Jean-Charles Dufour

A comprehensive repertoire of prokaryotic species identified in human beings

The compilation of the complete prokaryotic repertoire associated with human beings as commensals or pathogens is a major goal for the scientific and medical community. The use of bacterial culture techniques remains a crucial step to describe new prokaryotic species. The large number of officially acknowledged bacterial species described since 1980 and the recent increase in the number of recognised pathogenic species have highlighted the absence of an exhaustive compilation of species isolated in human beings. By means of a thorough investigation of several large culture databases and a search of the scientific literature, we built an online database containing all human-associated prokaryotic species described, whether or not they had been validated and have standing in nomenclature. We list 2172 species that have been isolated in human beings. They were classified in 12 different phyla, mostly in the Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes phyla. Our online database is useful for both clinicians and microbiologists and forms part of the Human Microbiome Project, which aims to characterise the whole human microbiota and help improve our understanding of the human predisposition and susceptibility to infectious agents.

Impact of a computerized decision support system on compliance with guidelines on antibiotics prescribed for urinary tract infections in emergency departments: a multicentre prospective before-and-after controlled interventional study

OBJECTIVES Urinary tract infections (UTIs) are one of the leading reasons for antibiotic prescriptions in emergency departments (EDs), with half of these antibiotics being inappropriately prescribed. Our objective was to assess the impact of a computerized decision support system (CDSS) on compliance with guidelines on empirical antibiotic prescriptions (antibiotic and duration) for UTIs in EDs. METHODS A multicentre prospective before-and-after controlled interventional study was conducted from 19 March to 28 October 2012. All adults diagnosed with community-acquired UTIs (cystitis, pyelonephritis or prostatitis) at three French EDs were included. The antibiotic therapy was considered compliant with guidelines if the antibiotic and the duration prescribed were in accordance with the national guidelines. Data were collected using electronic medical records. Paired tests were used when comparing periods within each ED and global analyses used multivariate logistic mixed models. RESULTS Nine hundred and twelve patients were included during the 30 week study period. The CDSS was used in 59% of cases (182/307). The CDSS intervention improved the compliance of antibiotic prescriptions in only one ED in a bivariate analysis (absolute increase +20%, P = 0.007). The choice of the antibiotic was improved in multivariate analyses but only when the CDSS was used [OR = 1.94 (95% CI 1.13-3.32)]. The CDSS also changed the initial diagnosis in 23% of cases, in all three EDs. CONCLUSIONS The CDSS only partially improved compliance with guidelines on antibiotic prescriptions in UTIs.

A semantic approach for the homogeneous identification of events in eight patient databases: A contribution to the European eu-ADR project

The overall objective of the eu-ADR project is the design, development, and validation of a computerised system that exploits data from electronic health records and biomedical databases for the early detection of adverse drug reactions. Eight different databases, containing health records of more than 30 million European citizens, are involved in the project. Unique queries cannot be performed across different databases because of their heterogeneity: Medical record and Claims databases, four different terminologies for coding diagnoses, and two languages for the information described in free text. The aim of our study was to provide database owners with a common basis for the construction of their queries. Using the UMLS, we provided a list of medical concepts, with their corresponding terms and codes in the four terminologies, which should be considered to retrieve the relevant information for the events of interest from the databases.

Design and evaluation of a semantic approach for the homogeneous identification of events in eight patient databases: a contribution to the European EU-ADR project

The overall objective of the EU-ADR project is the design, development, and validation of a computerised system that exploits data from electronic health records and biomedical databases for the early detection of adverse drug reactions. Eight different databases, containing health records of more than 30 million European citizens, are involved in the project. Unique queries cannot be performed across different databases because of their heterogeneity: Medical record and Claims databases, four different terminologies for coding diagnoses, and two languages for the information described in free text. The aim of our study was to provide database owners with a common basis for the construction of their queries. Using the UMLS, we provided a list of medical concepts, with their corresponding terms and codes in the four terminologies, which should be considered to retrieve the relevant information for the events of interest from the databases.

Designing and implementing health data and information providers

OBJECTIVES To model and implement web portals providing access to certified and high-quality information in the domain of health. MATERIAL AND METHODS The Unified Medical Language System (UMLS) knowledge sources of the U.S. National Library of Medicine and principles of implementation resulting from the previous ARIANE project are described. The XML technology that allows files transformations by the means of XSLT is briefly presented. RESULTS The design and implementation of software modules that exploit knowledge sources, operate the translation of a users query to selected information sources, and wrap obtained results are detailed. Querying documentary and factual medical databases are presented. DISCUSSION Current implementation and wrapping perspectives are discussed in terms of integration and interoperability of health information and data resources.

Coupling computer-interpretable guidelines with a drug-database through a web-based system – The PRESGUID project

BackgroundClinical Practice Guidelines (CPGs) available today are not extensively used due to lack of proper integration into clinical settings, knowledge-related information resources, and lack of decision support at the point of care in a particular clinical context.ObjectiveThe PRESGUID project (PREScription and GUIDelines) aims to improve the assistance provided by guidelines. The project proposes an online service enabling physicians to consult computerized CPGs linked to drug databases for easier integration into the healthcare process.MethodsComputable CPGs are structured as decision trees and coded in XML format. Recommendations related to drug classes are tagged with ATC codes. We use a mapping module to enhance computerized guidelines coupling with a drug database, which contains detailed information about each usable specific medication. In this way, therapeutic recommendations are backed up with current and up-to-date information from the database.ResultsTwo authoritative CPGs, originally diffused as static textual documents, have been implemented to validate the computerization process and to illustrate the usefulness of the resulting automated CPGs and their coupling with a drug database. We discuss the advantages of this approach for practitioners and the implications for both guideline developers and drug database providers. Other CPGs will be implemented and evaluated in real conditions by clinicians working in different health institutions.

An integrated approach to distance learning with digital video in the French-speaking Virtual Medical University

The aim of the French-speaking Virtual Medical University project (UMVF) is to share common resources and specific tools in order to improve medical training. Digital video on IP is an attractive tool for higher education but there are a number of obstacles to widespread implementation. This paper describes the UMVF approach to integrating digital video technologies and services in educational projects.

The contribution of culturomics to the repertoire of isolated human bacterial and archaeal species

After a decade of research and metagenomic analyses, our knowledge of the human microbiota appears to have reached a plateau despite promising results. In many studies, culture has proven to be essential in describing new prokaryotic species and filling metagenomic gaps. In 2015, only 2172 different prokaryotic species were reported to have been isolated at least once from the human body as pathogens or commensals. In this review, we update the previous repertoire by reporting the different species isolated from the human body to date, increasing it by 28% to reach a total of 2776 species associated with human beings. They have been classified into 11 different phyla, mostly the Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. Finally, culturomics contributed up to 66.2% towards updating this repertoire by reporting 400 species, of which 288 were novel. This demonstrates the need to continue the culturing work, which seems essential in order to decipher the hidden human microbial content.

Proposal for a European Public Health Research Infrastructure for Sharing of health and Medical administrative data (PHRIMA).

In Europe, health and medical administrative data is increasingly accumulating on a national level. Looking further than re-use of this data on a national level, sharing health and medical administrative data would enable large-scale analyses and European-level public health projects. There is currently no research infrastructure for this type of sharing. The PHRIMA consortium proposes to realise the Public Health Research Infrastructure for Sharing of health and Medical Administrative data (PHRIMA) which will enable and facilitate the efficient and secure sharing of healthcare data.

Halophilic & halotolerant prokaryotes in humans

Halophilic prokaryotes are described as microorganisms living in hypersaline environments. Here, we list the halotolerant and halophilic bacteria which have been isolated in humans. Of the 52 halophilic prokaryotes, 32 (61.54%) were moderately halophilic, 17 (32.69%) were slightly halophilic and three (5.76%) were extremely halophilic prokaryotes. At the phylum level, 29 (54.72%) belong to Firmicutes, 15 (28.84%) to Proteobacteria, four (7.69%) to Actinobacteria, three (5.78%) to Euryarchaeota and one (1.92%) belongs to Bacteroidetes. Halophilic prokaryotes are rarely pathogenic: of these 52 halophilic prokaryotes only two (3.92%) species were classified in Risk Group 2 (Vibrio cholerae, Vibrio parahaemolyticus) and one (1.96%), species in Risk Group 3 (Bacillus anthracis).