How TB bacteria change inside patients

Tuberculosis (TB) remains one of the world’s deadliest infectious diseases, driven by bacteria in the Mycobacterium tuberculosis complex (MTBC). As MTBC strains become more resistant to anti-TB drugs, treatment becomes harder and outcomes worse. To understand how the bacteria change while infecting people, Francesc Coll and colleagues gathered sequencing data from multiple clinical isolates taken from the same patients. They combined data from published studies and TB Portals, then applied stringent genomic QC criteria to keep only clonal isolates and used robust genomic pipelines to identify mutations that arose de novo during infection. The team used a convergent evolution approach to search across many patients for genes, operons and promoter regions that were repeatedly hit by mutations. In total, this large meta-analysis examined 5,899 high-quality genomes from 1,056 TB patients after ensuring clonality of isolate genomes, producing a dataset that captures how MTBC diversifies and adapts inside individual human hosts.

The analysis found limited within-host diversity overall, but still identified 3,296 fixed mutations across 501 patients. Statistically, 21 genes, 25 operons and 27 promoter regions were enriched by mutations compared to the rest of the genome, with other loci approaching significance. Importantly, many of the frequently mutated loci are already known or suspected to influence drug response: mutations affected genes involved in resistance to first-, second-, and last-line anti-TB drugs. The study also estimated how often drug resistance was acquired during treatment for the subset of patients with drug treatment data and found that fluoroquinolone resistance was acquired more frequently during treatment than resistance to any other anti-TB drug. Previously reported candidate drug-resistance and -tolerance genes were recovered, including prpR, Rv2571c, fadD11, helY, ndhA, Rv0139, fadE5, and the mce1 operon. Genes encoding regulators phoR, whiB6 and mycP 1 and effectors espK and eccE 1 of the virulence ESX-1 locus were also frequently mutated in host.

Taken together, these results show that studying mutations that arise during infection reveals both expected and new signals of bacterial adaptation. Much of the signal is linked to drug resistance, but changes also touch genes involved in pathogenesis, suggesting the bacteria are adapting to conditions inside the human body as well as to drug pressure. The higher rate of fluoroquinolone resistance acquisition observed during treatment may have important clinical relevance, because it points to a class of drugs where resistance can emerge more readily while patients are being treated. The study ends by providing a list of candidate loci that will require mechanistic characterisation and laboratory work to understand how specific mutations affect bacterial behavior and disease progression. These genomic clues give researchers concrete targets for follow-up studies that might lead to better diagnostics, monitoring and treatment strategies in the future.