Rapid adaptation of a complex trait during experimental evolution of Mycobacterium tuberculosis

Abstract

Tuberculosis (TB), caused by Mycobacterium tuberculosis (M. tb), is a leading cause of death due to infectious disease. TB is not traditionally associated with biofilms, but M. tb biofilms are linked with drug and immune tolerance and there is increasing recognition of their contribution to the recalcitrance of TB infections. Here, we used M. tb experimental evolution to investigate this complex phenotype and identify candidate loci controlling biofilm formation. We identified novel candidate loci, adding to our understanding of the genetic architecture underlying M. tb biofilm development. Under selective pressure to grow as a biofilm, regulatory mutations rapidly swept to fixation and were associated with changes in multiple traits, including extracellular matrix production, cell size, and growth rate. Genetic and phenotypic paths to enhanced biofilm growth varied according to the genetic background of the parent strain, suggesting that epistatic interactions are important in M. tb adaptation to changing environments.

Case Studies in the Assessment of Microbial Fitness: Seemingly Subtle Changes Can Have Major Effects on Phenotypic Outcomes

“…However, this approach comes with a long list of caveats, including the following assumptions: (1) the relationship between absorbance and CFU/ml is unchanged after evolution (i.e., no evolved changes in cell size/shape); (2) the environment in which the growth curve is measured is analogous to the evolved environment; and (3) the growth parameters used as indirect measures of fitness directly translate to fitness (i.e., there are no evolved adversarial interactions between the lines) (Concepción-Acevedo et al 2015 ; Ram et al 2019 ). These assumptions are often erroneous as large-scale phenotyping can result in contradictory observations, such as the relationship between absorbance and CFU/ml not being affected by evolution (Lenski and Travisano 1994 ; Grant et al 2021 ; Marshall et al 2022 ; Smith et al 2022 ). Thus, for our first case, we compared three approaches for indirectly estimating fitness through a microbial growth curve.…”

Adaptation of the Mycobacterium tuberculosis transcriptome to biofilm growth

“…We identified phenotypic changes during adaptation to biofilm growth including changes in cell morphology, increased extracellular matrix (ECM) production and alterations of growth rate. We also identified genetic changes accompanying enhanced biofilm growth that varied according to the genetic background of the population [ 17 ].…”

“…tb clinical isolates to biofilm growth, using an evolve and re-sequence approach. We discovered that the mutational pathway to enhanced biofilm growth varied between clinical isolates [ 17 ]. These results led us to hypothesize that the regulatory mechanisms underlying pellicle biofilm formation exhibit similar variation.…”

AllTheBacteria - all bacterial genomes assembled, available and searchable

“…It included assemblies of over 300,000 genomes which had not previously been available (the raw data only had been available). The assemblies and search indexes allowed multiple other studies of plasmids[5, 6], bacterial adaptation[7, 8, 9, 10], and compression/indexing algorithms[11, 12, 13, 14, 15]. However, there were a few limitations.…”