| description |
The analyses of single nucleotide polymorphisms (SNPs) in sequences derived from whole genome sequencing (WGS) are ideally suited to recognize precise evolutionary relationships of organisms and deriving their epidemiology. In this context, Mycobacterium caprae infections have been documented frequently in cattle and red deer along the Bavarian and Austrian Alps during the last decade. However, little is still known about the transmission dynamics within closed host populations, exchange of M. caprae between different hosts and a molecular evolution linked to such events. The aim of this study was to gain more detailed information about the molecular epidemiology of bovine tuberculosis (bTB) based on isolate-specific genome-wide SNP diversity of M. caprae to generate a phylogenetic network analysis. The complete genomes of 61 M. caprae isolates originating from eight cattle farms where bTB was detected in multiple animals within the herds were sequenced. The bTB events in cattle holdings were analyzed over a period of twelve years between 2004 and 2015. The whole genome data of the different M. caprae genomes revealed a direct cattle-to-cattle transmission within- the herds based on few or no SNP differences in their genomes. In contrast, the M. caprae genomes obtained from isolates not originating from the same study herd accounted for many more SNPs. This is shown by the fact that the dominant bTB- disease related molecular evolution of mycobacteria was maintained through interaction within rather than between herds. Furthermore, we assembled a nearly complete whole genome sequence |