ICO Amplicon NGS Data Analysis: A Web Tool for Variant Detection in Common High‐Risk Hereditary Cancer Genes Analyzed by Amplicon GS Junior Next‐Generation Sequencing

Next‐generation sequencing (NGS) has revolutionized genomic research and is set to have a major impact on genetic diagnostics thanks to the advent of benchtop sequencers and flexible kits for targeted libraries. Among the main hurdles in NGS are the difficulty of performing bioinformatic analysis of the huge volume of data generated and the high number of false positive calls that could be obtained, depending on the NGS technology and the analysis pipeline. Here, we present the development of a free and user‐friendly Web data analysis tool that detects and filters sequence variants, provides coverage information, and allows the user to customize some basic parameters. The tool has been developed to provide accurate genetic analysis of targeted sequencing of common high‐risk hereditary cancer genes using amplicon libraries run in a GS Junior System. The Web resource is linked to our own mutation database, to assist in the clinical classification of identified variants. We believe that this tool will greatly facilitate the use of the NGS approach in routine laboratories.     

Effect of layer thickness on the marginal and internal adaptation of laser-sintered metal frameworks

Statement of problemLaser sintering is commonly used for fabricating metal-ceramic restorations. The layer thickness of the sintering process may affect restoration adaptation. However, limited information is available regarding its impact.PurposeThe purpose of this in vitro study was to compare the marginal and internal adaptation of laser-sintered cobalt-chromium single crown frameworks sintered with layer thicknesses of 25 and 50 μm.Material and methodsThirty resin dies that represented prepared single molar abutment teeth were prepared by using a 3-dimensional printer and were divided into 3 groups (n=10) according to the method used for fabricating metal frameworks: group C, metal frameworks fabricated by using the lost-wax method (control); group L25, metal frameworks fabricated by using direct metal laser melting with a layer thickness of 25 μm; and group L50, metal frameworks fabricated by using direct metal laser melting with a layer thickness of 50 μm. After fabricating the metal frameworks, 15 vertical marginal discrepancy measurements were made in each axial region (mesial, distal, buccal, and lingual) using a stereomicroscope. Next, all the specimens were sectioned from the midline, and 5 internal discrepancy measurements were made in each internal region (inner marginal, axial, and occlusal). The data were analyzed statistically by using 1-way ANOVA, the Tukey honestly significant difference, and Tamhane T2 tests (α=.05).ResultsThe highest marginal and internal discrepancy values were obtained for metal frameworks in group C, and these values were significantly different (P<.001) from those obtained for metal frameworks in the other 2 groups. No significant difference was observed in the marginal and internal discrepancy values of metal frameworks in groups L25 and L50.ConclusionsThese results indicate that layer thickness does not affect the adaptation of laser-sintered metal frameworks, yet both sintering parameters yielded significantly lower mean marginal discrepancy values than the cast group.     

D-dimer level predicts in-hospital mortality in patients with infective endocarditis: A prospective single-centre study

Background

Increased circulating D-dimer levels have been correlated with adverse outcomes in various clinical conditions. To our knowledge, the association of on-admission D-dimer and in-hospital mortality in infective endocarditis (IE) has not been investigated. We hypothesized that increased on-admission D-dimer levels would correlate with adverse outcomes when prospectively studied in patients with IE.

Methods

In this prospective study, a total of 157 consecutive patients with the definite IE diagnosis met the inclusion criteria and underwent testing for on-admission D-dimer and CRP assays. The outcome measure was in-hospital death from any cause.

Results

In-hospital mortality occurred in 40 (26%) patients. Increased levels of plasma D-dimer (5.1 ± 1.7 vs 1.9 ± 0.8, p < 0.001), CRP [45(13-98) vs 12(5–28), p < 0.001] were found in dead patients compared with those survived. In addition to S. aureus infection, increased leukocyte count, end-stage renal disease, LVEF < 50%, vegetation size of > 10 mm, perivalvular abscess, on-admission D-dimer (HR: 1.32; 95% CI: 1.24-1.40; p < 0.001) and CRP (HR: 1.18; 95% CI: 1.09-1.36; p = 0.001) levels were significantly associated with in-hospital mortality. Furthermore, the sensitivity and specificity of D-dimer ≥ 4.2 mg/L in predicting in-hospital death in IE were 86% and 85%, respectively. Moreover, the sensitivity and specificity of CRP levels ≥ 13.6 mg/L were 72% and 69%, respectively.

Conclusion

Our findings suggest that on-admission D-dimer level may be a simple, available and valuable biomarker that allows us to identify high-risk IE patients for in-hospital mortality. D-dimer ≥ 4.2 mg/L, CRP ≥ 13.6 mg/L were independently associated with IE related in-hospital death.     

Identifying emerging trends in antimicrobial resistance using Salmonella surveillance data in poultry in Spain

Despite of controls and preventive measures implemented along the food chain, infection with non‐typhoidal Salmonella (NTS) remains one of the major causes of foodborne disease worldwide. Poultry is considered one of the major sources of NTS. This has led to the implementation of monitoring and control programmes in many countries (including Spain) to ensure that in poultry flocks infection is kept to a minimum and to allow the identification and monitoring of circulating NTS strains and their antimicrobial resistance (AMR) phenotypes. Here, we investigated the information from the monitoring programme for AMR in Salmonella from poultry in Spain in 2011–2017 to assess the diversity in phenotypic resistance and to evaluate the programme's ability to detect multi‐resistance patterns and emerging strains in the animal reservoir. Data on serotype and AMR to nine antimicrobials obtained from 3,047 NTS isolates from laying hens (n = 1,060), broiler (n = 765) and turkey (n = 1,222) recovered during controls performed by the official veterinary services and food business operators were analysed using univariate and multivariate methods in order to describe host and serotype‐specific profiles. Diversity and prevalence of phenotypic resistance to all but one of the antimicrobials (colistin) were higher in NTS from broiler and turkey compared with laying hen isolates. Certain combinations of serotype and AMR pattern (resistotype) were particularly linked with certain hosts (e.g. susceptible Enteritidis with laying hens, multi‐drug resistant (MDR) Derby in turkey, MDR Kentucky in turkey and broiler). The widespread presence of certain serotype‐resistotype combinations in certain hosts/years suggested the possible expansion of MDR strains in the animal reservoir. This study demonstrates the usefulness of the analysis of data from monitoring programmes at the isolate level to detect emerging threats and suggests aspects that should be subjected to further research to identify the forces driving the expansion/dominance of certain strains in the food chain.