Phylogenomic analysis of Mycoplasma bovis from Belgian veal, dairy and beef herds
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RESEARCH ARTICLE
Open Access
Phylogenomic analysis of Mycoplasma bovis from Belgian veal, dairy and beef herds Jade Bokma1* , Nick Vereecke2, Koen De Bleecker3, Jozefien Callens3, Stefaan Ribbens3, Hans Nauwynck2, Freddy Haesebrouck4, Sebastiaan Theuns2, Filip Boyen4† and Bart Pardon1†
Abstract M. bovis is one of the leading causes of respiratory disease and antimicrobial use in cattle. The pathogen is widespread in different cattle industries worldwide, but highest prevalence is found in the veal industry. Knowledge on M. bovis strain distribution over the dairy, beef and veal industries is crucial for the design of effective control and prevention programs, but currently undocumented. 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 long-read nanopore 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 the Belgian M. bovis isolates resulted in 5 major clusters and 1 outlier. No sector-specific M. bovis clustering was identified. On a world scale, Belgian isolates clustered with Israeli, European and American strains. Different M. bovis clusters circulated for at least 1.5 consecutive years throughout the country, affecting all observed industries. Therefore, the high prevalence in the veal industry is more likely the consequence of frequent purchase from the dairy and beef industry, than that a reservoir of veal specific strains on farm would exist. These results emphasize the importance of biosecurity in M. bovis control and prevention. Keywords: cattle, long-read nanopore sequencing, phylogenetic analysis, SNP analysis, whole genome Introduction Mycoplasma bovis (M. bovis) causes mostly pneumonia, arthritis, otitis in calves and mastitis in adult cattle [1, 2] resulting in high antimicrobial use (AMU) and enormous economic losses in cattle farming sectors worldwide [2– 4]. In Belgium, 100% of the veal farms are seropositive for M. bovis [5, 6], whereas M. bovis is involved in 33% of acute pneumonia outbreaks in beef and dairy farms [7]. Treatment of M. bovis is frequently unsatisfactory, probably due to a combination of intrinsic and acquired *Correspondence: [email protected] † Bart Pardon and Filip Boyen should be considered joint senior author 1 Department of Large Animal Internal Medicine, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium Full list of author information is available at the end of the article
antimicrobial resistance, immuno-evasive properties of the pathogen and failure of the animal to generate an effective immune response [8, 9]. Together with the absence of
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