Revisiting Mycobacterium bovis SB0121 genetic diversity reflects the complexity behind bovine tuberculosis persistence in Spain

Identifying the causes of tuberculosis (TB) chronicity in cattle herds in Spain is a complex endeavour, mainly due to the multiple factors involved in persistence and the clonal population structure of the Mycobacterium tuberculosis complex. This study assessed the genomic diversity among M. bovis isolates belonging to SB0121, the most prevalent genotype in Spain, in chronically-infected herds. A total of 70 M. bovis isolates from 22 herds, located in six Spanish provinces, in which M. bovis SB0121 was isolated in at least three different sampling events were sequenced. Forty-three isolates from wildlife and cattle herds from the same or neighbouring municipalities to the problem herds were also included to identify putative local transmission events. The within-herd analysis revealed a highly complex scenario, in which the majority (95.45 %; n = 21) of the herds were affected by highly distant strains (> 12 SNP differences), probably as a result of separate introductions. Highly similar isolates (< 6 SNPs) were retrieved in different sampling events from 11 herds, likely indicating active transmission of the outbreak strain or continued exposure to the same source of infection. The between-herd and interspecies comparison suggested the occurrence of several putative epidemiological links between cattle and wildlife species from the same or neighbouring municipalities, reflecting the complex epidemiology of the disease in some of the studied areas. The findings of this study highlight the usefulness of whole genome sequencing to study bTB breakdowns and pinpoints its potential for unravelling possible sources of persistence in cattle herds.