Detecting Single Nucleotide Polymorphisms in Mycobacterium orygis for the Creation of Standardized Diagnostic Markers
Mycobacterium orygis is an overlooked member of the Mycobacterium tuberculosis complex (MTBC). M. orygis had initially been detected in animals such as oryxes, cattle, antelopes, and rhesus monkeys. However, M. orygis has recently been isolated in patients presenting with tuberculosis from South Asia (Bangladesh, India, Nepal, and Pakistan). M. orygis has no accepted markers for identifying and tracking, which is a point of concern for rapid clinical diagnosis and epidemiological tracking.
Variant barcoding is an in silico technique that uses nucleotide markers, such as single nucleotide polymorphisms (SNPs), to distinguish variants.
We hypothesize that by using the variant barcoding methodology and validating our findings through Polymerase Chain Reaction and Sanger Sequencing, we would identify M. orygis specific SNPs that can be used as standard markers for M. orygis detection.
Pipeline detailing the various steps involved in quality checking, data clean-up, SNP generation and visualization, and phylogenetic tree generation and visualization. This pipeline has been modified and adapted to suit this project from the BAGEP pipeline (Source: BAGEP GitHub).
