The Evolution of Fluoroquinolone-Resistance in Mycobacterium tuberculosis is Modulated by the Genetic Background

Fluoroquinolones (FQ) form the backbone in experimental treatment regimens against drug-susceptible tuberculosis. However, little is known on whether the genetic variation present in natural populations ofMycobacterium tuberculosis(Mtb) affects the evolution of FQ-resistance (FQ-R). To investigate this question, we used a set ofMtbstrains that included nine genetically distinct drug-susceptible clinical isolates, and measured their frequency of resistance to the FQ ofloxacin (OFX)in vitro. We found that theMtbgenetic background led to differences in the frequency of OFX-resistance (OFX-R) that spanned two orders of magnitude and substantially modulated the observed mutational profiles for OFX-R. Furtherin vitroassays showed that the genetic background also influenced the minimum inhibitory concentration and the fitness effect conferred by a given OFX-R mutation. To test the clinical relevance of ourin vitrowork, we surveyed the mutational profile for FQ-R in publicly available genomic sequences from clinicalMtbisolates, and found substantialMtblineage-dependent variability. Comparison of the clinical and thein vitromutational profiles for FQ-R showed that 45% and 19% of the variability in the clinical frequency of FQ-RgyrAmutations in Lineage 2 and Lineage 4 strains, respectively, can be attributed to howMtbevolves FQ-Rin vitro. As theMtbgenetic background strongly influenced the evolution of FQ-Rin vitro, we conclude that the genetic background ofMtbalso impacts the evolution of FQ-R in the clinic.SignificanceNewer generations of fluoroquinolones form the backbone in many experimental treatment regimens againstM. tuberculosis(Mtb). While the genetic variation in natural populations ofMtbcan influence resistance evolution to multiple different antibiotics, it is unclear whether it modulates fluoroquinolone-resistance evolution as well. Using a combination ofin vitroassays coupled with genomic analysis of clinical isolates, we provide the first evidence illustrating theMtbgenetic background’s substantial role in fluoroquinolone-resistance evolution, and highlight the importance of bacterial genetics when studying the prevalence of fluoroquinolone-resistance inMtb. Our work may provide insights into how to maximize the timespan in which fluoroquinolones remain effective in clinical settings, whether as part of current standardized regimens, or in new regimens againstMtb.