A one-health approach revealed a hidden long-term role for Mycobacterium caprae as responsible for human tuberculosis

M. caprae, is a member of the Mycobacterium tuberculosis complex that is not routinely identified to the species level in many laboratories and its clinical presentation does not have specific features. That explains that infections involving this species may passed underidentified. The demands for higher discrimination in the analysis of a family tuberculosis microepidemic in Almeria, Spain, led to the application of WGS, which unexpectedly identified the involvement of M. caprae. Since this observation, we performed an extensive One Health strategy that allowed us to i) capture another 11 non-suspected M. caprae human infections along the last 18 years ii) analyze systematically an epidemiologically-related goat farm infected with M. caprae and iii) extend geographically the study by including 16 M. caprae isolates from other provinces. All 43 human and animal M. caprae isolates were analyzed by WGS to create an integrative genomic network which showed a high diversity of M. caprae strains. The infected animals showed a diversity compatible with a long-term infection of the farm studied and the comparison of the genomic data, proved the close relationships between the infected goats in the farm and the recent cases of M. caprae infection in humans. Our study revealed an extense endemic zoonotic problem involving M caprae strains, unnoticed for more than 10 years.