Tuberculosis at the animal-human interface in the Ugandan cattle corridor using a third-generation sequencing platform: A cross-sectional analysis study

Introduction Mycobacterial diseases are a significant source of disease burden, with Mycobacterium tuberculosis being the most common infectious cause of death worldwide. Given this, the emergence of antibiotic resistance in these species is of particular interest. By examining the epidemiology of mycobacteria in humans and cattle in an area of intense human-animal contact (the Ugandan cattle corridor [UCC]) and using a novel whole-genome sequencing technique to analyse organism diversity, this study will explore the role bidirectional transmission of mycobacteria plays in the local ecology, as well the significance of zoonotic Mycobacterium bovis in the human population. Methods and analysis This ongoing study includes both a cross-sectional analysis of the UCC mycobacteria-positive population and novel laboratory-based research focused on differentiating the species causing M. tuberculosis complex-linked disease. We will use a third-generation sequencing platform (the MinION sequencer from Oxford Nanopore Technology), comparing data from a sample subset to the Illumina platform as a means of measuring viability of the MinION platform in this specific setting. Our full sample set will be sequenced on Illumina and the data will be used to perform epidemiological and phylogenetic analyses. Ethics and dissemination Ethical approval was obtained from both the University of Minnesota IRB committee and the Ugandan National Council for Science and Technology - Research Ethics Committee. Samples were obtained after patients signed an informed consent indicating samples could be retained and used for research purposes. All samples are deidentified, with only basic demographic and geographic information being retained per national tuberculosis (TB) recording guidelines. Significant drug resistance results will be referred back to the local TB control officer to inform patient care. Final results of the study will be submitted to infectious disease-specific journals and will be submitted to the annual Infectious Diseases Society of America (IDSA) meeting.