PathoLive: pathogen detection while sequencing

Published on April 28, 2021   24 min

Other Talks in the Series: Genomics and Clinical Microbiology

Other Talks in the Series: Periodic Reports: Advances in Clinical Interventions and Research Platforms

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Hello, welcome to my presentation here at HSTalks. My name is Simon Tausch, and the work I'm presenting today was produced at the Robert Koch Institute, where I was working for the Center for Biological Threats and Special Pathogens, and also for the bioinformatics division. The title of the talk is 'PathoLive: Pathogen Detection While Sequencing'. The aim of the project was to enable medical doctors to diagnose patients using next-generation sequencing and to do that in a timely manner, meaning we are analyzing the data while the sequences are running to then detect pathogens in metagenomic samples.
The problem we were facing back at my time at the Robert Koch Institute was that we got many samples of patients with fever of unknown origin, or patients with zoonotic infections and that kind of illness. Generally, diagnostic methods often fail in these extraordinary cases because medical doctors do not really know what they are looking for in a sample. There are some obvious ways of diagnosing a patient when somebody has a cold, and the doctor can just look at him or her and see the result pretty quickly, but in more extraordinary cases it may be more difficult to get a good diagnosis. This is, as I said, often the case when we have novel pathogens which have just emerged and we do not know yet, or we may have zoonotic agents which also emerge from time to time. Especially in outbreak situations as we have recently seen in the huge and very bad Ebola outbreak in Africa, we need rapid diagnostic systems to tackle those outbreaks in a timely manner.

PathoLive: pathogen detection while sequencing

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