Next Generation Genome Based High Resolution Tracing of Pathogens (Patho-NGen-Trace)

Prof. Dr. Stefan Niemann (Research Center Borstel)
Project duration: 
01 Jan 2012 to 30 Jun 2016

Aim of the project: Development of new and widespread applications of NGS in clinical microbiology and disease surveillance, ranging from basic research to medical research, diagnostics, and pathogen genotyping.

Main objectives:

  1. Streamlining and implementation of new internal quality control procedures of the whole NGS process, from sample preparation protocols to final sequence assemblies or mapping.
  2. Development of new, completely integrated bioinformatics tools for fast and easy quality-controlled data extraction and interpretation for diagnostics, drug-resistance, virulence markers, DNA polymorphisms, public health applications, and genomics-based molecular epidemiology.

The newly developed bio-informatics and process tools will be tested for clinical and public health applications, namely for ultra-sensitive and early detection of drug-resistance and spread of:

  • Mycobacterium tuberculosis complex (the cause of tuberculosis)
  • Methicillin-resistant Staphylococcus aureus (major cause of hospital-acquired infections), and
  • Campylobacter spp. (most common cause of diarrhea).


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