An ancient Erysipelothrix rhusiopathiae genome recovered from 1400-year-old human remains in the Northern Caucasus

Erysipelothrix rhusiopathiae is a pathogenic bacterium infecting both humans and animals and causing erysipeloid, a disease that can leads to osteoarticular conditions, abscesses, and septic arthritis. Here, we report the sequenced ancient genome of E. rhusiopathiae obtained from teeth of an Alan child who lived in the North Caucasus in 6th-7th centuries AD. Differential diagnosis using paleopathological methods suggested that the child suffered from tuberculosis. However, analysis of tooth pulp revealed no signs of M. tuberculosis but a massive presence of ancient E. rhusiopathiae DNA. A complete high-quality ancient E. rhusiopathiae genome was assembled and found to belong to clade II of the extant E. rhusiopathiae phylogeny tree, nested in a subclade of closely related modern isolates infecting wild boars and domestic pigs. The ancient genome belongs to serotype 5 and encodes the key E. rhusiopathiae virulence factor SpaA group 1 along with vancomycin resistance genes. We propose that infection with E. rhusiopathiae, alone or together with other pathogens, is the likely cause of skeletal pathologies observed.