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Life (Basel, Switzerland) Nov 2021The diagnosis of COVID-19 is made using reverse transcription polymerase chain reaction (RT-PCR) but its sensitivity varies from 20 to 100%. The presence of gustatory... (Review)
Review
Exploring the Clinical Utility of Gustatory Dysfunction (GD) as a Triage Symptom Prior to Reverse Transcription Polymerase Chain Reaction (RT-PCR) in the Diagnosis of COVID-19: A Meta-Analysis and Systematic Review.
BACKGROUND
The diagnosis of COVID-19 is made using reverse transcription polymerase chain reaction (RT-PCR) but its sensitivity varies from 20 to 100%. The presence of gustatory dysfunction (GD) in a patient with upper respiratory tract symptoms might increase the clinical suspicion of COVID-19.
AIMS
To perform a systematic review and meta-analysis to determine the pooled sensitivity, specificity, positive likelihood ratio (LR+), negative likelihood ratio (LR-) and diagnostic odds ratio (DOR) of using GD as a triage symptom prior to RT-PCR.
METHODS
PubMed and Embase were searched up to 20 June 2021. Studies published in English were included if they compared the frequency of GD in COVID-19 adult patients (proven by RT-PCR) to COVID-19 negative controls in case control or cross-sectional studies. The Newcastle-Ottawa scale was used to assess the methodological quality of the included studies.
RESULTS
21,272 COVID-19 patients and 52,298 COVID-19 negative patients were included across 44 studies from 21 countries. All studies were of moderate to high risk of bias. Patients with GD were more likely to test positive for COVID-19: DOR 6.39 (4.86-8.40), LR+ 3.84 (3.04-4.84), LR- 0.67 (0.64-0.70), pooled sensitivity 0.37 (0.29-0.47) and pooled specificity 0.92 (0.89-0.94). While history/questionnaire-based assessments were predictive of RT-PCR positivity (DOR 6.62 (4.95-8.85)), gustatory testing was not (DOR 3.53 (0.98-12.7)). There was significant heterogeneity among the 44 studies (I = 92%, < 0.01).
CONCLUSIONS
GD is useful as a symptom to determine if a patient should undergo further testing, especially in resource-poor regions where COVID-19 testing is scarce. Patients with GD may be advised to quarantine while repeated testing is performed if the initial RT-PCR is negative.
FUNDING
None.
PubMed: 34947846
DOI: 10.3390/life11121315 -
Clinical Microbiology and Infection :... Mar 2023Streptococcus pneumoniae is a leading cause of bacterial meningitis worldwide. Conventional microbiological assays take several days and require the use of various drugs... (Meta-Analysis)
Meta-Analysis Review
BACKGROUND
Streptococcus pneumoniae is a leading cause of bacterial meningitis worldwide. Conventional microbiological assays take several days and require the use of various drugs for empirical treatment. Rapid antigen tests in cerebrospinal fluid (CSF) may be useful to triage pneumococcal meningitis immediately.
OBJECTIVES
To elucidate whether rapid antigen tests in CSF are useful in the triage of pneumococcal meningitis.
METHODS
Data sourcesCochrane CENTRAL, MEDLINE, EMBASE, World Health Organization International Clinical Trials Registry Platform, and ClinicalTrials.gov databases were searched. Study eligibility criteriaAll types of cohort studies except multiple-group studies, where the sensitivity and specificity of rapid antigen tests in CSF compared with CSF culture can be extracted. ParticipantsPatients with suspected meningitis. TestsRapid antigen tests in CSF. Reference standardsOne or more of the following: blood culture, CSF culture, and polymerase chain reaction in CSF. Assessment of risk of biasThe methodological quality of the included studies was assessed using QUADAS-2. Methods of data synthesisWe used a random-effects bivariate model for the meta-analysis. We conducted a subgroup analysis by dividing studies into types of antigen tests, adults and children, low-income and high-income countries, and with or without exposure to antibiotics before lumbar puncture.
RESULTS
Forty-four studies involving 14 791 participants were included. Most studies had a moderate-to-low methodological quality. Summary sensitivity and specificity were 99.5% (95% confidence interval (CI), 92.4-100%) and 98.2% (95% CI, 96.9-98.9%), respectively. Positive predictive values and negative predictive values at the median prevalence (4.2%) in the included studies were 70.8% (95% CI, 56.6-79.9%) and 100% (95% CI, 99.7-100%), respectively. The diagnostic accuracy was consistent across the various subgroups, except for slightly reduced sensitivity in high-income countries.
CONCLUSIONS
Rapid antigen tests in CSF would be useful in triaging pneumococcal meningitis. Further studies are warranted to investigate the clinical benefit of ruling out pneumococcal meningitis based on the results of rapid antigen tests.
Topics: Child; Adult; Humans; Meningitis, Pneumococcal; Streptococcus pneumoniae; Immunologic Tests; Cohort Studies; Sensitivity and Specificity
PubMed: 36503113
DOI: 10.1016/j.cmi.2022.12.002 -
Infectious Diseases and Therapy Mar 2019Capnocytophaga canimorsus infections are associated with dog bites, especially in asplenic or immunocompromised patients, and typically manifest as sepsis and/or...
INTRODUCTION
Capnocytophaga canimorsus infections are associated with dog bites, especially in asplenic or immunocompromised patients, and typically manifest as sepsis and/or bacteremia. Meningitis has been rarely described, and its diagnosis may be delayed due to poor or slow growth using traditional culture techniques. We provide our experience using polymerase chain reaction (PCR) to establish the diagnosis and perform a comprehensive review of C. canimorsus meningitis cases to provide summary data on the clinical manifestations, diagnosis, and outcomes of this unusual infection.
METHODS
A systematic review of the peer-reviewed English literature (PubMed, Embase, Ovid Medline) from January 1966 to March 2018 was conducted to identify cases of C. canimorsus meningitis. Data collected included demographics, risk factors, cerebrospinal fluid (CSF) findings, PCR results, treatments, and outcomes. Descriptive statistics are presented as numbers (percentages) and medians (ranges).
RESULTS
A total of 37 patients were reviewed with a median age of 63 years (12 days to 83 years) with a male predominance (76%). A relatively low proportion had an immunocompromised state (16% splenectomy and 5% steroid use); the most common risk factor was alcoholism (19%). Fifty-nine percent reported a dog bite (all within ≤ 14 days prior to presentation), while 22% reported a non-bite dog exposure, 3% reported cat bite, and 3% reported both dog and cat exposures; 11% reported no animal contact. CSF parameters included a median white count of 1024 cells/mm, 81% had neutrophilic predominance, median protein of 190 mg/dl, and median glucose CSF/serum ratio 0.23. In 54% of cases, blood cultures were positive for C. canimorsus (median, 4 days) and 70% had positive CSF cultures (median, 5 days). PCR established the diagnosis in eight (22%) cases. Antibiotic therapy was given for a median of 15 days (range, 7 to 42 days). Prognosis was overall favorable with only one (3%) death reported and adverse neurologic and/or physical sequelae in 19% of the survivors.
CONCLUSION
C. canimorsus meningitis is a rare but increasingly important clinical entity occurring in patients of all ages, typically after dog exposure. While classically considered an infection among immunocompromised patients, most cases have occurred in previously healthy, immunocompetent persons. Diagnosis may be rapidly established by PCR, and this test should be considered in culture-negative cases with associated exposures. Outcome was generally favorable after a median antibiotic duration of 15 days.
PubMed: 30706413
DOI: 10.1007/s40121-019-0233-6 -
Open Forum Infectious Diseases Sep 2021Cycle threshold (C) values are correlated with the amount of viral nucleic acid in a sample and may be obtained from some qualitative real-time polymerase chain reaction... (Review)
Review
Cycle threshold (C) values are correlated with the amount of viral nucleic acid in a sample and may be obtained from some qualitative real-time polymerase chain reaction tests used for diagnosis of most patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, C values cannot be directly compared across assays, and they must be interpreted with caution as they are influenced by sample type, timing of sample collection, and assay design. Presently, the correlation between C values and clinical outcomes is not well understood. We conducted a systematic review and meta-analysis of published studies through April 19, 2021, that reported an association between C values and hospitalization, disease severity, and mortality in patients ≥18 years old with SARS-CoV-2. A meta-analysis of 7 studies showed no significant difference in mean C values between hospitalized and nonhospitalized patients. Among hospitalized patients, those with C values <25 had a high risk of more severe disease and mortality than patients with C values >30 (odds ratio [OR], 2.31; 95% CI, 1.70 to 3.13; and OR, 2.95; 95% CI, 2.19 to 3.96; respectively). The odds of increased disease severity and mortality were less pronounced in patients with C values of 25-30 compared with >30.
PubMed: 34584900
DOI: 10.1093/ofid/ofab453 -
Diagnostics (Basel, Switzerland) Dec 2023Mismatch repair deficiency (d-MMR)/microsatellite instability (MSI), , and mutational status are crucial for treating advanced colorectal cancer patients. Traditional... (Review)
Review
Mismatch repair deficiency (d-MMR)/microsatellite instability (MSI), , and mutational status are crucial for treating advanced colorectal cancer patients. Traditional methods like immunohistochemistry or polymerase chain reaction (PCR) can be challenged by artificial intelligence (AI) based on whole slide images (WSI) to predict tumor status. In this systematic review, we evaluated the role of AI in predicting MSI status, , and mutations in colorectal cancer. Studies published in PubMed up to June 2023 were included ( = 17), and we reported the risk of bias and the performance for each study. Some studies were impacted by the reduced number of slides included in the data set and the lack of external validation cohorts. Deep learning models for the d-MMR/MSI status showed a good performance in training cohorts (mean AUC = 0.89, [0.74-0.97]) but slightly less than expected in the validation cohort when available (mean AUC = 0.82, [0.63-0.98]). Contrary to the MSI status, the prediction of and mutations was less explored with a less robust methodology. The performance was lower, with a maximum of 0.77 in the training cohort, 0.58 in the validation cohort for , and 0.82 AUC in the training cohort for .
PubMed: 38201408
DOI: 10.3390/diagnostics14010099 -
Iranian Journal of Public Health Nov 2021The loop-mediated isothermal amplification (LAMP) method is frequently used for identifying many microorganisms. The present review aimed to evaluate the sensitivity and... (Review)
Review
BACKGROUND
The loop-mediated isothermal amplification (LAMP) method is frequently used for identifying many microorganisms. The present review aimed to evaluate the sensitivity and specificity of LAMP method for detection of food-borne bacteria and to compare these features with those of polymerase chain reaction (PCR), as an alternative molecular diagnostic procedure, and with cultivation method, as the gold standard method.
METHODS
The literature was searched in electronic databases (PubMed, Scopus, Web of Science, and EMBASE) for recruiting publications within Jan 2000 to Jul 2021. We used the combinations of keywords including foodborne disease, LAMP, PCR, Loop-mediated isothermal amplification, and polymerase chain reaction. Meta-analysis was used to adjust the correlation and heterogeneity between the studies. The efficiency of the methods was presented by negative likelihood ratio, positive likelihood ratio, sensitivity, specificity, and odds ratio using forest plots. A value less than 0.05 was considered as statistical significance cut off. The confidence intervals were presented at the 95% interval.
RESULTS
Overall, 23 relevant studies were analyzed. The sensitivities of LAMP and PCR methods were estimated to be 96.6% (95% CI: 95.0-97.7) and 95.6% (95%CI: 91.5-97.8), respectively. The specificities of LAMP and PCR were also estimated to be 97.6% (95%CI: 92.6-99.3) and 98.7% (95%CI: 96.5-99.5), respectively.
CONCLUSION
The specificities of LAMP and PCR assays were determined by comparing their results with cultivation method as the gold standard. Overall, the specificity of both PCR and LAMP methods was low for detection of fastidious bacteria. Nevertheless, LAMP and PCR methods have acceptable specificities and sensitivities, and their application in clinical practice necessitates more studies.
PubMed: 35223591
DOI: 10.18502/ijph.v50i11.7571 -
Annals of Coloproctology Apr 2023Intestinal fibrosis is a common complication of inflammatory bowel diseases. However, the possible involvement of epithelial-mesenchymal transition (EMT) has been... (Review)
Review
PURPOSE
Intestinal fibrosis is a common complication of inflammatory bowel diseases. However, the possible involvement of epithelial-mesenchymal transition (EMT) has been scarcely investigated. This systematic review aims to search through research papers that are focusing on messenger RNA (mRNA) and protein expression profile in EMT in fistula or in intestinal fibrosis.
METHODS
Electronic exploration was performed until April 24, 2019 through PubMed, Ovid, Science Direct, and Scopus databases with the terms of "fistula" OR "intestinal fibrosis" AND "epithelial-mesenchymal transition". Two independent reviewers scrutinized the suitability of the title and abstract before examining the full text that met the inclusion criteria. For each study, the sample types that were used, methods for analysis, and genes expressed were identified. The list of genes was further analyzed using DAVID (Database for Annotation, Visualization, and Integrated Discovery) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway.
RESULTS
There were 896 citations found; however, only 3 studies fulfilled the requirements. Among the EMT-related genes, 5 were upregulated genes at mRNA level while 6 were at protein level. However, only 2 downregulated genes were found at each mRNA and protein level. Of the 4 inflammation-related genes found, 3 genes were upregulated at mRNA level and 1 at protein level. These genes were confirmed to be involved in the development of inflammatory induced fibrosis and fistula through EMT. Results from quantitative real-time polymerase chain reaction analysis were consistent with the process of EMT, confirmed by the western blot protein analysis.
CONCLUSION
Many significant genes which are involved in the process of EMT in fistula and intestinal fibrosis have been identified. With high-end technology many more genes could be identified. These genes will be good molecular targets in the development of biomarkers for precision drug targeting in the future treatment of intestinal fibrosis and fistula.
PubMed: 34856655
DOI: 10.3393/ac.2021.00584.0083 -
Tropical Animal Health and Production Sep 2021This study aimed to systematically collect and appraise the scientific evidence to answer the research question: What MAP genotypes have been isolated from cattle,... (Review)
Review
This study aimed to systematically collect and appraise the scientific evidence to answer the research question: What MAP genotypes have been isolated from cattle, sheep, and goats in Latin America and the Caribbean? An electronic search was conducted on three platforms (i.e., OVID®, Web of Science®, SciELO) as well as on the proceedings of the International Colloquium on Paratuberculosis. Inclusion and exclusion criteria were defined a priori and conserved through the systematic process and only articles published in peer-reviewed journals were considered. A total of 26 articles met the definitive inclusion criteria. All were published in English, in 15 different journals, and between 1989 and 2020. The relevant articles reported the use of six different genotyping techniques (i.e., polymerase chain reaction-restriction endonuclease analysis, restriction fragment length polymorphism, type-specific-PCR, mycobacterial interspersed repetitive units-variable number of tandem repeats, multi-locus short sequence repeat, single nucleotide polymorphism) in isolates from seven countries. Genotypes found so far in the region using typing techniques were mainly C type. MIRU-VNTR mostly reported INMV 1, INMV 2, and INMV 11 subtypes, among others. MLSSR reported genotypes from four different countries, reporting nine different subtypes of which 7g-10g-4ggt was the most common for loci 1, 2, and 8, respectively. Regardless the high diversity of techniques used so far to genotype Latin American and Caribbean MAP isolates, the original question of this systematic review has been answered. In addition, a relative genetic similarity between MAP strains recovered from cattle, goats, and sheep unrelatedly of the matrix and geographic origin was identified.
Topics: Animals; Cattle; Genotype; Goat Diseases; Goats; Latin America; Minisatellite Repeats; Mycobacterium avium subsp. paratuberculosis; Paratuberculosis; Sheep; Sheep Diseases
PubMed: 34546430
DOI: 10.1007/s11250-021-02923-9 -
PloS One 2015Pyrazinamide (PZA) is crucial for tuberculosis (TB) treatment, given its unique ability to eradicate persister bacilli. The worldwide burden of PZA resistance remains... (Meta-Analysis)
Meta-Analysis Review
BACKGROUND
Pyrazinamide (PZA) is crucial for tuberculosis (TB) treatment, given its unique ability to eradicate persister bacilli. The worldwide burden of PZA resistance remains poorly described.
METHODS
Systematic PubMed, Science Direct and Scopus searches for articles reporting phenotypic (liquid culture drug susceptibility testing or pyrazinamidase activity assays) and/or genotypic (polymerase chain reaction or DNA sequencing) PZA resistance. Global and regional summary estimates were obtained from random-effects meta-analysis, stratified by presence or risk of multidrug resistant TB (MDR-TB). Regional summary estimates were combined with regional WHO TB incidence estimates to determine the annual burden of PZA resistance. Information on single nucleotide polymorphisms (SNPs) in the pncA gene was aggregated to obtain a global summary.
RESULTS
Pooled PZA resistance prevalence estimate was 16.2% (95% CI 11.2-21.2) among all TB cases, 41.3% (29.0-53.7) among patients at high MDR-TB risk, and 60.5% (52.3-68.6) among MDR-TB cases. The estimated global burden is 1.4 million new PZA resistant TB cases annually, about 270,000 in MDR-TB patients. Among 1,815 phenotypically resistant isolates, 608 unique SNPs occurred at 397 distinct positions throughout the pncA gene.
INTERPRETATION
PZA resistance is ubiquitous, with an estimated one in six incident TB cases and more than half of all MDR-TB cases resistant to PZA globally. The diversity of SNPs across the pncA gene complicates the development of rapid molecular diagnostics. These findings caution against relying on PZA in current and future TB drug regimens, especially in MDR-TB patients.
Topics: Antitubercular Agents; Humans; Mycobacterium tuberculosis; Pyrazinamide; Tuberculosis, Multidrug-Resistant
PubMed: 26218737
DOI: 10.1371/journal.pone.0133869 -
The Kaohsiung Journal of Medical... Feb 2018Broad-range bacterial rDNA polymerase chain reaction (PCR) followed by sequencing may be identified as the etiology of infective endocarditis (IE) from surgically... (Meta-Analysis)
Meta-Analysis Review
Broad-range bacterial rDNA polymerase chain reaction (PCR) followed by sequencing may be identified as the etiology of infective endocarditis (IE) from surgically removed valve tissue; therefore, we reviewed the value of molecular testing in identifying organisms' DNA in the studies conducted until 2016. We searched Google Scholar, Scopus, ScienceDirect, Cochrane, PubMed, and Medline electronic databases without any time limitations up to December 2016 for English studies reporting microorganisms involved in infective endocarditis microbiology using PCR and real-time PCR. Most studies were prospective. Eleven out of 12 studies used valve tissue samples and blood cultures while only 1 study used whole blood. Also, 10 studies used the molecular method of PCR while 2 studies used real-time PCR. Most studies used 16S rDNA gene as the target gene. The bacteria were identified as the most common microorganisms involved in infective endocarditis. Streptococcus spp. and Staphylococcus spp. were, by far, the most predominant bacteria detected. In all studies, PCR and real-time PCR identified more pathogens than blood and tissue cultures; moreover, the sensitivity and specificity of PCR and real-time PCR were more than cultures in most of the studies. The highest sensitivity and specificity were 96% and 100%, respectively. The gram positive bacteria were the most frequent cause of infective endocarditis. The molecular methods enjoy a greater sensitivity compared to the conventional blood culture methods; yet, they are applicable only to the valve tissue of the patients undergoing cardiac valve surgery.
Topics: Endocarditis, Bacterial; Humans; Real-Time Polymerase Chain Reaction; Reproducibility of Results
PubMed: 29413230
DOI: 10.1016/j.kjms.2017.09.011