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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 -
International Health Mar 2022There is currently a lack of information regarding ocular tropism and the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Globally, the cumulative number... (Meta-Analysis)
Meta-Analysis
BACKGROUND
There is currently a lack of information regarding ocular tropism and the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Globally, the cumulative number of coronavirus disease 2019 (COVID-19) cases is increasing daily. Thus the potential for ocular transmission and manifestations of SARS-CoV-2 requires more investigation.
METHODS
A systematic search of electronic databases for ocular transmission and manifestations of SARS-CoV-2 was performed. Pooled cross-sectional studies were used for conducting a meta-analysis to estimate the prevalence of ocular transmission of SARS-CoV-2 to the respiratory system and ocular manifestations (associated symptoms) of SARS-CoV-2.
RESULTS
The highest prevalence of SARS-CoV-2-positive tears using reverse transcription polymerase chain reaction was found to be 7.5%. However, the highest prevalence of ocular conjunctivitis associated with SARS-CoV-2 was 32%. Thus, SARS-CoV-2 can evidently infect the eye, as revealed in the conjunctival secretions of COVID-19 patients.
CONCLUSION
The available data reflect the influence of the ocular structure on SARS-CoV-2. The analysis showed that ocular manifestation is an indication for SARS-CoV-2, particularly conjunctivitis. Moreover, there is no evidence that the ocular structure can be an additional path of transmission for SARS-CoV-2, however, it warrants further investigation.
Topics: COVID-19; Conjunctiva; Cross-Sectional Studies; Humans; SARS-CoV-2; Tears
PubMed: 34043796
DOI: 10.1093/inthealth/ihab028 -
Chronic Diseases and Translational... Sep 2022Around 450 million people are affected by pneumonia every year, which results in 2.5 million deaths. Coronavirus disease 2019 (Covid-19) has also affected 181 million... (Review)
Review
Around 450 million people are affected by pneumonia every year, which results in 2.5 million deaths. Coronavirus disease 2019 (Covid-19) has also affected 181 million people, which led to 3.92 million casualties. The chances of death in both of these diseases can be significantly reduced if they are diagnosed early. However, the current methods of diagnosing pneumonia (complaints + chest X-ray) and Covid-19 (real-time polymerase chain reaction) require the presence of expert radiologists and time, respectively. With the help of deep learning models, pneumonia and Covid-19 can be detected instantly from chest X-rays or computerized tomography (CT) scans. The process of diagnosing pneumonia/Covid-19 can become faster and more widespread. In this paper, we aimed to elicit, explain, and evaluate qualitatively and quantitatively all advancements in deep learning methods aimed at detecting community-acquired pneumonia, viral pneumonia, and Covid-19 from images of chest X-rays and CT scans. Being a systematic review, the focus of this paper lies in explaining various deep learning model architectures, which have either been modified or created from scratch for the task at hand. For each model, this paper answers the question of why the model is designed the way it is, the challenges that a particular model overcomes, and the tradeoffs that come with modifying a model to the required specifications. A grouped quantitative analysis of all models described in the paper is also provided to quantify the effectiveness of different models with a similar goal. Some tradeoffs cannot be quantified and, hence, they are mentioned explicitly in the qualitative analysis, which is done throughout the paper. By compiling and analyzing a large quantum of research details in one place with all the data sets, model architectures, and results, we aimed to provide a one-stop solution to beginners and current researchers interested in this field.
PubMed: 35572951
DOI: 10.1002/cdt3.17 -
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 -
Taiwan Journal of Ophthalmology 2020The coronavirus disease 2019 (COVID 19) pandemic has presented major challenges to ophthalmologists. Reports have shown that ocular manifestations can be the first... (Review)
Review
Ocular manifestation, comorbidities, and detection of severe acute respiratory syndrome-coronavirus 2 from conjunctiva in coronavirus disease 2019: A systematic review and meta-analysis.
The coronavirus disease 2019 (COVID 19) pandemic has presented major challenges to ophthalmologists. Reports have shown that ocular manifestations can be the first presenting symptoms of COVID 19 infection and conjunctiva may be a portal of entry for the severe acute respiratory syndrome (SARS) associated coronavirus 2 (SARS CoV 2). The purpose of this article is to provide general guidance for ophthalmologists to understand the prevalence of ocular presentation in COVID 19 patients and to reduce the risk of transmission during practice. Relevant studies published in the period of November 1, 2019, and July 15, 2020, regarding ocular manifestations of COVID 19 and detection of SARS CoV 2 in the eye were included in this systematic review and meta analysis. The pooled prevalence of the ocular manifestations has been estimated at 7% (95% confidence interval [CI]: 0.03-0.10) among COVID 19 patients. The pooled detection rate of SARS CoV 2 from conjunctiva was low (1%, 95% CI: 0.00-0.03). Conjunctival symptoms were the most common ocular manifestations in COVID 19, but the positive detection rate of the SARS CoV 2 virus by reverse transcription-polymerase chain reaction of conjunctival tears or secretions remained low. No study has shown a definite transmission of COVID 19 through ocular mucosa or secretions. In summary, ocular manifestations in COVID 19 patients commonly comprise ocular surface symptoms. Although a low prevalence of ocular symptoms was encountered among patients infected by SARS CoV 2, it is imperative for all ophthalmologists to understand the full spectrum of COVID 19 symptoms or signs including those of the eyes as well as to adopt appropriate protective measures during clinical practice.
PubMed: 33110745
DOI: 10.4103/tjo.tjo_53_20 -
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 -
Clinical Infectious Diseases : An... Dec 2021We aimed to review the evidence from studies relating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) culture with the results of reverse-transcription...
BACKGROUND
We aimed to review the evidence from studies relating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) culture with the results of reverse-transcription polymerase chain reaction (RT-PCR) and other variables that may influence the interpretation of the test, such as time from symptom onset.
METHODS
We searched LitCovid, medRxiv, Google Scholar, and the World Health Organization coronavirus disease 2019 (COVID-19) database for COVID-19 up to 10 September 2020. We included studies attempting to culture or observe SARS-CoV-2 in specimens with RT-PCR positivity. Studies were dual-extracted and the data summarized narratively by specimen type. Where necessary, we contacted corresponding authors of included papers for additional information. We assessed quality using a modified Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS 2) risk-of-bias tool.
RESULTS
We included 29 studies reporting attempts at culturing, or observing tissue infection by, SARS-CoV-2 in sputum, nasopharyngeal or oropharyngeal, urine, stool, blood, and environmental specimens. The quality of the studies was moderate with lack of standardized reporting. The data suggest a relationship between the time from onset of symptom to the timing of the specimen test, cycle threshold (Ct), and symptom severity. Twelve studies reported that Ct values were significantly lower and log copies higher in specimens producing live virus culture. Two studies reported that the odds of live virus culture were reduced by approximately 33% for every 1-unit increase in Ct. Six of 8 studies reported detectable RNA for >14 days, but infectious potential declined after day 8 even among cases with ongoing high viral loads. Four studies reported viral culture from stool specimens.
CONCLUSIONS
Complete live viruses are necessary for transmission, not the fragments identified by PCR. Prospective routine testing of reference and culture specimens and their relationship to symptoms, signs, and patient co-factors should be used to define the reliability of PCR for assessing infectious potential. Those with high Ct are unlikely to have infectious potential.
Topics: COVID-19; Humans; Prospective Studies; RNA, Viral; Reproducibility of Results; SARS-CoV-2; Serologic Tests
PubMed: 33270107
DOI: 10.1093/cid/ciaa1764 -
Annals of Saudi Medicine 2022Coronavirus disease 2019 (COVID-19) presents mainly with mild symptoms and involvement of the respiratory system. Acute pancreatitis has also been reported during the... (Review)
Review
BACKGROUND
Coronavirus disease 2019 (COVID-19) presents mainly with mild symptoms and involvement of the respiratory system. Acute pancreatitis has also been reported during the course of COVID-19.
OBJECTIVE
Our aim is to review and analyze all reported cases of COVID-19 associated acute pancreatitis, reporting the demographics, clinical characteristics, laboratory and imaging findings, comorbidities and outcomes.
DATA SOURCES
We conducted a systematic search of Pubmed/MEDLINE, SciELO and Google Scholar to identify case reports and case series, reporting COVID-19 associated acute pancreatitis in adults.
STUDY SELECTION
There were no ethnicity, gender or language restrictions. The following terms were searched in combination:"COVID-19" OR "SARS-CoV-2" OR "Coronavirus 19" AND "Pancreatic Inflammation" OR "Pancreatitis" OR "Pancreatic Injury" OR "Pancreatic Disease" OR "Pancreatic Damage". Case reports and case series describing COVID-19 associated acute pancreatitis in adults were included. COVID-19 infection was established with testing of nasal and throat swabs using reverse transcription polymerase chain reaction. The diagnosis of acute pancreatitis was confirmed in accordance to the revised criteria of Atlanta classification of the Acute Pancreatitis Classification Working Group. Exclusion of other causes of acute pancreatitis was also required for the selection of the cases.
DATA EXTRACTION
The following data were extracted from each report: the first author, year of publication, age of the patient, gender, gastrointestinal symptoms due to acute pancreatitis, respiratory-general symptoms, COVID-19 severity, underlying diseases, laboratory findings, imaging features and outcome.
DATA SYNTHESIS
Finally, we identified and analyzed 31 articles (30 case reports and 1 case series of 2 cases), which included 32 cases of COVID-19 induced acute pancreatitis.
CONCLUSION
COVID-19 associated acute pancreatitis affected mostly females. The median age of the patients was 53.5 years. Concerning laboratory findings, lipase and amylase were greater than three times the ULN while WBC counts and CRP were elevated in the most of the cases. The most frequent gastrointestinal, respiratory and general symptom was abdominal pain, dyspnea and fever, respectively. The most common imaging feature was acute interstitial edematous pancreatitis and the most frequent comorbidity was arterial hypertension while several patients had no medical history. The outcome was favorable despite the fact that most of the patients experienced severe and critical illness.
LIMITATIONS
Our results are limited by the quality and extent of the data in the reports. More specifically, case series and case reports are unchecked, and while they can recommend hypotheses they are not able to confirm robust associations.
CONFLICT OF INTEREST
None.
Topics: Acute Disease; Adult; COVID-19; Critical Illness; Female; Humans; Male; Middle Aged; Pancreatitis; SARS-CoV-2
PubMed: 35933608
DOI: 10.5144/0256-4947.2022.276