Lara Urban from the Helmholtz AI Institute, Helmholtz Pioneer Campus, & the Technical University of Munich in Germany spoke at London Calling 2023 about “Real-time genomics for One Health.” They explained that the concept of One Health is that the health of everything on our planet is interrelated. Urban explained how nanopore sequencing can unlock information about DNA modifications. With computational power and mobile devices, real-time genomics can be available in a variety of contexts. Urban and colleagues wrote an article about how real-time genomics can be used for One Health by generating genomes, performing surveillance, and monitoring wildlife trafficking. Urban also noted opportunities to include the community and decentralizing data. Urban’s research included monitoring the health of endangered species in the field. With colleagues, they have also monitored air quality and water sources. Urban’s research group attended London Calling and presented work. Urban explained that their work is using non-invasive approaches to monitor water from several sources. In one study, they performed amplicon sequencing and identified potential pathogens in sewage outlets. They also found organisms of concern in others sites. They focused more on these samples by doing whole genome sequencing. The shotgun approach correlated well with the amplicon sequencing and provided functional annotation of potential pathogens. Using similar approaches, the team analyzed air. They used “cyclonic technologies” to sample air and noticed a lot of variability in a greenhouse. Interestingly, there was a lot of variability with longer sampling runs but consistency could be achieved with 2-3 hour sampling periods. Urban also noted they used the Rapid Barcoding Kit v14 and could use smaller quantities of DNA. This is great as we are using this approach. They have improved the sampling protocols and are now trying to distinguish between DNA from live and dead organisms! The team is trying to determine if they can use Nanopore sequencing to differentiate squiggle data from live and dead E. coli. They trained their algorithm to make binary predictions. The model is able to detect live/dead bacteria. This is really exciting! I would love to use this approach. Urban also spoke about the equitable and inclusive access to real-time genomics. The cost of reagents and accessibility to suppliers is an issue. Urban also noted that automatization can increase access with both library preparation and data analyses. Urban also spoke about “helicopter research” and being careful about equitable inclusion. This was a thought-provoking session that I will share with PORES participants!
