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 ultimative whole genome information.

However, technical and bioinformatics constraints restrict the application of NGS to few highly experienced laboratories. The goal of the project was 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 was achieved by establishing a unique European consortium that brought 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 Mycobacterium tuberculosis complex). 

Particularly we

  1. developed bio-informatics pipelines for quality-controlled and easy interpretation of NGS data,
  2. optimized sample preparation steps and evaluated newest NGS (Ion Torrent) and Optical Mapping (OM) technologies, and
  3. developed new, dedicated NGS-based pathogen diagnostic kits.

Ultimate goal was 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” were developed. Product-like prototypic software development for automatic analysis of microbial NGS-data were guided by two leading SMEs.

The development of new and improved tools/technologies in this SME-targeted project helped overcome existing obstacles of NGS and opened the door for a wide application of NGS for European scientists and clinical microbiologists, thus fostering competitiveness of Europe in NGS research and medical applications.