Sacbrood viruses and select Lake Sinai virus variants dominated Apis mellifera colonies symptomatic for European foulbrood

European foulbrood (EFB) is a prevalent disease of the European honey bee (Apis mellifera) in the US, which can lead to colony decline and collapse. The bacterial components of EFB are well studied, but the diversity of viral infections within infected colonies has not been explored. Here we use meta-transcriptomics sequencing of 12 honey bee hives, symptomatic (+) and asymptomatic (-) for EFB to explore viral infection associated with the disease. We identified 41 viral genomes, belonging to two families, with a predominant occurrence of 34 genomes observed in colonies with severe EFB. This is in contrast to fewer, and a complete absence of Dicistroviridae genomes, recovered from healthy colonies (7 genomes). Identified viruses included multiple lineages previously reported in honey bees, namely Lake Sinai virus, Deformed wing virus, Sacbrood virus, Black queen cell virus, and Israeli acute paralysis virus. We observed specific Lake Sinai virus clades associated exclusively with EFB+ or EFB- colonies, in addition to EFB-afflicted colonies that exhibited an increase in relative abundance of sacbrood viruses. Multivariant analyses highlighted that a combination of site and EFB disease status influenced RNA virome composition, while EFB status alone didn't significantly impact it, presenting a challenge for comparisons between colonies kept in different yards. These findings contribute to the understanding of viral dynamics in honey bee colonies compromised by EFB and underscore the need for future investigations to consider viral composition when investigating EFB.