SYSTOMONAS — an integrated database for systems biology analysis of Pseudomonas

To provide an integrated bioinformatics platform for a systems biology approach to the biology of pseudomonads in infection and biotechnology the database SYSTOMONAS (SYSTems biology of pseudOMONAS) was established. Besides our own experimental metabolome, proteome and transcriptome data, various additional predictions of cellular processes, such as gene-regulatory networks were stored. Reconstruction of metabolic networks in SYSTOMONAS was achieved via comparative genomics. Broad data integration is realized using SOAP interfaces for the well established databases BRENDA, KEGG and PRODORIC. Several tools for the analysis of stored data and for the visualization of the corresponding results are provided, enabling a quick understanding of metabolic pathways, genomic arrangements or promoter structures of interest. The focus of SYSTOMONAS is on pseudomonads and in particular Pseudomonas aeruginosa, an opportunistic human pathogen. With this database we would like to encourage the Pseudomonas community to elucidate cellular processes of interest using an integrated systems biology strategy. The database is accessible at

Screening for multi-drug-resistant Gram-negative bacteria: what is effective and justifiable?

Effectiveness is a key criterion in assessing the justification of antibiotic resistance interventions. Depending on an intervention's effectiveness, burdens and costs will be more or less justified, which is especially important for large scale population-level interventions with high running costs and pronounced risks to individuals in terms of wellbeing, integrity and autonomy. In this paper, we assess the case of routine hospital screening for multi-drug-resistant Gram-negative bacteria (MDRGN) from this perspective. Utilizing a comparison to screening programs for Methicillin-Resistant Staphylococcus aureus (MRSA) we argue that current screening programmes for MDRGN in low endemic settings should be reconsidered, as its effectiveness is in doubt, while general downsides to screening programs remain. To accomplish justifiable antibiotic stewardship, MDRGN screening should not be viewed as a separate measure, but rather as part of a comprehensive approach. The program should be redesigned to focus on those at risk of developing symptomatic infections with MDRGN rather than merely detecting those colonised

The visualization of metabolic pathways from KEGG in SYSTOMONAS is based on GraphViz using the dot layout

<p><b>Copyright information:</b></p><p>Taken from "SYSTOMONAS — an integrated database for systems biology analysis of "</p><p>Nucleic Acids Research 2007;35(Database issue):D533-D537.</p><p>Published online Jan 2007</p><p>PMCID:PMC1899106.</p><p>© 2006 The Author(s)</p> All known metabolic reactions are depicted here for the ‘Urea cycle and metabolism of amino groups’ pathway. Rectangles depict metabolic reactions, ellipses represent metabolites whose names are abbreviated with an asterisk * when the length exceeds 10 letters. Both types of nodes are clickable. Different colours for rectangles specify distinct species, which catalyse the corresponding reaction. These pathways can be obtained from metabolic pathway entries. An abbreviation code for the species is provided with the visualization output (AO1 = PAO1, A14 = PA14, P = KT2440, Pf-5 = F5, F01 = PfO-1, ST = pv tomato, SP = pv , SS = pv