Genomic Characterization of Non-Tuberculous Mycobacteria Using Whole Genome Sequencing

Abstract

Introduction:The study aims to identify and characterize nontuberculous mycobacteria at the molecular level in patients suspected of having tuberculosis, as standardized identification criteria are recommended by the American Thoracic Society for quicker clinical and laboratory procedures.
Method: 772 samples were collected from 386 patients (2 each) in selected districts of Jammu and Kashmir. In addition to phenotypic, molecular methods were also used to detect the number, species/ sub-species and AMR gene/SNP’s detection of Non tuberculosis mycobacteria. Records of patients were collected for clinical information, such as symptoms and radiological findings.
Results:Out of 772 samples, 180 (23.31%) were positive for acid-fast bacteria, with 164 (21.24%) and 16 (2.07%) identified as M. tuberculosis complex and NTM respectively. Mycobacterium abscessus and M. intracellular isolates were the most frequent, identified by restriction endonuclease assay (REA-PCR) and whole genome sequencing. Furthermore, whole genome sequencing helps in detection of AMR gene and SNP’s. Common symptoms included cough, fever, shortness of breath, weight loss, sputum production, appetite loss, night sweating, and thrombocytosis.
Conclusion:A study of 386 patients revealed that most were over 40 years old, with a higher rate of non-tuberculous mycobacteria (NTM) infections in males. Common symptoms included cough, fever, shortness of breath, weight loss, and sputum production. Positive cultures showed 21.24% MTB complexes and 2.07% NTM growth. Although biochemical testing is time-consuming, the study found five distinct mycobacterial species with 100% concordance across REA-PCR, whole genome sequencing, and biochemical tests. Whole genome sequencing not only helped find NTM at the species level but also at the sub-species level. It also aids in the discovery of AMR genes and SNPs.