Field+Genomics Workshop: an initiative to build Nanopore sequencing capacity in field-based host-pathogen research

Abstract

Wildlife disease surveillance has received considerable attention following recent emergence of high-consequence zoonotic pathogens in humans. Increased portability and affordability of sequencing technologies over the last decade have made real-time sequencing of wild animals and their pathogens a reality. Wildlife samples screened for pathogens, however, are rarely permanently archived in museum biorepositories, which limits potential for scientific validation and prevents extension by related disciplines (e.g., ecology, evolution, conservation). To better connect biodiversity and biomedical sciences, the Museums and Emerging Pathogens in the Americas (MEPA) network developed the Field+Genomics Workshop to build capacity for surveillance of wildlife and their pathogens in biodiverse countries. Here, we share workshop resources, in English and Spanish, to facilitate reproducibility and expansion of the workshop into the future. The workshop lasted 10 days, 6 days of fieldwork and 4 days of molecular lab and bioinformatic techniques. The field component emphasized the importance of holistic collecting—that is, permanently preserving many parts and symbionts from each sampled organism—as a critical step in wildlife and pathogen surveillance and to build foundational scientific infrastructure. The molecular component of the workshop used samples collected during the field portion to identify hosts and pathogens in real-time. For this component, we trained participants in methods of DNA extraction, library preparation, and Nanopore Adaptive Sampling (a software feature for real-time selective enrichment or depletion of target sequences). Bioinformatic training consisted of a basic introduction to computational genomics, a worked example to analyze a small sequence dataset, and an exercise using data generated from samples collected during the workshop. In total, the workshop cost ~$37K (~$3K per participant), however, ~25% of those funds are invested in basic equipment and infrastructure that is reusable in future workshops (e.g., sequencer, computer, etc.). This workshop highlights the effort and expertise required to conduct voucher-backed surveillance of wildlife and their pathogens and the many benefits of uniting biodiversity and biomedical sciences to build local capacity.