• A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2.

      Thiele, Ines; Hyduke, Daniel R; Steeb, Benjamin; Fankam, Guy; Allen, Douglas K; Bazzani, Susanna; Charusanti, Pep; Chen, Feng-Chi; Fleming, Ronan M T; Hsiung, Chao A; et al. (BioMed Central Ltd, 2011)
      Metabolic reconstructions (MRs) are common denominators in systems biology and represent biochemical, genetic, and genomic (BiGG) knowledge-bases for target organisms by capturing currently available information in a consistent, structured manner. Salmonella enterica subspecies I serovar Typhimurium is a human pathogen, causes various diseases and its increasing antibiotic resistance poses a public health problem.
    • Functional metabolic map of Faecalibacterium prausnitzii, a beneficial human gut microbe.

      Heinken, Almut; Khan, M Tanweer; Paglia, Giuseppe; Rodionov, Dmitry A; Harmsen, Hermie J M; Thiele, Ines; Univ Luxembourg, Luxembourg Ctr Syst Biomed, Belval, Luxembourg [ 2 ] Univ Iceland, Ctr Syst Biol, Reykjavik, Iceland [ 3 ] Univ Groningen, Univ Med Ctr Groningen, Dept Med Microbiol, Groningen, Netherlands [ 4 ] Sanford Burnham Med Res Inst, La Jolla, CA USA [ 5 ] Russian Acad Sci, AA Kharkevich Inst Informat Transmiss Problems, Moscow, Russia (Amer Soc Microbiology, 2014-09)
      The human gut microbiota plays a central role in human well-being and disease. In this study, we present an integrated, iterative approach of computational modeling, in vitro experiments, metabolomics, and genomic analysis to accelerate the identification of metabolic capabilities for poorly characterized (anaerobic) microorganisms. We demonstrate this approach for the beneficial human gut microbe Faecalibacterium prausnitzii strain A2-165. We generated an automated draft reconstruction, which we curated against the limited biochemical data. This reconstruction modeling was used to develop in silico and in vitro a chemically defined medium (CDM), which was validated experimentally. Subsequent metabolomic analysis of the spent medium for growth on CDM was performed. We refined our metabolic reconstruction according to in vitro observed metabolite consumption and secretion and propose improvements to the current genome annotation of F. prausnitzii A2-165. We then used the reconstruction to systematically characterize its metabolic properties. Novel carbon source utilization capabilities and inabilities were predicted based on metabolic modeling and validated experimentally. This study resulted in a functional metabolic map of F. prausnitzii, which is available for further applications. The presented workflow can be readily extended to other poorly characterized and uncharacterized organisms to yield novel biochemical insights about the target organism.
    • Inpatient drug utilization in Europe: nationwide data sources and a review of publications on a selected group of medicines (PROTECT project).

      Sabaté, Mònica; Ferrer, Pili; Ballarín, Elena; Rottenkolber, Marietta; Amelio, Justyne; Schmiedl, Sven; Reynolds, Robert; Klungel, Olaf; Ibáñez, Luisa; Addresses: [ 1 ] Fundacio Inst Catala Farmacol, Barcelona, Spain [ 2 ] Univ Hosp Vall dHebron, Dept Clin Pharmacol, Barcelona, Spain [Show the Organization-Enhanced name(s)] [ 3 ] Autonomous Univ Barcelona, Hosp Univ Vall dHebron, Dept Pharmacol Toxicol & Clin Therapeut, Barcelona 08029, Spain [Show the Organization-Enhanced name(s)] [ 4 ] Univ Munich, Inst Med Informat Sci Biometry & Epidemiol, Munich, Germany [ 5 ] Amgen Inc, Uxbridge, Middx, England [ 6 ] Helios Klin Wuppertal, Philipp Klee Inst Clin Pharmacol, Wuppertal, Germany [Show the Organization-Enhanced name(s)] [ 7 ] Univ Witten Herdecke, Fac Hlth, Sch Med, Dept Clin Pharmacol, Witten, Germany [Show the Organization-Enhanced name(s)] [ 8 ] Pfizer Res & Dev, Epidemiol, New York, NY USA [Show the Organization-Enhanced name(s)] [ 9 ] Univ Utrecht, Div Pharmacoepidemiol & Clin Pharmacol, Utrecht, Netherlands (Wiley-Blackwell, 2015-03)
      Drug utilization (DU) studies in inpatient settings at a national level are rarely conducted. The main objective of this study was to review the general information on hospital medicine management in Europe and to report on the availability and characteristics of nationwide administrative drug consumption databases. A secondary objective was to perform a review of published studies on hospital DU of a group of selected drugs, focusing on methodological characteristics (ATC/DDD). General information on hospital drug management was retrieved from several websites, nationwide administrative drug consumption databases and reports published by governmental organizations. A PubMed search was conducted using keywords related to the selected group of drugs AND 'hospital drug utilization'. The data sources for hospital DU information varied widely and included 14 databases from 25 reviewed countries. Bulgaria, Croatia, Denmark, Estonia, Finland, France, Hungary, Iceland, Latvia, Norway and Sweden obtain information on inpatient DU at a national level from wholesalers/manufacturers. In Belgium, Italy and Portugal, drugs dispensed to patients in hospitals are registered at a national level. Data are freely available online only for Denmark and Iceland. From the PubMed search, of a total of 868 retrieved studies, only 13 studies used the ATC/DDD methodology. Although the number of DDD/100 bed-days was used in four studies, other units of measure were also used. The type of information provided for the inpatient sector allowed primarily for conducting DU research at an aggregated data level. The existence of national administrative structures to monitor hospital DU would contribute to promoting the rational use of medicines and improving the safety and quality of prescribing.