Metagenomic and Genomic Analyses Reveal Prevalent Spread and Evolution of the Bat White-Nose Pathogen Pseudogymnoascus destructans in Western Canada

Bats play a crucial role in the ecosystem. However, North American bat populations have experienced a dramatic decline since 2006 due to white-nose syndrome, a disease caused by <i>Pseudogymnoascus destructans</i> (<i>Pd</i>). This fungus can invade and damage the skin on bat wings and muzzles during hibernation. Since 2021, <i>Pd</i> has been reported at selected sites in western Canada, the region with the highest bat diversity in Canada, eliciting urgent calls for action among diverse stakeholders. Here we analyze nine metagenomes of bat guanos and wing swabs and the genomes of five <i>Pd</i> strains from western Canada to investigate the distribution and diversity of <i>Pd</i> in this region. <i>Pd</i> was found in all nine metagenomic samples and the metagenome sequences enabled us to identify the associated bat species. Divergence time estimates of <i>Pd</i> based on whole-genome sequences suggest that <i>Pd</i> likely entered Alberta two to five years before its first official report. Furthermore, we found evidence of abundant gene copy number variations in this species. Together, our metagenomic and genomic analyses indicate that <i>Pd</i> is more prevalent than currently recognized and is evolving and diversifying. Continued surveillance with more comprehensive methods is needed to accurately track its spread and facilitate timely management of white-nose syndrome in North America.