The objective of this study is to describe the general approaches to network meta-analysis that are available for quantitative data synthesis using R software. We conducted a network meta-analysis using two approaches: Bayesian and frequentist methods. The corresponding R packages were “gemtc” for the Bayesian approach and “netmeta” for the frequentist approach. In estimating a network meta-analysis model using a Bayesian framework, the “rjags” package is a common tool. “rjags” implements Markov chain Monte Carlo simulation with a graphical output. The estimated overall effect sizes, test for heterogeneity, moderator effects, and publication bias were reported using R software. The authors focus on two flexible models, Bayesian and frequentist, to determine overall effect sizes in network meta-analysis. This study focused on the practical methods of network meta-analysis rather than theoretical concepts, making the material easy to understand for Korean researchers who did not major in statistics. The authors hope that this study will help many Korean researchers to perform network meta-analyses and conduct related research more easily with R software.

BackgroundThe usefulness of the quick Sequential (Sepsis-related) Organ Failure Assessment (qSOFA) score in providing bedside criteria for early prediction of poor outcomes in patients with suspected infection remains controversial. We investigated the prognostic performance of a positive qSOFA score outside the intensive care unit (ICU) compared with positive systemic inflammatory response syndrome (SIRS) criteria.MethodsA systematic literature search was performed using MEDLINE, Embase, and the Cochrane Central Register of Controlled Trials. Data were pooled on the basis of sensitivity, specificity, and diagnostic OR. Overall test performance was summarized using a hierarchical summary ROC and the AUC. Meta-regression analysis was used to identify potential sources of bias.ResultsWe identified 23 studies with a total of 146,551 patients. When predicting in-hospital mortality in our meta-analysis, we identified pooled sensitivities of 0.51 for a positive qSOFA score and 0.86 for positive SIRS criteria, as well as pooled specificities of 0.83 for a positive qSOFA score and 0.29 for positive SIRS criteria. Discrimination for in-hospital mortality had similar AUCs between the two tools (0.74 vs. 0.71; P = 0.816). Using meta-regression analysis, an overall mortality rate ≥ 10% and timing of qSOFA score measurement could be significant sources of heterogeneity. For predicting acute organ dysfunction, although the AUC for a positive qSOFA score was higher than that for positive SIRS criteria (0.87 vs. 0.76; P < 0.001), the pooled sensitivity of positive qSOFA score was very low (0.47). In addition, a positive qSOFA score tended to be inferior to positive SIRS criteria in predicting ICU admission (0.63 vs. 0.78; P = 0.121).ConclusionsA positive qSOFA score had high specificity outside the ICU in early detection of in-hospital mortality, acute organ dysfunction, and ICU admission, but low sensitivity may have limitations as a predictive tool for adverse outcomes. Because between-study heterogeneity was highly represented among the studies, our results should be interpreted with caution.Electronic supplementary materialThe online version of this article (10.1186/s13054-018-1952-x) contains supplementary material, which is available to authorized users.

The objective of this paper is to describe general approaches of diagnostic test accuracy (DTA) that are available for the quantitative synthesis of data using R software. We conduct a DTA that summarizes statistics for univariate analysis and bivariate analysis. The package commands of R software were “metaprop” and “metabin” for sensitivity, specificity, and diagnostic odds ratio; forest for forest plot; reitsma of “mada” for a summarized receiver-operating characteristic (ROC) curve; and “metareg” for meta-regression analysis. The estimated total effect sizes, test for heterogeneity and moderator effect, and a summarized ROC curve are reported using R software. In particular, we focus on how to calculate the effect sizes of target studies in DTA. This study focuses on the practical methods of DTA rather than theoretical concepts for researchers whose fields of study were non-statistics related. By performing this study, we hope that many researchers will use R software to determine the DTA more easily, and that there will be greater interest in related research.

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Background Timely and accurate diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is crucial to reduce the risk of viral transmission. We investigated the diagnostic accuracy of rapid antigen detection tests (RADTs) in the diagnosis of SARS-CoV-2 infection. Methods A systematic literature search was performed using Pubmed, Embase, and the Cochrane Central Register. The sensitivity, specificity, diagnostic odds ratio (DOR), and a hierarchical summary receiver-operating characteristic curve (HSROC) of RADTs were pooled using meta-analysis. We used commercial and laboratory-developed reverse transcriptase-polymerase chain reaction (RT-PCR) as reference standards. Results We identified 24 studies comprising 14,188 patients. The overall pooled sensitivity, specificity, and DOR of RADTs for diagnosis of SARS-CoV-2 were 0.68 (95%CI, 0.59 to 0.76), 0.99 (95%CI, 0.99 to 1.00), and 426.70 (95% CI, 168.37 to 1081.65), respectively. RADTs and RT-PCR had moderate agreement with an estimated pooled Cohen's kappa statistic of 0.75 (95%CI, 0.74-0.77), and area under the HSROC of 0.98 (95%CI, 0.96 to 0.99). The pooled sensitivity of RADTs was significantly increased in subjects with viral load of Ct-value ≤25 or in those within 5 days after symptom onset than it was in subjects with lower viral loads or longer symptom duration. Conclusions The overall sensitivity of RADTs was inferior to that of the RT-PCR assay. The RADTs were more sensitive for samples of Ct-value ≤25 and might be suitable for subjects in the community within 5 days of symptom onset.

PurposePeramivir is the first intravenously administered neuramidase inhibitor for immediate delivery of an effective single-dose treatment in patients with influenza. However, limited data are available on intravenous (IV) peramivir treatment compared to oral oseltamivir for these patients.Materials and MethodsWith a systematic review and meta-analysis, we compared the efficacy of IV peramivir with oral oseltamivir for treatment of patients with seasonal influenza. MEDLINE, EMBASE, and Cochrane Central Register were searched for relevant clinical trials.ResultsA total of seven trials [two randomized controlled trials (RCTs) and five non-randomized observational trials] involving 1676 patients were finally analyzed. The total number of peramivir- and oseltamivir-treated patients was 956 and 720, respectively. Overall, the time to alleviation of fever was lower in the peramivir-treated group compared with the oseltamivir-treated group [mean difference (MD), -7.17 hours; 95% confidence interval (CI) -11.00 to -3.34]. Especially, pooled analysis of observational studies (n=4) and studies of outpatients (n=4) demonstrated the superiority of the peramivir-treated group (MD, -7.83 hours; 95% CI -11.81 to -3.84 and MD, -7.71 hours; 95% CI -11.61 to -3.80, respectively). Mortality, length of hospital stay, change in virus titer 48 hours after admission, and the incidence of adverse events in these patients were not significantly different between the two groups.ConclusionIV peramivir therapy might reduce the time to alleviation of fever in comparison with oral oseltamivir therapy in patients with influenza; however, we could not draw clear conclusions from a meta-analysis because of the few RCTs available and methodological limitations.

Background/Aims:Nursing home-acquired pneumonia (NHAP) is included under healthcare-associated pneumonia. However, the optimal treatment strategy for NHAP has been controversial in several studies. We evaluated the clinical features of NHAP compared to community-acquired pneumonia (CAP) in elderly patients admitted with pneumonia.Methods:This was a retrospective study in elderly patients aged ≥ 65 years with NHAP or CAP who were hospitalized at Jeju National University Hospital between January 2012 and April 2013.Results:A total of 209 patients were enrolled, and 58 (27.7%) had NHAP. The patients with NHAP were older, had more frequent central nervous system disorders, and showed worse clinical parameters. Potential drug-resistant pathogens were more frequently detected in the NHAP group (22.4% vs. 9.9%, p = 0.018), and the incidences of Pseudomonas aeruginosa and methicillin-resistant Staphylococcus aureus were 8.6% and 10.3%, respectively. In-hospital mortality occurred in 13 patients (22.4%) with NHAP and 17 patients (11.2%) with CAP (p = 0.039). In multivariate analyses, only higher pneumonia severity index (PSI) score was associated with increased mortality (p < 0.001), and the PSI score was higher in the NHAP group than that in the CAP group.Conclusions:Elderly patients admitted with NHAP showed more severe pneumonia at onset, higher rates of potentially drug-resistant pathogens, and worse clinical outcomes than those with CAP. However, higher in-hospital mortality in those with NHAP seemed to be related to the PSI score reflecting host factors and severity of pneumonia rather than the type of pneumonia or the presence of drug-resistant pathogens.