Two Cases of Pulmonary Tuberculosis Caused by Mycobacterium tuberculosis subsp. canetti

We identified an unusual strain of mycobacteria from two patients with pulmonary tuberculosis by its smooth, glossy morphotype and, primarily, its genotypic characteristics. Spoligotyping and restriction fragment length polymorphism typing were carried out with the insertion sequence IS6110 patterns. All known cases of tuberculosis caused by Mycobacterium canetti have been contracted in the Horn of Africa

Profil épidémio-clinique des pneumonies aiguës communautaires hospitalisées en 2010 au sein de l'Hôpital d'Instruction des Armées Laveran

INTRODUCTION: La pneumopathie aiguë communautaire (PAC) est une pathologie courante. En hospitalisation la mortalité est non négligeable. Il est intéressant de connaître les facteurs de risque de décès, afin d'optimiser leur prise en charge. PATIENTS ET METHODE: Il s'agit d'une étude rétrospective descriptive monocentrique réalisée sur un an au sein de l'HIA Laveran à partir de données du PMSI. Elle a pour objectifs de décrire les caractéristiques épidémio-cliniques des PAC hospitalisées et de rechercher des facteurs de risque de décès, hors sévérité de l'épisode infectieux. RESULTATS: En 2010, 396 patients ont été hospitalisés, dont 77% âgés de plus de 65 ans. 12,9% des patients hospitalisés hors réanimation sont décédés. En réanimation, 47,9% sont décédés. Les facteurs de risque identifiés en analyse multivariée étaient l'âge supérieur à 65 ans (p=0,01), l'existence d'un séjour en réanimation (p<0,005), d'une démence (p=0,003) et d'un antécédent de pathologie cardiaque rythmique (p=0,03). DISCUSSION ET CONCLUSION: Ces résultats nous incitent à investiguer les causes du sur-risque de décès par pneumopathie en cas d'antécédent rythmique cardiaque et à réaliser des études de plus haut niveau de preuve pour optimiser la prise en charge de ces patients. Les patients présentant une démence sont une population également à risque sur laquelle des actions préventives et thérapeutiques pourraient être mises en place, comme le dépistage des troubles de la déglutition, l'optimisation de la kinésithérapie, de la nutrition et de l'environnement du patientAIX-MARSEILLE2-BU Méd/Odontol. (130552103) / SudocPARIS-Bib. Serv.Santé Armées (751055204) / SudocSudocFranceF

Le tabagisme dans la Marine nationale

AIX-MARSEILLE2-BU Méd/Odontol. (130552103) / SudocPARIS-Bib. Serv.Santé Armées (751055204) / SudocPARIS-BIUM (751062103) / SudocSudocFranceF

Mieux collecter les données personnelles sur Internet. Une étude qualitative auprès d’internautes français

National audienceAs Web users are more and more concerned regarding how their personal data are used, how can firms reduce their concerns, reassure them and even incite them to divulge more personal data? In order to answer this question, a qualitative study has been conducted with 30 French Internet users. This study underlines seven context variables (i.e. usefulness and aim of the data request, vocabulary used, request tone, quantity of requested data, responses modes, opportunity of not being asked next time) that represent useful strategies that firms could use when they collect personal data in order to bypass this concern.Dans un contexte de méfiance des internautes vis-à-vis de l’utilisation qui peut être faite des informations personnelles qu’ils fournissent sur Internet, quelles stratégies les entreprises peuvent-elles mettre en place afin de contourner leurs craintes, de les rassurer voire de les inciter à divulguer davantage leurs données ? Afin d’apporter des éléments de réponse à cette question, une étude qualitative a été conduite auprès de trente internautes français. Elle permet de mettre à jour sept variables relatives au contexte de sollicitation (exposé de l’utilité et de la finalité de la demande, vocabulaire employé, tonalité de la sollicitation, quantité de données demandées, modalités de réponse proposées, possibilité offerte aux internautes de ne plus être sollicité ultérieurement) constituant autant de leviers d’action que les entreprises peuvent mobiliser dans leurs pratiques de collecte

VarAFT: a variant annotation and filtration system for human next generation sequencing data

International audienceWith the rapidly developing high-throughput sequencing technologies known as next generation sequencing or NGS, our approach to gene hunting and diagnosis has drastically changed. In <10 years, these technologies have moved from gene panel to whole genome sequencing and from an exclusively research context to clinical practice. Today, the limit is not the sequencing of one, many or all genes but rather the data analysis. Consequently, the challenge is to rapidly and efficiently identify disease-causing mutations within millions of variants. To do so, we developed the VarAFT software to annotate and pinpoint human disease-causing mutations through access to multiple layers of information. VarAFT was designed both for research and clinical contexts and is accessible to all scientists, regardless of bioinformatics training. Data from multiple samples may be combined to address all Mendelian inheritance modes, cancers or population genetics. Optimized filtration parameters can be stored and re-applied to large datasets. In addition to classical annotations from dbNSFP, VarAFT contains unique features at the disease (OMIM), phenotypic (HPO), gene (Gene Ontology, pathways) and variation levels (predictions from UMD-Predictor and Human Splicing Finder) that can be combined to optimally select candidate pathogenic mutations. VarAFT is freely available at: http://varaft.eu

UMD-Predictor: A High-Throughput Sequencing Compliant System for Pathogenicity Prediction of any Human cDNA Substitution

International audienceWhole-exome sequencing (WES) is increasingly applied to research and clinical diagnosis of human diseases. It typically results in large amounts of genetic variations. Depending on the mode of inheritance, only one or two correspond to pathogenic mutations responsible for the disease and present in affected individuals. Therefore , it is crucial to filter out nonpathogenic variants and limit downstream analysis to a handful of candidate mutations. We have developed a new computational combi-natorial system UMD-Predictor (http://umd-predictor.eu) to efficiently annotate cDNA substitutions of all human transcripts for their potential pathogenicity. It combines biochemical properties, impact on splicing signals, localiza-tion in protein domains, variation frequency in the global population, and conservation through the BLOSUM62 global substitution matrix and a protein-specific conservation among 100 species. We compared its accuracy with the seven most used and reliable prediction tools, using the largest reference variation datasets including more than 140,000 annotated variations. This system consistently demonstrated a better accuracy, specificity, Matthews correlation coefficient, diagnostic odds ratio, speed, and provided the shortest list of candidate mutations for WES. Webservices allow its implementation in any bioinfor-matics pipeline for next-generation sequencing analysis. It could benefit to a wide range of users and applications varying from gene discovery to clinical diagnosis

Actionable Genes, Core Databases, and Locus-Specific Databases

International audienceAdoption of next-generation sequencing (NGS) in a diagnostic context raises numerous questions with regard to identification and reports of secondary variants (SVs) in actionable genes. To better understand the whys and wherefores of these questioning, it is necessary to understand how they are selected during the filtering process and how their proportion can be estimated. It is likely that SVs are underestimated and that our capacity to label all true SVs can be improved. In this context, Locus-specific databases (LSDBs) can be key by providing a wealth of information and enabling classifying variants. We illustrate this issue by analyzing 318 SVs in 23 actionable genes involved in cancer susceptibility syndromes identified through sequencing of 572 participants selected for a range of atherosclerosis phenotypes. Among these 318 SVs, only 43.4% are reported in Human Gene Mutation Database (HGMD) Professional versus 71.4% in LSDB. In addition, 23.9% of HGMD Professional variants are reported as pathogenic versus 4.8% for LSDB. These data underline the benefits of LSDBs to annotate SVs and minimize overinterpretation of mutations thanks to their efficient curation process and collection of unpublished data. (C) 2016 Wiley Periodicals, Inc

Molecular and epidemiological investigation of a colistin-resistant OXA-23-/NDM-1-producing Acinetobacter baumannii outbreak in the Southwest Indian Ocean Area

International audienc

Novel heterozygous mutation in ANO3 responsible for craniocervical dystonia.

International audienc