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BACKGROUND: The rapid expansion of Whole-Genome Sequencing has revolutionized the fields of clinical and food microbiology. However, its implementation as a routine laboratory technique remains challenging due to the growth of data at a faster rate than can be effectively analyzed and critical gaps in bioinformatics knowledge. RESULTS: To address both issues, CamPype was developed as a new bioinformatics workflow for the genomics analysis of sequencing data of bacteria, especially Campylobacter, which is the main cause of gastroenteritis worldwide making a negative impact on the economy of the public health systems. CamPype allows fully customization of stages to run and tools to use, including read quality control filtering, read contamination, reads extension and assembly, bacterial typing, genome annotation, searching for antibiotic resistance genes, virulence genes and plasmids, pangenome construction and identification of nucleotide variants. All results are processed and resumed in an interactive HTML report for best data visualization and interpretation. CONCLUSIONS: The minimal user intervention of CamPype makes of this workflow an attractive resource for microbiology laboratories with no expertise in bioinformatics as a first line method for bacterial typing and epidemiological analyses, that would help to reduce the costs of disease outbreaks, or for comparative genomic analyses. CamPype is publicly available at https://github.com/JoseBarbero/CamPype .

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Campylobacter spp. is the leading cause of foodborne gastrointestinal infections in humans worldwide. This study reports the first case of four family members who had contact with the same source of Campylobacter jejuni contamination with different results. Only the little siblings were infected by the same C. jejuni strain, but with different symptoms. Whereas the daughter was slightly affected with mild enteritis, the son suffered a longer campylobacteriosis followed with a perimyocarditis. This is the first case of the youngest patient affected by C. jejuni-related perimyocarditis published to date. The genomes of both strains were characterized by whole-genome sequencing and compared with the C. jejuni NCTC 11168 genome to gain insights into the molecular features that may be associated with perimyocarditis. Various comparison tools were used for the comparative genomics analysis, including the identification of virulence and antimicrobial resistance genes, phase variable (PV) genes, and single nucleotide polymorphisms (SNPs) identification. Comparisons of the strains identified 16 SNPs between them, which constituted small but significant changes mainly affecting the ON/OFF state of PV genes after passing through both hosts. These results suggest that PV occurs during human colonization, which modulates bacteria virulence through human host adaptation, which ultimately is related to complications after a campylobacteriosis episode depending on the host status. The findings highlight the importance of the relation between host and pathogen in severe complications of Campylobacter infections.

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Immune checkpoint inhibitors (ICIs) are soluble antibodies that have dramatically changed the outcomes including overall survival in a subset of kidney tumors, specifically in renal cell carcinoma (RCC). To date, there is no a single predictive biomarker approved to be used to select the patients that achieve benefit from ICIs targeting. It seems reasonable to analyze whether the programmed death-ligand 1 (PD-L1) expression could be useful. To assess the role of PD-L1 expression as a potential predictive biomarker for benefit of ICIs in RCC patients, we performed a search of randomized clinical trials (RCTs) comparing ICIs (monotherapy or in combination with other therapies) to standard of care in metastatic RCC patients according to PRISMA guidelines. Trials must have included subgroup analyses evaluating the selected outcomes (progression-free survival (PFS) and overall survival (OS)) in different subsets of patients according to PD-L1 expression on tumor samples. Hazard ratios with confidence intervals were used as the measure of efficacy between groups. A total of 4635 patients (six studies) were included (ICIs arm: 2367 patients; standard of care arm: 2268 patients). Globally, PFS and OS results favored ICIs. Differential expression of PD-L1 on tumor samples could select a subset of patients who could benefit more in terms of PFS (those with higher levels; p-value for difference between subgroups: <0.0001) but it did not seem to impact in OS results (p-value for difference: 0.63). As different methods to assess PD-L1 positivity were used among trials, this heterogeneity could have an influence on the results. PD-L1 could represent a biomarker to test PFS in clinical trials but its value for OS is less clear. In this meta-analysis, the usefulness of PD-L1 expression as a predictive biomarker to select treatment in metastatic RCC patients was not clearly shown.

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Anorexia nervosa (AN) is the most prevalent of eating disorders in children and adolescents, and its treatment is long and complex, involving a multidisciplinary team. Nutritional rehabilitation and restoration of a healthy body weight is one of the central goals in the initial stages of inpatient treatment. However, current recommendations on initial energy requirements for these patients are inconsistent, with a clear lack of controlled studies, available scientific evidence and global consensus on the most effective and safe refeeding practices in hospitalized adolescents with anorexia nervosa (AN). Conservative refeeding recommendations have been classically established in order to prevent the refeeding syndrome. Nevertheless, various works have recently appeared advocating a higher initial caloric intake, without observing more complications or refeeding syndrome, and allowing a shorter average stay. We present our experience in the treatment of restricting AN with a conservative progressive treatment. We have obtained good results with this approach, which was well tolerated by patients, with no observing complications. As a consequence, the medical team could establish a pact about the therapeutic goals with the patients in an easier way.

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Anorexia nervosa (AN) is the most prevalent of eating disorders in children and adolescents, and its treatment is long and complex, involving a multidisciplinary team. Nutritional rehabilitation and restoration of a healthy body weight is one of the central goals in the initial stages of inpatient treatment. However, current recommendations on initial energy requirements for these patients are inconsistent, with a clear lack of controlled studies, available scientific evidence and global consensus on the most effective and safe refeeding practices in hospitalized adolescents with anorexia nervosa (AN). Conservative refeeding recommendations have been classically established in order to prevent the refeeding syndrome. Nevertheless, various works have recently appeared advocating a higher initial caloric intake, without observing more complications or refeeding syndrome, and allowing a shorter average stay. We present our experience in the treatment of restricting AN with a conservative progressive treatment. We have obtained good results with this approach, which was well tolerated by patients, with no observing complications. As a consequence, the medical team could establish a pact about the therapeutic goals with the patients in an easier way (AU)

La anorexia nerviosa (AN) es el trastorno del comportamiento alimentario más prevalente en niños y adolescentes; su tratamiento es largo y complejo, e involucra a múltiples profesionales. La rehabilitación nutricional y la recuperación de un peso corporal normal es uno de los objetivos centrales en las fases iniciales del tratamiento del paciente ingresado. Sin embargo, las recomendaciones actuales sobre los requerimientos energéticos iniciales para estos pacientes son inconsistentes, con una clara ausencia de estudios controlados, evidencia científica disponible y consenso global sobre la forma de realimentación más efectiva y segura en adolescentes ingresados con anorexia nerviosa (AN). Clásicamente se han recomendado una realimentación conservadora para prevenir el síndrome de realimentación. No obstante, han aparecido recientemente varios trabajos recomendado una ingesta calórica inicial más elevada, sin observar más complicaciones ni síndrome de realimentación, y asociadas a estancias medias más cortas. Presentamos aquí nuestra experiencia en el tratamiento de la AN restrictiva con un tratamiento progresivo conservador. Hemos obtenido buenos resultados con este abordaje, bien tolerando por los pacientes, y sin observar complicaciones. Gracias a él, el equipo médico pudo establecer más fácilmente un acuerdo sobre los objetivos terapéuticos con el paciente (AU)

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The maintenance of an adequate oxygen supply to tissues after congenital heart surgery is essential for good outcomes. The objective of this study was to assess the usefulness of near-infrared spectroscopy (NIRS) for estimating central venous oxygen saturation (ScvO2) using both cerebral and renal measurements, explore its relation with cardiac output measurements and check its ability to detect low cardiac output. A prospective observational pilot study was conducted in patients weighing <10 kg undergoing cardiopulmonary bypass surgery. Spectroscopy probes were placed on the forehead and renal area, and serial cardiac output measurements were obtained by femoral transpulmonary thermodilution over the first 24 h after surgery. In the 15 patients studied, ScvO2 was correlated with cerebral (r = 0.58), renal (r = 0.60) and combined (r = 0.71) measurements. Likewise, the systolic index was correlated with the NIRS signals: cerebral (r = 0.60), renal (r = 0.50) and combined (r = 0.66). Statistically significant differences were found in the NIRS measures registered in the 29 low cardiac output events detected by thermodilution: cerebral: 62 % (59-65) versus 69 % (63-76); renal: 83 % (70-89) versus 89 % (83-95); and combined 64 % (60-69) versus 72 % (67-76). In our series, combined cerebral and renal monitoring was correlated with central venous oxygen saturation and cardiac output; low cardiac output detection associated a different spectroscopy pattern.

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