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VirulenceFinder for Enterococcus faecium and Enterococcus lactis: an enhanced database for detection of putative virulence markers by using whole-genome sequencing data.
No full text20.500.12530/87854Enterococcus faecium (Efm) is a leading cause of hospital-associated (HA) infections, often enriched in putative virulence markers (PVMs). Recently, the Efm clade B was assigned as Enterococcus lactis (Elts), which usually lack HA-Efm infection markers. Available databases for extracting PVM are incomplete and/or present an intermix of genes from Efm and Enterococcus faecalis, with distinct virulence profiles. In this study, we constructed a new database containing 27 PVMs [acm, scm, sgrA, ecbA, fnm, sagA, hylEfm, ptsD, orf1481, fms15, fms21-fms20 (pili gene cluster 1, PGC-1), fms14-fms17-fms13 (PGC-2), empA-empB-empC (PGC-3), fms11-fms19-fms16 (PGC-4), ccpA, bepA, gls20-glsB1, and gls33-glsB] from nine reference genomes (seven Efm + two Elts). The database was validated against these reference genomes and further evaluated using a collection of well-characterized Efm (n = 43) and Elts (n = 7) control strains, by assessing PVM presence/absence and its variants together with a genomic phylogeny constructed as single-nucleotide polymorphisms. We found a high concordance between the phylogeny and in silico findings of the PVM, with Elts clustering separately and mostly carrying Elts-specific PVM gene variants. Based on our validation results, we recommend using the database with raw reads instead of assemblies to avoid missing gene variants. This newly constructed database of 27 PVMs will enable a more comprehensive characterization of Efm and Elts based on WGS data. The developed database exhibits scalability and boasts a range of applications in public health, including diagnostics, outbreak investigations, and epidemiological studies. It can be further used in risk assessment for distinguishing between safe and unsafe enterococci.IMPORTANCEThe newly constructed database, consisting of 27 putative virulence markers, is highly scalable and serves as a valuable resource for the comprehensive characterization of these closely related species using WGS data. It holds significant potential for various public health applications, including hospital outbreak investigations, surveillance, and risk assessment for probiotics and feed additives
Long-term results of total hip arthroplasty in severe congenital hip disease: A ten- to 20-year follow-up study.
No full textThe impact of bone deformities, previous surgeries, and the surgical technique in total hip arthroplasty (THA) for congenital dislocation of the hip (CDH) at a long-term has not been clearly defined yet. In this single-centre observational study we sought to assess patients undergoing THA due to osteoarthritis secondary to severe CDH with low or high dislocation ten- to 20-years after surgery. To determine this purpose, we assessed: (1) THA-related complications and reoperations; (2) the clinical outcome, patients' satisfaction and radiological results; and (3) the possible risk factors for reoperation with particular attention to the surgical technique and the influence of prior surgeries. We hypothesized that an anatomical reconstruction of the hip would decrease the reoperations rates in patients undergoing THA with severe CDH. Seventy-five patients (85 hips) operated between 1999 and 2012 at our large tertiary hospital were analyzed. Fifty-six hips were diagnosed as low dislocation (group 1) and 29 hips as high dislocation (group 2). The existence of prior surgeries was frequent: group 1, pelvic osteotomies 6 hips, femoral osteotomies 7, tectoplasty (shelf) 6, resection arthroplasty 1 and lowering of the greater trochanter 1; group 2 included pelvic osteotomies 10 hips, femoral osteotomies 10, and a femoral lengthening 2. The number of additional procedures during THA was: group 1 (19/56 [34%]), acetabular roof bone autograft 8 hips, acetabular medial wall autograft 2, hardware removal 6, extended femoral osteotomy 2, and a femoral shortening 1; group 2 (20/29 [69%]), acetabular bone autograft 12 hips, medial autograft 1, hardware removal 1, extended femoral osteotomy 2, and a femoral shortening 4 hips. The clinical and the radiological analysis were compared in both groups for a minimum follow-up of ten years. Cox regression models were used to detect risk factors for reoperation. Nine patients (13.8%) required reoperation for the following reasons: cup loosening (5 hips), periprosthetic femoral fracture (3) and stem loosening (1); seven had prior surgeries. The 12-year survival rate for reoperation for any reason was 96.3% (95% confidence interval [CI] 91.2-100) in group 1 and 75.7% (95% CI, 65.8-90.8) in group 2 (p=0.003). Patients with high dislocation (p=0.02, hazard ratio [HR]: 6.25, 95% CI, 1.26-30.9) and those with an acetabular component inclination placed out of the target zone between 35° and 50° (p=0.03, HR: 4.27, 95% CI, 1.13-16.1) had a higher risk of reoperation. An optimal placement of the acetabular component decreased the reoperation rates in patients undergoing THA for severe CDH. Hips with high dislocation and the existence of prior surgery can affect THA implantation. III; retrospective; comparative
Association between physician burnout and patient safety: study protocol for an overview of systematic reviews and meta-analyses.
No full text20.500.12530/87907Burnout, a disorder caused by chronic stress at work, involves emotional exhaustion, depersonalisation and reduced professional efficacy. The prevalence of burnout appears to be high among physicians worldwide. Burnout may affect different dimensions of healthcare, such as patient safety. Several systematic reviews and meta-analyses have examined the relationship between physician burnout and quality of care, although with some controversial results. To our knowledge, no overview of systematic reviews and meta-analyses has been conducted, specifically evaluating physician burnout, patient safety and other relevant aspects of quality of care. The main objective of this study will be to evaluate the available evidence of the association between physician burnout and patient safety. An overview of systematic reviews and meta-analyses will be carried out. Systematic reviews with or without meta-analyses assessing the relationship between burnout in physicians and quality of care will be included. The primary outcome will be patient safety (ie, the occurrence of any adverse event related to healthcare which could have resulted, or did result, in unnecessary harm to patients). Secondary outcomes will be patient satisfaction and professionalism. Literature searches will be conducted (from their inception onwards) in PubMed/MEDLINE, EMBASE and Cochrane Database of Systematic Reviews. Two researchers will select studies that meet the predefined eligibility criteria and proceed to extract information from each included study. The methodological characteristics, measures of association and qualitative conclusions of the reviews will be assessed. The methodological quality of each review will also be analysed using the AMSTAR-2 (A MeaSurement Tool to Assess systematic Reviews) tool. A descriptive synthesis will be carried out using evidence tables and graphs. The proposed research mainly involves the analysis of existing studies, approval from a research ethics committee is not required. This overview of systematic reviews will help to gain a better understanding of the association between physician burnout and patient safety. Our findings could support future research, recommendations and policies in this area. We plan to publish the full study in a peer-reviewed journal. Open Science Framework: https://osf.io/wr73u/
Sex-Based Differences in the Causes of Myocardial Ischemia in Patient With Chronic Coronary Syndromes Undergoing Angiography: Insights From the AID Angio- Study
No full textThe RICA-2 registry: design and baseline characteristics of the first 1,000 patients.
No full text20.500.12530/87897Heart failure (HF) is a syndrome of epidemic proportions and one of the main reasons for hospital admission. Patient registries provide real-world clinical practice information which is complementary to clinical trials. RICA-2 is a registry of the Spanish Society of Internal Medicine. Its main goal is to know the clinical and epidemiological characteristics and prognostic factors of patients with HF treated in Internal Medicine Departments. The objective of this study is to present the design of the RICA-2, the baseline characteristics of the first 1000 patients included and their comparison with those of the historical cohort of the RICA registry. Observational, multicentre and prospective study of patients with HF with the following inclusion criteria: age equal to or greater than 18 years old, diagnosis of HF according to the European Guidelines, indistinct inclusion in decompensation or stable phase, of patients with de novo HF or chronic HF, regardless of left ventricular ejection fraction, aetiology and comorbidities. RICA-2 patients have advanced age (83 years old) and 51% are women. The comorbidity burden is higher than in the RICA registry (5 points in the Charlson comorbidity index), with predominating chronic decompensated HF (74%), hypertensive aetiology (39%) and preserved ejection fraction (52%). Most patients are pre-frail or vulnerable and are at risk of malnutrition. The RICA-2 represents a contemporary cohort of patients that will provide us with clinical, epidemiological and prognostic information on patients with acute and chronic HF treated in Internal Medicine
Longitudinal outcomes of obeticholic acid therapy in ursodiol-nonresponsive primary biliary cholangitis: Stratifying the impact of add-on fibrates in real-world practice.
No full text20.500.12530/87852Suboptimal response to ursodeoxycholic acid occurs in 40% of primary biliary cholangitis (PBC) patients, affecting survival. Achieving a deep response (normalisation of alkaline phosphatase [ALP] and bilirubin ≤0.6 upper limit of normal) improves survival. Yet, the long-term effectiveness of second-line treatments remains uncertain. To evaluate the long-term effectiveness of obeticholic acid (OCA) ± fibrates. Focusing on biochemical response (ALP ≤1.67 times the upper limit of normal, with a decrease of at least 15% from baseline and normal bilirubin levels), normalisation of ALP, deep response and biochemical remission (deep response plus aminotransferase normalisation). We conducted a longitudinal, observational, multicentre study involving ursodeoxyccholic acid non-responsive PBC patients (Paris-II criteria) from Spain and Portugal who received OCA ± fibrates. Of 255 patients, median follow-up was 35.1 months (IQR: 20.2-53). The biochemical response in the whole cohort was 47.2%, 61.4% and 68.6% at 12, 24 and 36 months. GLOBE-PBC and 5-year UK-PBC scores improved (p Triple therapy was superior in achieving therapeutic goals in UDCA-nonresponsive PBC. Decompensation was linked to pre-existing portal hypertension
COFAITH and COMFA: A Collective Roadmap for Past and Future Food Allergy Clinical Trials and Observational Research on Interventions.
No full text20.500.12530/8789
Systematic Minigene-Based Splicing Analysis and Tentative Clinical Classification of 52 CHEK2 Splice-Site Variants.
No full textDisrupted pre-mRNA splicing is a frequent deleterious mechanism in hereditary cancer. We aimed to functionally analyze candidate spliceogenic variants of the breast cancer susceptibility gene CHEK2 by splicing reporter minigenes. A total of 128 CHEK2 splice-site variants identified in the Breast Cancer After Diagnostic Gene Sequencing (BRIDGES) project (https://cordis.europa.eu/project/id/634935) were analyzed with MaxEntScan and subsetted to 52 variants predicted to impact splicing. Three CHEK2 minigenes, which span all 15 exons, were constructed and validated. The 52 selected variants were then genetically engineered into the minigenes and assayed in MCF-7 (human breast adenocarcinoma) cells. Of 52 variants, 46 (88.5%) impaired splicing. Some of them led to complex splicing patterns with up to 11 different transcripts. Thirty-four variants induced splicing anomalies without any trace or negligible amounts of the full-length transcript. A total of 89 different transcripts were annotated, which derived from different events: single- or multi-exon skipping, alternative site-usage, mutually exclusive exon inclusion, intron retention or combinations of the abovementioned events. Fifty-nine transcripts were predicted to introduce premature termination codons, 7 kept the original open-reading frame, 5 removed the translation start codon, 6 affected the 5'UTR (Untranslated Region), and 2 included missense variations. Analysis of variant c.684-2A > G revealed the activation of a non-canonical TG-acceptor site and exon 6 sequences critical for its recognition. Incorporation of minigene read-outs into an ACMG/AMP (American College of Medical Genetics and Genomics/Association for Molecular Pathology)-based classification scheme allowed us to classify 32 CHEK2 variants (27 pathogenic/likely pathogenic and 5 likely benign). However, 20 variants (38%) remained of uncertain significance, reflecting in part the complex splicing patterns of this gene
Diagnosis and approach of pseudohypoparathyroidism type 1A and related disorders during long term follow-up: a case report
No full textObjectives: Pseudohypoparathyroidism type 1A (PHP1A) encompasses the association of resistance to multiple hormones, features of Albright hereditary osteodystrophy and decreased Gs alpha activity. Little is known about the early signs of PHP1A, with a delay in diagnosis. We report two PHP1A cases and their clinical and biochemical findings during a 20-year follow-up. Case presentation: Clinical suspicion was based on obesity, TSH resistance and ectopic ossifications which appeared several months before PTH resistance, at almost 3 years of age. Treatment with levothyroxine, calcitriol and calcium was required in both patients. DNA sequencing of GNAS gene detected a heterozygous pathogenic variant within exon 7 (c.569_570delAT) in patient one and a deletion from XLAS to GNAS-exon 5 on the maternal allele in patient 2. In patient 1, ectopic ossifications that required surgical excision were found. Noticeably, patient 2 displayed adult short stature, intracranial calcifications and psychomotor delay. In terms of weight, despite early diagnosis of obesity, dietary measures were established successfully in both cases. Conclusions: GNAS mutations should be considered in patients with obesity, ectopic ossifications and TSH resistance presented in early infancy. These cases emphasize the highly heterogeneous clinical picture PHP1A patients may present, especially in terms of final height and cognitive impairment