Project: Healthcare Associated Infections bacteria characterization directly from clinical samples with faster time to result

Healthcare-Associated Infections (HCAI) are unpredictable infections, which develop during the course of health care treatment and result in significant patient illnesses and deaths. These in turn require additional medical interventions, and represent a growing occurrence (5 to 10% of hospitalized patients are concerned, 1% of whose deaths are directly attributable to the infection; with HCAI contributing to 2.7% of overall patient morbidity in the EU– HELICS report, 2005) causing a real burden on communities (e.g. the medical costs of HCAI to hospitals range from €12-24 billion/yr in Europe and from $28-45 billion/year in the USA - CDC report, 2009). _x000D_But since initial hospital stays may be shorter than the incubation period of the infecting agent (bacteria, viruses, fungi, and protozoa), the true incidence of HCAI is still likely to be underestimated. _x000D_Streptococcus pneumoniae, Staphylococcus aureus, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa are the most frequent infectious agents responsible for HCAI in hospitals worldwide. For the majority of these pathogens, drug resistance is an important issue showing a constant evolution yielding to the situation of 70% of them are considered as multi -resistant (CDC, 2008), which in turn emerges as a major hospital problem affecting patient outcomes by enhancing microbial virulence and limiting options for efficient therapy._x000D_The presence of HCAI agents must be detected at the earliest possible opportunity. However the diagnostic technologies currently in use are not adapted to such a time trial context. Indeed the current 2-step diagnostic process requiring bacterial growth and the successive use of (i) isolation agar plates (ii) species identification technologies (MALDI-TOF , culture, or immunochemistry) while antibiotic susceptibility testing and virulence characterization technology (molecular biology, immunology or polymerase chain reaction- PCR) may take generally 2 to 3 days._x000D_The key element is to gain time on the infection spread. This is the precise scope of the NOSO-FIGHT project that will allow clinicians to undertake the direct identification of HCAI-related strains on patient fluid samples and will simultaneously evaluate their virulence potential and determine antimicrobial susceptibility profile based on the use of an innovative database of biomarkers able to identify and characterize the CO 7 species involved in HCAI (E.coli, S.aureus, Enterococci, K. pneumoniae, S. pneumoniae, P. aeruginosa). _x000D__x000D_With this new technique, clinicians will be offered new simplified methods to directly detect protein in patient samples with an optimized protein extraction followed by a LC-ESI-MS/MS method which, combined with the use of a biomarker database populated with relevant information in HCAI bacteria strain virulence and antimicrobial resistance mechanisms, will provide clinicians with relevant information regarding therapeutic approach within a time frame of only 12 hours. _x000D__x000D_Within this context, and with a view to providing clinicians with a fast diagnostic test, the research and development (R&D) performing French small and medium sized (SME) company, PHYLOGENE (PHYLO), asked the leading Swiss genomic research laboratory of University of Geneva Hospitals, GENOMIC (GENOMIC) to work on the NOSO-FIGHT project._x000D_This 36-month project aims to develop Healthcare Associated Infections bacteria characterization directly from clinical samples with reduced time to result._x000D__x000D_Innovative work will be performed on:_x000D_• An innovative biomarker discovery approach combining genomic, transcriptomic and proteomic data, in particular RNA sequencing and MS/MSall (SWATH),_x000D_• An innovative diagnosis method which multiplexing properties will allow determination of parameters required by clinicians to determine best therapeutic: identification and characterization (virulence, antibiotic resistance) of infecting bacteria._x000D_• An improve sample treatment allowing determination directly in clinical samples reducing time to result_x000D__x000D_The business model will involve licensing of validated markers database and know-how to hospitals and/or diagnosis companies._x000D__x000D_At the end, NOSO-FIGHT patient’s care and safety as well as healthcare organization will both benefit enormously from the success of the project._x000D_

Acronym NOSO-FIGHT (Reference Number: 7916)
Duration 01/06/2013 - 31/05/2016
Project Topic Healthcare Associated Infections bacteria characterization (identification, virulence and antimicrobial resistance mechanisms) directly from clinical sample using proteomic and genomic approaches with faster time to result
Network Eurostars
Call Eurostars Cut-Off 9

Project partner

Number Name Role Country
2 Genomic Research Laboratory Partner Switzerland
2 PHYLOGENE Coordinator France