PT25 – Detecting Horizontal Gene Transfer by Mapping Sequencing Reads Across Species Boundaries

Proceeding talk – Theme: Genes.

Abstract

Horizontal gene transfer (HGT) is a fundamental mechanism that enables bacteria to easily acquire new traits such as antibiotic resistance or pathogenic toxins. Next-generation sequencing (NGS) technologies facilitate rapid analysis of unknown pathogens but so far no approach detects HGTs directly from NGS reads. NGS-based HGT detection has clear advantages, especially in outbreak scenarios with HGT mediated emergence of new pathogens, like the EHEC outbreak in Germany 2011. We present Daisy, a novel mapping-based HGT detection tool, which successfully determines HGT regions with base pair resolution in both simulated and real data. It is also transferable to HGT-like scenarios present in genetically modified organisms, as shown by a successful case study with a transgenic E. coli.

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Authors

Kathrin Trappe, Robert Koch Institute, Germany
Tobias Marschall, Saarland University / Max Planck Institute for Informatics, Germany
Bernhard Renard, Robert Koch Institute, Germany