Phylogenetically Informative Mutations in Drug Resistance Genes of Human-Infecting Mycobacterium bovis

The diagnosis of drug-resistant tuberculosis (TB) by molecular testing of Mycobacterium tuberculosis drug resistance genes is becoming increasingly common clinically. However, M. bovis, as an uncommon pathogen of human TB, may interfere with the test results. A comprehensive understanding of phylogenetically informative mutations in the drug resistance genes of M. bovis is required to distinguish true resistance-conferring mutations. We analyzed 53 drug resistance genes in 165 M. bovis isolated from humans using whole-genome sequencing data and found that 98.2% (162/165) of isolates have pyrazinamide intrinsic genotypic resistance, owing to the H57D mutation in the pncA gene. 12.1% (20/165) of M. bovis isolates were resistant to drugs other than pyrazinamide. Furthermore, we discovered 18 phylogenetically informative mutations that differed between M. bovis and the major lineages 1-4 of M. tuberculosis. Additionally, we reported false-positive ethambutol resistance caused by M. bovis infection due to the phylogenetically informative mutation embB E378A. This study is crucial for gaining insights into the genetic characterization and drug resistance of M. bovis prevalent in humans, as well as contributing to the development of more accurate molecular diagnostic methods and detection tools for drug resistance.