Identification of drug resistance mutations among Mycobacterium bovis lineages in the Americas

Identifying the Mycobacterium tuberculosis resistance mutation patterns is of the utmost importance to assure proper patient's management and devising of control programs aimed to limit spread of disease. Zoonotic Mycobacterium bovis infection still represents a threat to human health, particularly in dairy production regions. Routinary, molecular characterization of M. bovis is performed primarily by spoligotyping and mycobacterial interspersed repetitive units (MIRU) while next generation sequencing (NGS) approaches are often performed by reference laboratories. However, spoligotyping and MIRU methodologies lack the resolution required for the fine characterization of tuberculosis isolates, particularly in outbreak settings. In conjunction with sophisticated bioinformatic algorithms, whole genome sequencing (WGS) analysis is becoming the method of choice for advanced genetic characterization of tuberculosis isolates. WGS provides valuable information on drug resistance and compensatory mutations that other technologies cannot assess. Here, we performed an analysis of the most frequently identified mutations associated with tuberculosis drug resistance and their genetic relationship among 2,074 Mycobacterium bovis WGS recovered primarily from non-human hosts. Full-length gene sequences harboring drug resistant associated mutations and their phylogenetic relationships were analyzed. The results showed that M. bovis isolates harbor mutations conferring resistance to both first- and second-line antibiotics. Mutations conferring resistance for isoniazid, fluoroquinolones, streptomycin, and aminoglycosides were identified among animal strains. Our findings highlight the importance of molecular surveillance to monitor the emergence of mutations associated with multi and extensive drug resistance in livestock and other non-human mammals. Author summary Here we describe the identification of high confidence mutations among Mycobacterium bovis lineages associated with resistance to first- and second-line antituberculosis drugs. Resistance to isoniazid, aminoglycosides and fluoroquinolones among non-human hosts is of importance because of the risk of emergence of multi- and extensively-drug resistance. Further research is warranted for the identification of the mechanisms responsible for acquisition of such mutations as well as the routes of transmissions involved in this process, including selective use of antibiotics or anthroponotic transmission. Our findings highlight the importance of molecular surveillance to monitor the emergence or introduction of strains carrying mutations related to MDR and XDR. This could potentially help to limit the transmission of pathogenic and difficult to treat TB.

Automated summary

Identifying tuberculosis resistance mutation patterns is crucial for patient management and disease control. Whole genome sequencing is becoming the preferred method for genetic characterization of tuberculosis isolates. Monitoring emergence of mutations related to multi and extensive drug resistance is essential for controlling transmission of drug-resistant TB strains.