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Abstract We assessed whether multiplex real-time PCR plus conventional microbiological testing is safe and more effective than conventional microbiological testing alone for reducing antibiotic use in community-acquired pneumonia (CAP). In this randomised trial, we recruited adults hospitalised with CAP at four Spanish hospitals. Patients were randomly assigned (1:1) to undergo either multiplex real-time PCR in non-invasive respiratory samples plus conventional microbiological testing or conventional microbiological testing alone. The primary endpoint was antibiotic use measured by days of antibiotic therapy (DOT). Between February 20, 2020, and April 24, 2023, 242 patients were enrolled; 119 were randomly assigned to multiplex real-time PCR plus conventional microbiological testing and 123 to conventional microbiological testing alone. All but one of the patients allocated to multiplex real-time PCR plus conventional microbiological testing underwent PCR, which was performed in sputum samples in 77 patients (65.2%) and in nasopharyngeal swabs in 41 (34.7%). The median DOT was 10.04 (IQR 7.98, 12.94) in the multiplex PCR plus conventional microbiological testing group and 11.33 (IQR 8.15, 16.16) in the conventional microbiological testing alone group (difference −1.04; 95% CI, −2.42 to 0.17; p = 0.093). No differences were observed in adverse events and 30-day mortality. Our findings do not support the routine implementation of multiplex real-time PCR in the initial microbiological testing in hospitalised patients with CAP. Clinicaltrials.gov registration: NCT04158492.

Abstract Background Research Electronic Data CAPture (REDCap) is a web application for creating and managing online surveys and databases. Clinical data management is an essential process before performing any statistical analysis to ensure the quality and reliability of study information. Processing REDCap data in R can be complex and often benefits from automation. While there are several R packages available for specific tasks, none offer an expansive approach to data management. Results The REDCapDM is an R package for accessing and managing REDCap data. It imports data from REDCap to R using either an API connection or the files in R format exported directly from REDCap. It has several functions for data processing and transformation, and it helps to generate and manage queries to clarify or resolve discrepancies found in the data. Conclusion The REDCapDM package is a valuable tool for data scientists and clinical data managers who use REDCap and R. It assists in tasks such as importing, processing, and quality-checking data from their research studies.

Abstract In this study, we modelled the incidence of COVID-19 cases and hospitalisations by basic health areas (ABS) in Catalonia. Spatial, temporal and spatio-temporal incidence trends were described using estimation methods that allow to borrow strength from neighbouring areas and time points. Specifically, we used Bayesian hierarchical spatio-temporal models estimated with Integrated Nested Laplace Approximation (INLA). An exploratory analysis was conducted to identify potential ABS factors associated with the incidence of cases and hospitalisations. High heterogeneity in cases and hospitalisation incidence was found between ABS and along the waves of the pandemic. Urban areas were found to have a higher incidence of COVID-19 cases and hospitalisations than rural areas, while socio-economic deprivation of the area was associated with a higher incidence of hospitalisations. In addition, full vaccination coverage in each ABS showed a protective effect on the risk of COVID-19 cases and hospitalisations.

Abstract Background The use of remote consultation modalities has exponentially grown in the past few years, particularly since the onset of the COVID-19 pandemic. Although a huge body of the literature has described the use of phone (tele) and video consultations, very few of the studies correspond to randomized controlled trials, and none of them has assessed the safety of these consultation modalities as the primary objective. The primary objective of this trial was to assess the safety of remote consultations (both video and teleconsultation) in the follow-up of patients in the hospital setting. Methods Multicenter, randomized controlled trial being conducted in four centers of an administrative healthcare area in Catalonia (North-East Spain). Participants will be screened from all individuals, irrespective of age and sex, who require follow-up in outpatient consultations of any of the departments involved in the study. Eligibility criteria have been established based on the local guidelines for screening patients for remote consultation. Participants will be randomly allocated into one of the two study arms: conventional face-to-face consultation (control) and remote consultation, either teleconsultation or video consultation (intervention). Routine follow-up visits will be scheduled at a frequency determined by the physician based on the diagnostic and therapy of the baseline disease (the one triggering enrollment). The primary outcome will be the number of adverse reactions and complications related to the baseline disease. Secondary outcomes will include non-scheduled visits and hospitalizations, as well as usability features of remote consultations. All data will either be recorded in an electronic clinical report form or retrieved from local electronic health records. Based on the complications and adverse reaction rates reported in the literature, we established a target sample size of 1068 participants per arm. Recruitment started in May 2022 and is expected to end in May 2024. Discussion The scarcity of precedents on the assessment of remote consultation modalities using randomized controlled designs challenges making design decisions, including recruitment, selection criteria, and outcome definition, which are discussed in the manuscript. Trial registration NCT05094180. The items of the WHO checklist for trial registration are available in Additional file 1. Registered on 24 November 2021.

Background: The differential diagnosis between patients with celiac disease (CD) and non-celiac gluten sensitivity (NCGS) is difficult when a gluten-free diet (GFD) has been initiated before the diagnostic work-up. Isolated increases in TCRγδ+ and celiac lymphogram (increased TCRγδ+ plus decreased CD3−) may enable differential diagnosis in this challenging clinical setting. This study evaluated: (1) the accuracy of %TCRγδ+ and celiac lymphogram for diagnosing CD before and after GFD and for differentiation with NCGS; (2) TCRγδ+ kinetics at baseline and after starting GFD in both CD and NCGS. Methods: The inclusion criteria were patients with CD (n = 104), NCGS (n = 37), and healthy volunteers (n = 18). An intestinal biopsy for intraepithelial lymphogram by flow cytometry was performed at baseline and after GFD. The optimal cutoff for CD diagnostic accuracy was established by maximizing the Youden index and via logistic regression. Results: %TCRγδ+ showed better diagnostic accuracy than celiac lymphogram for identifying CD before and after GFD initiation. With a cutoff > 13.31, the accuracy for diagnosing CD in patients under GFD was 0.88 [0.80–0.93], whereas the accuracy for diagnosing NCGS (%TCRγδ+ ≤ 13.31) was 0.84 [0.76–0.89]. The percentage of TCRγδ+ cells showed differential kinetics between CD (baseline 22.7% [IQR, 16.4–33.6] vs. after GFD 26.4% [IQR, 17.8–36.8]; p = 0.026) and NCGS (baseline 9.4% [IQR, 4.1–14.6] vs. after GFD 6.4% [IQR, 3.2–11]; p = 0.022). Conclusion: TCRγδ+ T cell assessment accurately diagnoses CD before and after a GFD. Increased TCRγδ+ was maintained in the long term after GFD in CD but not in NCGS. Altogether, this suggests the potential usefulness of this marker for the differential diagnosis of these two entities in patients on a GFD.

Abstract Background Stenosis is one of the most common complications in patients with Crohn’s disease (CD). Endoscopic balloon dilation (EBD) is the treatment of choice for a short stenosis adjacent to the anastomosis from previous surgery. Self-expandable metal stents (SEMS) may be a suitable treatment option for longer stenoses. To date, however, there is no scientific evidence as to whether endoscopic (EBD/SEMS) or surgical treatment is the best approach for de novo or primary stenoses that are less than 10 cm in length. Methods/design Exploratory study as “proof-of-concept”, multicentre, open-label, randomized trial of the treatment of de novo stenosis in the CD; endoscopic treatment (EBD/SEMS) vs surgical resection (SR). The type of endoscopic treatment will initially be with EDB; if a therapeutic failure occurs, then a SEMS will be placed. We estimate 2 years of recruitment and 1 year of follow-up for the assessment of quality of life, costs, complications, and clinical recurrence. After the end of the study, patients will be followed up for 3 years to re-evaluate the variables over the long term. Forty patients with de novo stenosis in CD will be recruited from 15 hospitals in Spain and will be randomly assigned to the endoscopic or surgical treatment groups. The primary aim will be the evaluation of the patient quality of life at 1 year follow-up (% of patients with an increase of 30 points in the 32-item Inflammatory Bowel Disease Questionnaire (IBDQ-32). The secondary aim will be evaluation of the clinical recurrence rate, complications, and costs of both treatments at 1-year follow-up. Discussion The ENDOCIR trial has been designed to determine whether an endoscopic or surgical approach is therapeutically superior in the treatment of de novo stenosis in CD. Trial registration ClinicalTrials.gov NCT 04330846. Registered on 1 April 1 2020. https://clinicaltrials.gov/ct2/home

Information on the long-term effects of non-restrictive antimicrobial stewardship (AMS) strategies is scarce. We assessed the effect of a stepwise, multimodal, non-restrictive AMS programme on broad-spectrum antibiotic use in the intensive care unit (ICU) over an 8-year period. Components of the AMS were progressively implemented. Appropriateness of antibiotic prescribing was also assessed by monthly point-prevalence surveys from 2013 onwards. A Poisson regression model was fitted to evaluate trends in the reduction of antibiotic use and in the appropriateness of their prescription. From 2011 to 2019, a total of 12,466 patients were admitted to the ICU. Antibiotic use fell from 185.4 to 141.9 DDD per 100 PD [absolute difference, −43.5 (23%), 95% CI −100.73 to 13.73; p = 0.13] and broad-spectrum antibiotic fell from 41.2 to 36.5 [absolute difference, −4.7 (11%), 95% CI −19.58 to 10.18; p = 0.5]. Appropriateness of antibiotic prescribing rose by 11% per year [IRR: 0.89, 95% CI 0.80 to 1.00; p = 0.048], while broad-spectrum antibiotic use showed a dual trend, rising by 22% until 2015 and then falling by 10% per year since 2016 [IRR: 0.90, 95% CI 0.81 to 0.99; p = 0.03]. This stepwise, multimodal, non-restrictive AMS achieved a sustained reduction in broad-spectrum antibiotic use in the ICU and significantly improved appropriateness of antibiotic prescribing.

Metabolic syndrome (MetS) is associated with alterations of lipoprotein structure and function that can be characterized with advanced lipoprotein testing (ADLT). The effect of the Mediterranean diet (MedDiet) and weight loss on the lipoprotein subclass profile has been scarcely studied. Within the PREDIMED-Plus randomized controlled trial, a sub-study conducted at Bellvitge Hospital recruiting center evaluated the effects of a weight loss program based on an energy-reduced MedDiet (er-MedDiet) and physical activity (PA) promotion (intervention group) compared with energy-unrestricted MedDiet recommendations (control group) on ADLT-assessed lipoprotein subclasses. 202 patients with MetS (n = 107, intervention; n = 95, control) were included. Lipid profiles were determined, and ADLT was performed at baseline, 6, and 12 months. Linear mixed models were used to assess the effects of intervention on lipoprotein profiles. Compared to the control diet, at 12 months, the er-MedDiet+PA resulted in a significant additional 4.2 kg of body weight loss, a decrease in body mass index by 1.4 kg/m2, reduction in waist circumference by 2.2 cm, decreased triglycerides, LDL-cholesterol and non-HDL-cholesterol, and increased HDL-cholesterol. In er-MedDiet+PA participants, ADLT revealed a decrease in small dense-LDL-cholesterol (sd-LDL-C), intermediate-density lipoproteins, VLDL-triglyceride, and HDL-Triglyceride, and an increase in large LDL and large VLDL particles. In conclusion, compared to an ad libitum MedDiet (control group), er-MedDiet+PA decreased plasma triglycerides and the triglyceride content in HDL and VLDL particles, decreased sd-LDL-C, and increased large LDL particles, indicating beneficial changes against cardiovascular disease.

ABSTRACT We investigated whether the difference of antigen tube 2 (TB2) minus antigen tube 1 (TB1) (TB2−TB1) of the QuantiFERON-TB gold plus test, which has been postulated as a surrogate for the CD8+ T-cell response, could be useful in identifying recent tuberculosis (TB) exposure. We looked at the interferon gamma (IFN-γ) responses and differences in TB2 and TB1 tubes for 686 adults with QFT-plus positive test results. These results were compared among groups with high (368 TB contacts), low (229 patients with immune-mediated inflammatory diseases [IMID]), and indeterminate (89 asylum seekers or people from abroad [ASPFA]) risks of recent TB exposure. A TB2−TB1 value >0.6 IU·ml−1 was deemed to indicate a true difference between tubes. In the whole cohort, 13.6%, 10.9%, and 11.2% of cases had a TB2>TB1 result in the contact, IMID, and ASPFA groups, respectively (P = 0.591). The adjusted odds ratios (aORs) for an association between a TB2−TB1 result of >0.6 IU·ml−1 and risk of recent exposure versus contacts were 0.71 (95% confidence interval [CI], 0.31 to 1.61) for the IMID group and 0.86 (95% CI, 0.49 to 1.52) for the ASPFA group. In TB contact subgroups, 11.4%, 15.4%, and 17.7% with close, frequent, and sporadic contact had a TB2>TB1 result (P = 0.362). The aORs versus the close subgroup were 1.29 (95% CI, 0.63 to 2.62) for the frequent subgroup and 1.55 (95% CI, 0.67 to 3.60) for the sporadic subgroup. A TB2−TB1 difference of >0.6 IU·ml−1 was not associated with increased risk of recent TB exposure, which puts into question the clinical potential as a proxy marker for recently acquired TB infection. IMPORTANCE Contact tuberculosis tracing is essential to identify recently infected people, who therefore merit preventive treatment. However, there are no diagnostic tests that can determine whether the infection is a result of a recent exposure or not. It has been suggested that by using the QuantiFERON-TB gold plus, an interferon gamma (IFN-γ) release assay, a difference in IFN-γ production between the two antigen tubes (TB2 minus TB1) of >0.6 IU·ml−1 could serve as a proxy marker for recent infection. In this large multinational study, infected individuals could not be classified according to the risk of recent exposure based on differences in IFN-γ in TB1 and TB2 tubes that were higher than 0.6 IU·ml−1. QuantiFERON-TB gold plus is not able to distinguish between recent and remotely acquired tuberculosis infection, and it should not be used for that purpose in contact tuberculosis tracing.

Meta-analysis is a useful tool in clinical research, as it combines the results of multiple clinical studies to improve precision when answering a particular scientific question. While there has been a substantial increase in publications using meta-analysis in various clinical research topics, the number of published meta-analyses in metabolomics is significantly lower compared to other omics disciplines. Metabolomics is the study of small chemical compounds in living organisms, which provides important insights into an organism's phenotype. However, the wide variety of compounds and the different experimental methods used in metabolomics make it challenging to perform a thorough meta-analysis. Additionally, there is a lack of consensus on reporting statistical estimates, and the high number of compound naming synonyms further complicates the process. Easy-Amanida is a new tool that combines two R packages, "amanida" and "webchem", to enable meta-analysis of aggregate statistical data, like p-value and fold-change, while ensuring the compounds naming harmonization. The Easy-Amanida app is implemented in Shiny, an R package add-on for interactive web apps, and provides a workflow to optimize the naming combination. This article describes all the steps to perform the meta-analysis using Easy-Amanida, including an illustrative example for interpreting the results. The use of aggregate statistics metrics extends the use of Easy-Amanida beyond the metabolomics field.

Abstract Background Less invasive monitoring, such as radial arterial pulse contour analysis (ProAQT® sensor), represents an alternative when hemodynamic monitoring is necessary to guide postoperative management and invasive monitoring is not technically feasible. The aim of the study is to evaluate the accuracy of the ProAQT® sensor cardiac output measurements in comparison with Pulmonary Artery Catheter (PAC) during the postoperative course of patients who underwent cardiac surgery with cardiopulmonary bypass. Case presentation Prospective observational study in a Surgical Intensive Care Unit of a tertiary university hospital. Ten patients with a mean age of 73.5 years were included. The main comorbidities were hypertension, diabetes, dyslipidemia and the preoperative left ejection fraction was 43.8 ± 14.5%. Regarding the type of surgery, six patients underwent valve surgery, two underwent coronary artery bypass grafting and two underwent aortic surgery. The cardiac index measured simultaneously by the ProAQT® sensor was compared with the PAC. The parameters were evaluated at predefined time points during the early postoperative courses (6 h, 12 h, 24 h, 48 h and 72 h). The degree of agreement with the cardiac index between the PAC and the ProAQT® sensor along the time points was measured using the concordance correlation coefficient, Bland–Altman analysis, and four-quadrant plot. Sixty-three pairs of measurements were analyzed. We showed that measurements of cardiac index were slightly higher with PAC (β ̂ = − 0.146, p-value = 0.094). The concordance correlation coefficient for the additive model of cardiac index was 0.64 (95% Confidence Interval: 0.36, 0.82), indicating a high concordance between both sensors. Bland-Altmann analysis showed a mean bias of 0.45 L·min−1·m−2, limits of agreement from − 1.65 to 2.3 L·min−1·m−2, and percentage of error was 82.5%. Four-quadrant plot of changes in cardiac index showed a good concordance rate (75%), which increases after applying the exclusion zone (87%). Conclusions In patients undergoing cardiac surgery, the ProAQT® sensor may be useful to monitor cardiac index during the postoperative period, especially when more invasive monitoring is not possible.

Abstract Background It is unclear whether the insertion of an axis-orienting double-pigtail plastic stent (DPS) through biliary lumen-apposing meal stent (LAMS) in EUS-guided choledochoduodenostomy (CDS) improves the stent patency. The aim of this study is to determine whether this technical variant offers a clinical benefit in EUS-guided biliary drainage (BD) for the management of distal malignant biliary obstruction. Methods/design This is a multicenter open-label, randomized controlled trial with two parallel groups. Eighty-four patients with malignant biliary obstruction will undergo EUS-BD (CDS type) using LAMS in 7 tertiary hospitals in Spain and will be randomized to the LAMS and LAMS plus DPS groups. The primary endpoint is the rate of recurrent biliary obstruction, as a stent dysfunction parameter, detected during follow-up. Secondary endpoints: technical and clinical success (reduction in bilirubin > 50% within 14 days of stent placement), safety, and others (number of reinterventions, time to biliary obstruction, prognostic factors, survival rate). Discussion The BAMPI trial has been designed to determine whether the addition of a coaxial axis-orienting DPS through LAMS is superior to LAMS alone to prevent stent dysfunction. Trial registration ClinicalTrials.gov NCT04595058 . Registered on October 14, 2020.