Isolation, identification and genomic analysis of Mycobacterium caprae strain SY-1 from Chinese sika deer (Cervus nippon)

Mycobacterium caprae, a member of the Mycobacterium tuberculosis complex, has been infrequently reported and studied in China. Recently, its emerging potential for cross-host transmission and drug resistance has raised public health concerns. This study reports the first isolation and whole-genome sequencing of M. caprae from Chinese sika deer (Cervus nippon), providing a detailed characterization of its genomic features. The isolate SY-1 was identified as Mycobacterium caprae, a member of the Mycobacterium tuberculosis complex (MTBC), based on morphological characteristics and PCR analysis. Whole-genome sequencing (WGS) revealed that isolate SY-1 possesses a genome of 4,346,248 bp with a GC content of 65.63%, encoding 4,162 predicted protein-coding sequences (CDSs). Furthermore, SY-1 harbors multiple virulence factors associated with pathogenicity and immune evasion, along with genes conferring resistance to isoniazid (katG) and ethambutol (embB, embC). Phylogenetic analysis demonstrated that SY-1 exhibits close relatedness to strains isolated from diverse host species. Phylogenetic analysis revealed that the SY-1 strain exhibits close phylogenetic relatedness to isolates derived from diverse host species. Furthermore, SY-1 clusters within a clade predominantly comprising isolates from Japan and China. These findings provide the first evidence of M. caprae infection in Chinese sika deer. Strain SY-1 exhibits region-specific characteristics, demonstrating a high degree of host adaptability and cross-species transmission potential. This underscores its role as a potential zoonotic pathogen capable of facilitating the spread of tuberculosis and the dissemination of drug resistance, thereby posing a significant public health threat.