Microevolution of Mycobacterium tuberculosis strains during long-term observation of chronic patients

A significant proportion of TB patients undergo multiple courses of long-term treatment. To gain molecular insight into Mycobacterium tuberculosis variation during long-term observation and treatment of chronic tuberculosis (TB) patients. The retrospective study enrolled nine tuberculosis patients who had multiple episodes of receiving anti-TB chemotherapy during long-term observation (up to 7 years). M. tuberculosis isolates (2-3 per patient) were available and subjected to whole genome sequencing using MiSeq (Illumina) followed by bioinformatics analysis with Geneious R (Biomatters), SAM-TB and Phyresse online tools. This research was supported by Russian Science Foundation (grant 24-44-00004). Analysis of serial isolates from the same patient recovered in the course of long-term observation showed an increase in mutations in the drug resistance genes in strains of the Beijing B0/W148 cluster (Russian epidemic strain). The first isolates from 8 patients were MDR, from 5 – pre-XDR. In the follow-up, XDR strains were isolated from three more MDR-TB patients (2 strains of cluster B0/W148 and 1 strain of cluster 94-32). Mutations in eis, folC, pncA emerged in the last available isolates. In one isolate, Rv0678 Arg134Stop mutation (bedaquiline resistance) was present. Beijing B0/W148 cluster strains showed capacity to readily acquire drug resistance mutations during long-term treatment. In contrast, Beijing Central Asian/Russian clade was more stable with regard to mutations associated with drug resistance over a long period of observation. While strain itself did not change, fluctuating resistance mutations, emerging/disappearing in some consecutive isolates may reflect compartmentalization of TB infection in a patient.