Phylogenomic analysis of Mycoplasma bovis from Belgian veal, dairy and beef herds with nanopore sequencing

Mycoplasma bovis associated diseases are mostly feared because of their poor response to antimicrobial therapy and high economic losses in cattle farming worldwide. Treatment is frequently unsatisfactory, while the absence of a commercially available vaccine makes the control of M. bovis challenging in most parts of the world. It is currently not clear whether specific M. bovis strains are associated with certain cattle sectors. Therefore, the present study evaluated the molecular epidemiology and genetic relatedness of M. bovis isolates obtained from Belgian beef, dairy and veal farms, and how these relate to M. bovis strains obtained worldwide. Full genomes of one hundred Belgian M. bovis isolates collected over a 5-year period (2014-2019), obtained from 27 dairy, 38 beef and 29 veal farms, were sequenced by MinION long-read sequencing. Consensus sequences were used to generate a phylogenetic tree in order to associate genetic clusters with cattle sector, geographical area and year of isolation. The phylogenetic analysis of 100 M. bovis isolates resulted in 5 major clusters: 3 large clusters (n ≥ 10 isolates), 2 smaller clusters (n < 10) and 1 outlier. No sector-specific M. bovis strains could be identified. Belgian isolates clustered with Israeli, European and a few American M. bovis strains. Representative isolates of all clusters were continuously detected for at least 1.5 consecutive years throughout the country. These results show important insights into the epidemiology of M. bovis in Belgium, and can also contribute to the prevention and control of M. bovis in Europe.