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Background <p><i>Mycobacterium caprae</i>, a member of the <i>Mycobacterium tuberculosis</i> 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 <i>M. caprae</i> from Chinese sika deer (<i>Cervus nippon</i>), providing a detailed characterization of its genomic features.</p> Results <p>The isolate SY-1 was identified as <i>Mycobacterium caprae</i>, a member of the <i>Mycobacterium tuberculosis</i> 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&#xa0;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 (<i>katG</i>) and ethambutol (<i>embB</i>, <i>embC</i>). 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.</p> Conclusions <p>These findings provide the first evidence of <i>M. caprae</i> 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.</p>

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

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年1月17日

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  • Guiyang Ge,
  • Zewei Cheng,
  • Jianhui Xu,
  • Bing Yue,
  • Haozhe Hou,
  • Yiwen Liu,
  • Chenxi Zhu,
  • Hongbei Ge,
  • Shang Shi,
  • Jiaquan Li,
  • Qinglong Gong,
  • Yuhao Song,
  • Xinxin Meng,
  • Ruopeng Cai,
  • Rui Du

摘要

Background

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.

Results

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.

Conclusions

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.