Insights into genomic variations between Mycobacterium tuberculosis compartmentalized in the lungs and blood of HIV-infected individuals in Uganda

Abstract

Introduction: Mycobacterium tuberculosis (MTB), particularly clinical strains present a genomic diversity that ranges from several single nucleotide polymorphisms (SNPs) to insertions and deletions (INDELS). This study assessed the genetic variations between sequences of isolates belonging to the MTB Uganda family, a sub-lineage of the MTB lineage 4, from the lungs and blood of TB-HIV positive individuals in Uganda with the hypothesis that sequences of isolates from the blood have unique SNPs and INDELs that characterize MTB survival. Methods: A case-control study was conducted in-silico. Twenty-four MTB blood and lung sequences were examined in this study. The sequences were aligned against the H37Rv (RefSeq: NC_000962.3) reference genome using BWA-MEM. The alignment quality was checked using IGV. SAMtools was used to sort and index the alignment⁠. FreeBayes was used to identify SNPs and INDELs. The SNPs and INDELs were annotated using SnpEff. The 'cat' and 'grep' commands were used to compare and analyze variants between the MTB blood and lung sequences, and then the functions of the genes in which the variants unique to the blood sequences occurred were identified. Results: Comparative analysis of the genetic variation of the samples showed that MTB blood isolates had 11 virulence genes with distinctive non-synonymous SNPs, which were absent in MTB lung isolates. The majority of the INDELs were found in non-virulence genes, with the remainder found in both blood and lung isolate sequences. Discussion: Overall, the 11 virulence genes identified in this study that had distinctive non-synonymous SNPs are implicated in pathways that increase CFUs in the lungs and organs, as well as lower host survival, increase host tissue damage, and enhance tissue pathology, allowing for human host persistence. The true role of all SNPs mentioned in this study is difficult to determine. This supports the theory that MTB-blood isolates have SNPs that let them survive longer than MTB-pulmonary isolates, allowing these strains to stay in the blood of their hosts. Conclusions: MTB blood sequences have distinctive SNPs, which could explain the capacity of MTB blood isolates to persist outside of the lungs (in blood) of HIV-infected individuals.