Experimental evolution in the cystic fibrosis chemical environment reveals early TCA cycle flux as a central regulator of Mycobacterium abscessus biofilm formation

<i>Mycobacterium abscessus</i> (MAB) is an emerging opportunistic pathogen that can cause severe, recalcitrant pulmonary infections in susceptible groups, including people with cystic fibrosis (CF). MAB forms biofilms during human infection and in environmental reservoirs such as household plumbing systems, and biofilm formation renders MAB more drug tolerant. However, our limited understanding of the regulatory systems governing mycobacterial biofilm formation undercuts our ability to disperse MAB biofilms and potentially increase treatment efficacy. Using experimental evolution, we demonstrate that selective pressure from synthetic cystic fibrosis sputum medium (SCFM1) drives the emergence of evolved MAB lineages that more readily aggregate in different environmental conditions. Whole-genome sequencing identified mutations in genes coding for two putative IclR family transcriptional regulators, which we named MraA and MraB, as responsible for the increase in aggregation. Using RNA-seq, we revealed that MraA and MraB share a regulon composed largely of genes involved in the early tricarboxylic acid (TCA) cycle and glutamate metabolism. Targeted metabolomic analysis confirmed that both mutants had increased levels of TCA cycle intermediates citrate/isocitrate and α-ketoglutarate (AKG), suggesting that in WT both MraA and MraB suppress flux through those metabolites. We found we could increase both citrate/isocitrate and AKG pools in WT MAB by supplementing SCFM1 with acetate, thereby increasing biofilm formation without increasing expression of the MraA/B regulon and demonstrating a specific causal relationship between those metabolites and biofilm formation. Finally, we show that acetate-induced, agar-suspended biofilms confer antibiotic tolerance. Altogether, we demonstrate how MAB carbon flux can be redirected by selective pressures in a CF sputum-like chemical environment to increase biofilm formation and drug tolerance. We propose a model in which MraA and MraB control flux of citrate/isocitrate/AKG and thereby feed into a metabolism-based biofilm regulatory system in MAB.