Tests for Tuberculous Meningitis

2019 ◽  
Vol 57 (6) ◽  
Author(s):  
Ali Pormohammad ◽  
Mohammad Javad Nasiri ◽  
Timothy D. McHugh ◽  
Seyed Mohammad Riahi ◽  
Nathan C. Bahr
Keyword(s):  
Systematic Review ◽  
Nucleic Acid ◽  
Diagnostic Accuracy ◽  
Likelihood Ratio ◽  
Tuberculous Meningitis ◽  
Meta Analysis ◽  
Nucleic Acid Amplification ◽  
Data Sets ◽  
Reference Standard ◽  
Sensitivity Specificity

ABSTRACTThe diagnosis of tuberculous meningitis (TBM) is difficult and poses a significant challenge to physicians worldwide. Recently, nucleic acid amplification (NAA) tests have shown promise for the diagnosis of TBM, although their performance has been variable. We undertook a systematic review and meta-analysis to evaluate the diagnostic accuracy of NAA tests with cerebrospinal fluid (CSF) samples against that of culture as the reference standard or a combined reference standard (CRS) for TBM. We searched the Embase, PubMed, Web of Science, and Cochrane Library databases for the relevant records. The QUADAS-2 tool was used to assess the quality of the studies. Diagnostic accuracy measures (i.e., sensitivity and specificity) were pooled with a random-effects model. All statistical analyses were performed with STATA (version 14 IC; Stata Corporation, College Station, TX, USA), Meta-DiSc (version 1.4 for Windows; Cochrane Colloquium, Barcelona, Spain), and RevMan (version 5.3; The Nordic Cochrane Centre, the Cochrane Collaboration, Copenhagen, Denmark) software. Sixty-three studies comprising 1,381 cases of confirmed TBM and 5,712 non-TBM controls were included in the final analysis. These 63 studies were divided into two groups comprising 71 data sets (43 in-house tests and 28 commercial tests) that used culture as the reference standard and 24 data sets (21 in-house tests and 3 commercial tests) that used a CRS. Studies which used a culture reference standard had better pooled summary estimates than studies which used CRS. The overall pooled estimates of sensitivity, specificity, positive likelihood ratio (PLR), and negative likelihood ratio (NLR) of the NAA tests against culture were 82% (95% confidence interval [CI], 75 to 87%), 99% (95% CI, 98 to 99%), 58.6 (95% CI, 35.3 to 97.3), and 0.19 (95% CI, 0.14 to 0.25), respectively. The pooled sensitivity, specificity, PLR, and NLR of NAA tests against CRS were 68% (95% CI, 41 to 87%), 98% (95% CI, 95 to 99%), 36.5 (95% CI, 15.6 to 85.3), and 0.32 (95% CI, 0.15 to 0.70), respectively. The analysis has demonstrated that the diagnostic accuracy of NAA tests is currently insufficient for them to replace culture as a lone diagnostic test. NAA tests may be used in combination with culture due to the advantage of time to result and in scenarios where culture tests are not feasible. Further work to improve NAA tests would benefit from the availability of standardized reference standards and improvements to the methodology.

scholarly journals Meta-analysis of diagnostic accuracy of nucleic acid amplification tests for abdominal tuberculosis: A protocol

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0243765
Author(s):  
Yanqin Shen ◽  
Likui Fang ◽  
Bo Ye ◽  
Guocan Yu
Keyword(s):  
Systematic Review ◽  
Nucleic Acid ◽  
Diagnostic Accuracy ◽  
Meta Analysis ◽  
Extrapulmonary Tuberculosis ◽  
Abdominal Tuberculosis ◽  
Nucleic Acid Amplification ◽  
Cochrane Library ◽  
China National Knowledge Infrastructure ◽  
Nucleic Acid Amplification Tests

Background Abdominal tuberculosis is a severe extrapulmonary tuberculosis, which can lead to serious complications. Early diagnosis and treatment are very important for the prognosis and the diagnosis of abdominal tuberculosis is still difficult. This study aims to evaluate the diagnostic accuracy of nucleic acid amplification tests (NAATs) for abdominal tuberculosis using meta-analysis method. Methods We will search PubMed, the Cochrane Library, Embase, China National Knowledge Infrastructure, and the Wanfang database for studies evaluating the diagnostic accuracy of NAATs for abdominal tuberculosis until May 2020. We will include a systematic review and meta-analysis that evaluated the accuracy of NAATs for abdominal tuberculosis. Any types of study design with full text will be sought and included. The risk of bias will be assessed using the Quality Assessment of Diagnostic Accuracy Studies tool. Stata version 15.0 with the midas command packages will be used to carry out meta-analyses. Results The results will provide clinical evidence for diagnostic accuracy of NAATs for abdominal tuberculosis, and this systematic review and meta-analysis will be submitted to a peer-reviewed journal for publication. Conclusion This overview will provide evidence of NAATs for diagnosis of abdominal tuberculosis. Systematic review registration INPLASY202060030.

scholarly journals Diagnostic Accuracy of Nucleic Acid Amplification-Based Assays for Clostridium perfringens-Associated Diseases: a Systematic Review and Meta-analysis

2020 ◽  
Vol 58 (9) ◽  
Author(s):  
Ke Chen ◽  
Sarfraz Ahmed ◽  
Yun-Juan Sheng ◽  
Changfeng Sun ◽  
Cun-Liang Deng ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Diagnostic Accuracy ◽  
Likelihood Ratio ◽  
Clostridium Perfringens ◽  
Meta Analysis ◽  
Reference Standards ◽  
Nucleic Acid Amplification ◽  
Content Type ◽  
Microbiological Culture ◽  
Associated Diseases

ABSTRACT Timely and accurate methods for detecting Clostridium perfringens-associated diseases (CPAD) are crucial to improve patient care. A number of studies have evaluated the accuracy of nucleic acid amplification tests (NAAT) in detecting CPAD, but decisive results about their effectiveness have not been reported. We conducted a meta-analysis to evaluate the diagnostic performance of NAAT for detecting C. perfringens in clinical diarrheal samples. Five databases including PubMed, Embase, Scopus, Web of Science, and the Cochrane library were systematically probed for studies published before 6 December 2019. From 2,632 citations, we identified five eligible studies comprising 817 samples. Three studies (n = 695 samples) compared NAAT with a microbiological culture while the other three studies (n = 322 samples) compared NAAT with an immunoassay. NAAT revealed higher diagnostic accuracy against immunoassay (sensitivity, 0.53 [95% confidence interval [CI], 0.35 to 0.7]; specificity, 0.97 [95% CI, 0.95 to 0.99]; positive likelihood ratio [PLR], 23.2 [95% CI, 3.49 to 153.98]; negative likelihood ratio [NLR], 0.25 [95% CI, 0 to 245.28]; diagnostic odds ratio [DOR], 74.11 [95% CI, 2.11 to 2,593.7]) than microbiological culture (sensitivity, 0.31 [95% CI, 0.22 to 0.41]; specificity, 0.95 [95% CI, 0.93 to 0.97]; PLR, 11.56 [95% CI, 3.87 to 34.6]; NLR, 0.57 [95% CI, 0.27 to 1.21]; DOR, 18.1 [95% CI, 4.83 to 67.8]). NAAT pooled specificity was consistently ≥95% against that of applied reference standards. A meta-regression and subgroup analysis of sample condition, gene target, study design, and reference standards could not explain the heterogeneity (P > 0.05) in the diagnostic efficiency. The analysis has demonstrated that the diagnostic accuracy of NAAT is relatively insufficient to replace traditional reference standards as a single diagnostic test. NAAT can be applied in combination with microbiological culture because of the advantage of time to result and in scenarios where traditional tests are not feasible. Further investigations in this direction with larger sample sizes are still warranted to support our findings.

scholarly journals Diagnostic Accuracy of Stool Xpert MTB/RIF for Detection of Pulmonary Tuberculosis in Children: a Systematic Review and Meta-analysis

2019 ◽  
Vol 57 (6) ◽  
Author(s):  
Emily MacLean ◽  
Giorgia Sulis ◽  
Claudia M. Denkinger ◽  
James C. Johnston ◽  
Madhukar Pai ◽  
...  
Keyword(s):  
Systematic Review ◽  
Pulmonary Tuberculosis ◽  
Diagnostic Accuracy ◽  
Sensitivity And Specificity ◽  
Meta Analysis ◽  
Target Population ◽  
Nucleic Acid Amplification ◽  
Reference Standard ◽  
Noninvasive Method ◽  
High Data

ABSTRACT Invasive collection methods are often required to obtain samples for the microbiological evaluation of children with presumptive pulmonary tuberculosis (PTB). Nucleic acid amplification testing of easier-to-collect stool samples could be a noninvasive method of diagnosing PTB. We conducted a systematic review and meta-analysis to evaluate the diagnostic accuracy of testing stool with the Xpert MTB/RIF assay (“stool Xpert”) for childhood PTB. Four databases were searched for publications from January 2008 to June 2018. Studies assessing the diagnostic accuracy among children of stool Xpert compared to a microbiological reference standard of conventional specimens tested by mycobacterial culture or Xpert were eligible. Bivariate random-effects meta-analyses were performed to calculate pooled sensitivity and specificity of stool Xpert against the reference standard. From 1,589 citations, 9 studies (n = 1,681) were included. Median participant ages ranged from 1.3 to 10.6 years. Protocols for stool processing and testing varied substantially, with differences in reagents and methods of homogenization and filtering. Against the microbiological reference standard, the pooled sensitivity and specificity of stool Xpert were 67% (95% confidence interval [CI], 52 to 79%) and 99% (95% CI, 98 to 99%), respectively. Sensitivity was higher among children with HIV (79% [95% CI, 68 to 87%] versus 60% [95% CI, 44 to 74%] among HIV-uninfected children). Heterogeneity was high. Data were insufficient for subgroup analyses among children under the age of 5 years, the most relevant target population. Stool Xpert could be a noninvasive method of ruling in PTB in children, particularly those with HIV. However, studies focused on children under 5 years of age are needed, and generalizability of the evidence is limited by the lack of standardized stool preparation and testing protocols.

scholarly journals Effectiveness of practices to reduce blood culture contamination: A Laboratory Medicine Best Practices systematic review and meta-analysis

2012 ◽  
Vol 45 (13-14) ◽  
pp. 999-1011 ◽  
Author(s):  
Susan R. Snyder ◽  
Alessandra M. Favoretto ◽  
Rich Ann Baetz ◽  
James H. Derzon ◽  
Bereneice M. Madison ◽  
...  
Keyword(s):  
Systematic Review ◽  
Blood Culture ◽  
Best Practices ◽  
Meta Analysis ◽  
Laboratory Medicine

scholarly journals A systematic review and meta-analysis of the sensitivity of antibody tests for the laboratory confirmation of COVID-19

2021 ◽  
Author(s):  
Nigel A Makoah ◽  
Thomas Tipih ◽  
Matefo M Litabe ◽  
Mareza Brink ◽  
Joseph B Sempa ◽  
...  
Keyword(s):  
Systematic Review ◽  
Nucleic Acid ◽  
Symptom Onset ◽  
Meta Analysis ◽  
Nucleic Acid Amplification ◽  
Serological Tests ◽  
Nucleic Acid Amplification Tests ◽  
Laboratory Confirmation ◽  
Using Data ◽  
Low Sensitivity

Aim: The aim of this study was to investigate the utility of serological tests for the diagnosis of COVID-19 during the first week of symptom onset in patients confirmed with the real-time RT-PCR. Materials & methods: A systematic review and meta-analysis of 58 publications were performed using data obtained from Academic Search Ultimate, Africa-wide, Scopus, Web of Science and MEDLINE. Results: We found that the highest pooled sensitivities were obtained with ELISA IgM-IgG and chemiluminescence immunoassay IgM tests. Conclusion: Serological tests have low sensitivity within the first week of symptom onset and cannot replace nucleic acid amplification tests. However, serological assays can be used to support nucleic acid amplification tests.

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