Deciphering the role of host species in Mycobacterium bovis SB0120 spoligotype circulation within a cattle-badger-wild boar multi-hosts system (2nd area)

Conventional genotyping of Mycobacterium bovis (spoligotyping and VNTR) does not allow the reconstruction of the transmission chain in areas of high incidence, where the dominant genotypic profile is shared by almost all isolates. The objective of this project was to determine, via whole genome sequencing, in two study areas in Dordogne/Haute Vienne (DHV) (n=218 samples collected between 2010 and 2017) and Côte-d'Or (CdO) (n=144 samples between 2009 and 2014), the links between infected individuals from cattle herds and from wildlife. We used the marginal approximation of the structured coalescent model implemented in the package Mascot of BEAST2. Strains were isolated from cattle (BV, n=160 in DHV and n=77 in CdO), badgers (BL, n=41 in DHV and n=52 in CdO) and wild boars (SG, n=17 in DHV and n=15 in CdO). Two hundred and ninety SNPs (single nucleotide polymorphisms) in HDV and 123 SNPs in CdO were identified. Using this model, we predicted that the most recent common ancestor was hosted by wildlife in both areas. The backward migration rates suggested that M. bovis would circulate from cattle to badger to wild boar to cattle. The use of a mathematical model integrating genomic and epidemiological data provides new insights into understanding the circulation of M. bovis within this multi-host system and highlight the interactions between two wildlife species and cattle.