A 14^th century CE Brucella melitensis genome and the recent expansion of the Western Mediterranean clade

Author summaryWe describe the reconstruction of a high-quality ancient B. melitensis genome isolated from the kidney stone of a 14(th) C. CE Italian friar. We confirm the presence of a B. melitensis genome from the Western Mediterranean clade in Italy during this time period and refine previous estimates for the diversification of this phylogenetic group. In addition, we propose that the speciation event separating B. abortus and B. melitensis occurred during the domestication of sheep and goats approximately 9000 BCE.By comparing the gene content of the ancient B. melitensis genome with modern isolates, we provide evidence that neither the B. melitensis phylogenetic groups nor their respective sequence types necessarily correspond with the genetic components of their strains. The accessory genome of B. melitensis appears to be influenced by its geographic location, more so than its sequence type. We propose splitting the Eastern Mediterranean clade into three smaller groups to better reflect these genomic differences. Brucellosis is a disease caused by the bacterium Brucella and typically transmitted through contact with infected ruminants. It is one of the most common chronic zoonotic diseases and of particular interest to public health agencies. Despite its well-known transmission history and characteristic symptoms, we lack a more complete understanding of the evolutionary history of its best-known species-Brucella melitensis. To address this knowledge gap we fortuitously found, sequenced and assembled a high-quality ancient B. melitensis draft genome from the kidney stone of a 14(th)-century Italian friar. The ancient strain contained fewer core genes than modern B. melitensis isolates, carried a complete complement of virulence genes, and did not contain any indication of significant antimicrobial resistances. The ancient B. melitensis genome fell as a basal sister lineage to a subgroup of B. melitensis strains within the Western Mediterranean phylogenetic group, with a short branch length indicative of its earlier sampling time, along with a similar gene content. By calibrating the molecular clock we suggest that the speciation event between B. melitensis and B. abortus is contemporaneous with the estimated time frame for the domestication of both sheep and goats. These results confirm the existence of the Western Mediterranean clade as a separate group in the 14(th) CE and suggest that its divergence was due to human and ruminant co-migration.