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Genomic methods for tracking bacterial pathogens for clinical and public health benefit: the need for genomic surveillance
Published on September 29, 2022 20 min
Other Talks in the Series: Genomics and Clinical Microbiology
PathoLive: pathogen detection while sequencing
- Dr. Simon Tausch
- Robert Koch Institute, Germany
Application of whole genome sequencing in tuberculosis clinical trials
- Prof. Stephen Gillespie
- University of St. Andrews, UK
Hello, I'm Martin Maiden. I'm in the Department of Biology at the University of Oxford with my colleague Charlene Rodrigues. We're going to be presenting a talk on genomic methods for tracking bacterial pathogens for clinical and public health benefit. This is the first of two talks. In the second talk, Charlene will be taking us through a number of case studies.
Here's the outline of the two talks. In the first talk, today, I'm going to discuss why genomic surveillance is needed. Describe how to perform genomic surveillance, including the pitfalls and difficulties. In the second talk, Charlene will talk about case studies that demonstrate the use of genomic surveillance in clinical and public health settings. That's a very important part of what we're talking about in these two talks, is not just genomics, but how genomics can be used for translational benefit in the public health and clinical health space.
We'll discuss why we track the pathogens. The questions which we're addressing this particular application of clinical and public health applications are crucial to why and how we do this tracking. Firstly is diagnosis. We need often to identify the causes of disease and to subtype those causes of diseases for reasons that I'll mention in a moment. Then we might want to do localised epidemiology, which is the surveillance of resistance organisms or the investigation of hospital outbreaks and so on, so that we can determine what localised public health measures might need to be done. As we get up onto yet another scale, we get on to regional and national epidemiology. In this situation, usually national, regional or international bodies are trying to identify trends in disease and characterising pathogen variance, very much in the way we've seen in the COVID-19 pandemic in order to tailor both interventions and to track how a disease is progressing. That leads into, finally, international global disease surveillance, which is typically done over the global scale and over very long periods of time to identify pathogens of interest, pathogens of concern, to identify when outbreaks occur, particularly international outbreaks and pandemics. All of these feed into research and development of novel treatments and interventions.