The contribution of Mycobacterium bovis to the proportion of tuberculosis cases in humans is unknown. A retrospective study was undertaken on archived Mycobacterium tuberculosis complex (MTBC) isolates from a reference laboratory in Uganda to identify the prevalence of human M. bovis infection. A total of 5676 isolates maintained in this repository were queried and 136 isolates were identified as pyrazinamide resistant, a hallmark phenotype of M. bovis. Of these, 1.5% (n = 2) isolates were confirmed as M. bovis by using regions of difference PCR analysis. The overall size of whole genome sequences (WGSs) of these two M. bovis isolates were ~4.272 Mb (M. bovis Bz_31150 isolated from a captive chimpanzee) and 4.17 Mb (M. bovis B2_7505 from a human patient), respectively. Alignment of these genomes against 15 MTBC genome sequences revealed 7248 single nucleotide polumorphisms (SNPs). Theses SNPs were used for phylogenetic analysis that indicated a strong relationship between M. bovis and the chimpanzee isolate (Bz_31150) while the other M. bovis genome from the human patient (B2_7505) analyzed did not cluster with any M. bovis or M. tuberculosis strains. WGS analysis also revealed multidrug resistance genotypes; these genomes revealed pncA mutations at positions H57D in Bz_31150 and B2_7505. Phenotypically, B2_7505 was an extensively drug-resistant strain and this was confirmed by the presence of mutations in the major resistance-associated proteins for all anti-tuberculosis (TB) drugs, including isoniazid (KatG (S315T) and InhA (S94A)), fluoroquinolones (S95T), streptomycin (rrs (R309C)), and rifampin (D435Y, a rare but disputed mutation in rpoB). The presence of these mutations exclusively in the human M. bovis isolate suggested that these occurred after transmission from cattle. Genome analysis in this study identified M. bovis in humans and great apes, suggesting possible transmission from domesticated ruminants in the area due to a dynamic and changing interface, which has created opportunity for exposure and transmission.
Bibliographical noteFunding Information:
Funding: This project was supported by NIH Research Training Grant # R25 TW009345 funded by the Fogarty International Center, the National Institute of Mental Health, the NIH Office of the Director Office of Research on Women’s Health, and the NIH Office of the Director the Office of AIDS Research.
Permission to use isolates for molecular characterization was obtained from the research committee of the JCRC; the JCRC Uganda-Case Western Reserve University (CWRU) Research Collaboration and the Molecular Diagnostics Laboratory Department of Medical Microbiology, College of Health Sciences (CHS), Makerere University Kampala. Institutional Review Board (IRB) approval was obtained from the Makerere University, School of Biomedical Sciences Research and Ethics Committee. Scientific and ethical clearance was obtained from the Uganda National Council for Science and Technology (UNCST) reference number HS 1478. Since the work was a retrospective study using archived isolates, this work was exempt from University of Minnesota IRB approval.
© 2019 by the authors. Licensee MDPI, Basel, Switzerland.
- Bovine TB
- Whole genome sequencing