PATHONGEN-TRACE

Next Generation Genome Based High Resolution Tracing of Pathogens

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 Obiettivo del progetto (Objective)

'Next generation sequencing (NGS) has fundamentally altered genomic research. New developments will bring NGS costs and performance down to an everybody's technology with extreme potential for ultra fast and accurate molecular typing and diagnostic as it provides the ultimate whole genome information. However, technical and bioinformatics constraints, restrict the application of NGS to few highly experienced laboratories. The goal of this project is the transition of NGS from a basic research tool to a highly efficient technology for pathogen typing and diagnostics on the EU level. This objective will be achieved by establishing a unique European consortium that brings together three SMEs leading in the fields of 'data to knowledge' and 'NGS genome research' with leading experts in clinical microbiology of three model pathogens of high European and worldwide importance (methicillin-resistant Staphylococcus aureus, Campylobacter spp., and M. tuberculosis complex. Particularly we will i) develop bio-informatics pipelines for quality-controlled and easy interpretation of NGS data, ii) optimize sample preparation steps and evaluate newest NGS (Ion Torrent) and Optical Mapping (OM) technologies, and iii) develop new, dedicated NGS-based pathogen diagnostic kits. Ultimate goal is to generate automatically plain language reports and to implement GIS and space-time cluster detections for automatic early-warning systems based on NGS-data. Application programming interfaces and a microbial typing ontology for a “linked web” will be developed. Product-like prototypic software development for automatic analysis of microbial NGS-data will be guided by two leading SMEs. The development of new and improved tools/technologies in this SME-targeted project will overcome existing obstacles of NGS and open the door for a wide application of NGS for European scientists and clinical microbiologist, thus fostering competitiveness of Europe in NGS research and medical applications.'

Introduzione (Teaser)

EU-funded researchers are developing next generation sequencing (NGS) technology for clinical microbiology and disease surveillance applications.

Descrizione progetto (Article)

NGS has fundamentally altered genomic research through ultra-fast and accurate molecular typing. It offers whole genome information in a fraction of the time of standard methods. New developments in the field also promise to bring down the cost of NGS methods and ensure their widespread utilisation for diagnostics.

The key objective of the EU-funded 'Next generation genome based high resolution tracing of pathogens' (http://www.patho-ngen-trace.eu (PATHONGEN-TRACE)) project is to apply the NGS technology for the high-resolution typing of microbial pathogens. Consortium partners have selected pathogens that pose a significant global medical threat, namely Mycobacterium tuberculosis, methicillin-resistant Staphylococcus aureus (MRSA), and human-pathogenic Campylobacter species. The proposed technology will overcome problems associated with conventional typing and diagnosis, and convert pathogen genotyping into standard diagnosis. Additionally, the study hopes to validate NGS for epidemiological tracing of these pathogens.

Apart from sample preparation, project members worked on selecting an appropriate sequencing platform and developing a completely integrated bioinformatics tool for data extraction. This tool also includes an interpretation add-on that would be useful in the future for general diagnostics.

NGS is currently being used for whole genome analysis of over 86 different M. tuberculosis strains involved in disease outbreaks over the past 10 years. Similarly, a retrospective MRSA outbreak analysis will verify if the generated information holds epidemiological value. With respect to Campylobacter, the data from the 561 isolates investigated to date suggest very high levels of accuracy and effectiveness.

Taken together, the PATHONGEN-TRACE deliverables are expected to promote a major technological shift towards NGS for medical research and diagnostics. Especially in medical microbiology, the accuracy and sensitivity of NGS-mediated pathogen typing will bring about a new era in pathogen diagnosis.