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

Abstract

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.

Diversity of glpK Gene and Its Effect on Drug Sensitivity in Mycobacterium bovis

“…Since the glpK gene encodes an enzyme involved in glycerol metabolism ( Supplementary Figure 1 ), and early studies concluded that the growth of M. tuberculosis was strongly promoted by the addition of glycerol to the medium during in vitro culture, 27 , 28 we monitored the growth curves of different M. bovis glpK HT strains. Similar to M. tuberculosis H37Rv, the growth of M. bovis glpK 7C HT strain was promoted in the glycerol-based medium compared to pyruvate ( Figure 1A ).…”

“… 34 However, in many countries, first and second line antibiotics against TB are not approved for animal consumption. 28 This further complicates the identification of the sources implicated in the acquisition of mutations conferring resistance to these drugs since multiple factors could participate in this process. Canonical mechanisms of resistance are generally grouped into three broad categories: target modification, drug inactivation, and drug transport.…”

“… 49 Moreover, there is growing evidence of the epidemic of MDR M. bovis , resulting in significant economic losses and threats to human health. 13 , 14 , 28 , 50–52 Rifampicin, isoniazid, and ethambutol are used to treat disease due to M. bovis in humans. Treatment duration is generally extended to 9 months due to the exclusion of pyrazinamide, since all strains of M. bovis are resistant to it.…”

Whole-Genome SNP Analysis Identifies Putative Mycobacterium bovis Transmission Clusters in Livestock and Wildlife in Catalonia, Spain

“…While it is not rare in M. tuberculosis , further studies targeting this mutation in M. bovis might provide more insight into this mechanism of resistance in this species. Similarly, isoniazid (INH) resistance, though less common, has been demonstrated from animal-recovered isolates and is a cause for concern [ 82 , 83 , 84 , 85 ]. INH resistance can be associated with mutations in several genes ( fabG1 , inhA , iniC , kasA , and katG ); here, the five genomes with this predicted mutation involved fabG1 .…”

“…INH resistance can be associated with mutations in several genes ( fabG1 , inhA , iniC , kasA , and katG ); here, the five genomes with this predicted mutation involved fabG1 . A previous study identified the katG mutation only among a set of 2074 genomes of M. bovis lineages in the Americas [ 85 ]. Another study previously performed in Catalonia also identified polyresistant M. bovis infection in human and sympatric sheep [ 86 ], highlighting the importance of a One Health approach in TB control to prevent the spread of TB between humans and livestock, considering the drug resistance in strains circulating among livestock.…”