Comparative genomic analysis of Paenibacillus larvae from archived beehive samples

The Western honey bee, Apis mellifera, plays a vital role in ecology, agriculture, and the economy. With an important contribution to the world's food production, compromised health and colony losses in honey bees pose a global concern. The decline of A. mellifera populations has intensified the need to understand diseases such as American Foulbrood, caused by Paenibacillus larvae. Our study employs genomic sequencing to investigate P. larvae diversity in Denmark over 17 years. Using Illumina technology, we shotgun sequenced DNA from brood comb samples collected in Denmark between the years 2003 to 2020, which we used to assemble genomes of P. larvae. Furthermore, we sequenced DNA extracted from museum specimens dating back to the 19th century, screened it for the presence of P. larvae, and compared the identified historical genomes with the modern ones. The study demonstrates the advantages of shotgun sequencing over traditional culturing methods, including faster processing, detection of multiple strains, and identification of historical P. larvae genomes from museum specimens.