Whole-genome sequencing reveals genetic diversity and transmission dynamics of Mycobacterium bovis in South African wildlife

Abstract

Mycobacterium bovis infection poses a significant threat to the biodiversity and conservation of South African wildlife. Despite this, few studies have explored transmission dynamics within these complex multi-host systems. This study used wholegenome sequencing to investigate the genetic diversity and relatedness of M. bovis strains across various wildlife species and regions in South Africa to explore transmission patterns. A total of 112 M. bovis isolates from 106 individuals representing 12 species underwent short-read sequencing. Two animal-adapted sub-lineages, La1.7.1 (clonal complex Eu2) and La1.8.1 (Eu1), exhibited geographic clustering and notable genomic diversity. Closely related isolates (≤5 SNP differences) were primarily found within single host species, particularly African buffalo (Syncerus caffer), indicating intra-species transmission and potential source identification. In contrast, other genetically similar isolates (≤12 SNP differences), collected over 25 years, suggest historical inter-species transmission. Understanding these transmission patterns is essential for developing effective strategies to control the spread of M. bovis and protect vulnerable wildlife populations.