NEW YORK – A team from Japan and Thailand has tallied genetic variation across the genome in the tuberculosis-causing bacteria Mycobacterium tuberculosis, identifying large insertions and deletions and other variants linked to drug resistance and clinical outcomes in Thailand.
"This study provides a comprehensive catalog of genetic variations and highlights their potential impact for the future treatment and risk prediction of tuberculosis," co-senior and co-corresponding authors Akihiro Fujimoto, a human genetics researcher affiliated with the University of Tokyo, and Surakameth Mahasirimongkol, with Thailand's Ministry of Public Health, and their colleagues wrote in Cell Host & Microbe on Monday.
With the help of a computational tool established for finding large insertions and deletions (indels), the team searched for informative single-nucleotide changes, small indels, and large indels in 1,960 M. tuberculosis genomes generated from sputum samples collected from 1,186 tuberculosis patients treated in the northern Thailand province of Chiangrai between 2002 and 2011, or from 774 tuberculosis cases from 2015 that were documented through Thailand's Ministry of Public Health.
The team noted that a subset of 17 M. tuberculosis isolates was assessed by long-read sequencing using Oxford Nanopore Technology, while two isolates were sequenced with a Pacific Biosciences long-read platform.
"[W]e developed a computational method for highly accurate large indel calling based on a systematic comparison of long-read and short-read data," the authors explained. "Using these methods, we revealed a genome-wide pattern of genetic variations, a signature of natural selection, and genes associated with disease outcomes and drug resistance."
Among the variants found in the clinical isolate genomes, the team highlighted 1,181 large indels. While variants classified as partially deleterious appeared to be particularly common in the M. tuberculosis isolates, variants expected to disrupt gene functions turned up less frequently in genes known for having essential, survival-related roles in the pathogen.
"Our analysis revealed that non-essential genes had a higher percentage of genes with large indels than essential genes," the authors explained, "indicating the importance of large indels in gene functions."
By bringing in clinical data and findings from drug susceptibility testing on the tuberculosis-causing clinical isolates, meanwhile, the investigators performed genome-wide association and gene burden testing to find genes containing variants linked to tuberculosis outcomes or drug resistance.
Along with prognostic alterations in the bacterial virulence-related gene eccB2, for example, the team identified nearly two-dozen non-canonical drug resistance genes in the isolates. Again, large indels appeared to have "crucial roles" in such processes, the authors suggested, contributing to drug response or clinical outcomes associations involving five genes.
The authors noted that the comprehensive analysis of genetic variations is "indispensable" for the study of M. tuberculosis and thus will contribute to future treatments and risk prediction. They also noted that additional association, long-read sequencing, and functional studies are expected to validate and further expand knowledge of the large indels and candidate genes involved in such processes.