Widespread loss-of-function mutations implicating preexisting resistance to new or repurposed anti-tuberculosis drugs

Area of Science:

• Genomics
• Microbiology
• Drug Discovery

Background:

• Five new or repurposed drugs (NRDs) approved for multi-drug resistant tuberculosis face emerging resistance.
• Resistance to these NRDs appears faster than anticipated, possibly due to pre-existing resistance in naive strains.
• Previous studies on rapid resistance emergence primarily focused on short genetic variants.

Purpose of the Study:

• To comprehensively study the rapid emergence of resistance to new or repurposed drugs (NRDs) in tuberculosis.
• To utilize de novo-assembled genomes and systematically include structural variations (SV) and heterogeneity.
• To identify novel markers of resistance and lay the foundation for preventing pre-existing resistance in future drug development.

Main Methods:

• Conducted a systematic literature review identifying 313 NRD resistance variants across 13 genes.
• Analyzed 409 diverse clinical tuberculosis isolates (collected pre-programmatic drug use) for conventional, structural, and heterogeneous variants in these 13 genes.
• Employed de novo genome assembly for 106 of the isolates to comprehensively assess genetic variations.

Main Results:

• Identified 72 putative NRD resistance variants, including 5 previously reported and 67 novel ones.
• Observed various mutation types: promoter mutations, frameshifts, structural variations (SVs), and heterogeneous frameshifts/SVs.
• Delamanid and pretomanid resistance mutations were most prevalent (48/409 isolates), while linezolid resistance mutations were least prevalent (8/409 isolates).

Conclusions:

• Pre-existing mutations conferring resistance to at least one NRD were highly prevalent (21% of isolates).
• These mutations were primarily loss-of-function variants in genes involved in prodrug activation and efflux pump regulation.
• The comprehensive assessment methods, particularly for SVs and heterogeneity, can help mitigate the risk of pre-existing resistance in early-stage drug development.