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Automated Next Generation Sequencing for Diagnostic Microbiology (PATHSEEK)
Start date: Sep 1, 2012, End date: Feb 29, 2016 PROJECT  FINISHED 

"Sequencing platforms in diagnostic laboratories may aid both patient management by detecting resistance associated mutations, and public health measures, by determining phylogenetic relationships between infections from different patients. Current platforms are limited by the timeframe required for generating a result and by the limited sequence information provided on pathogens. To overcome these limitations PATHSEEK, a 42-month project, proposes to set up a disruptive diagnostic technological pathogen sequencing platform that will deliver in 24-48H, all possible drug resistance mutation as well as data on nosocomial infection, from one patient sample in one single assay. The PATHSEEK platform will open up a new era in clinical diagnosis and patient management by delivering, in one to two days, all the results needed to provide personalized treatment. The rapid delivery of results will ensure early, appropriate therapy thereby helping to reduce the development of drug- resistance and minimizing unnecessary, extra medical expense from the use of inappropriate drugs. Through its multiplex, ultra-deep sequencing capabilities, the platform will also impact public health management of nosocomial infections. At the local level, it will provide, in a simple and efficient manner, all data to control hospital-acquired infections and identify community clusters and transmission chains. At a larger scale, it will permit European and WHO Reference centres to follow, in real time, the spread of infection, allowing earlier interventions to mitigate pandemics.To achieve automated high coverage deep sequencing of any pathogens directly from clinical material for timely identification of drug resistance and outbreaks, PATHSEEK will develop a user-friendly diagnostic platform based on Next Generation Sequencing (NGS). PATHSEEK will overcome real and perceived barriers to the use of NGS for routine microbiology, by the innovative inclusion of customized, automated targeted-enrichment of pathogen nucleic acid prior to sequencing. This will improve the sensitivity and specificity of NGS methods for pathogen sequencing. Together with state of the art bench-top sequencing machines and novel bioinformatics tools to facilitate interpretation of results, these measures will provide rapid, personalized results, which are appropriate to real-life diagnostic workflows and clinical needs. To evaluate the performance of the proposed platform in clinical diagnostic settings, the consortium has selected eight key pathogens whose characteristics include a clear unmet clinical and public health need and/or for which the threat is of global importance. The pathogens will be used as proof of concept to show the benefit of new target enrichment and library preparation methods on pathogen purification and quality. New software and bioinformatics tools will tackle genuine concerns about data-interpretation complexity and results turn-around times for routine diagnostic applications."
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