High-throughput laboratory evolution and evolutionary constraints inEscherichia coli

Abstract

These authors contributed equally to this work. SUMMARYUnderstanding the constraints that shape the evolution of antibiotic resistance is critical for predicting and controlling drug resistance. Despite its importance, however, a systematic investigation for evolutionary constraints is lacking. Here, we performed a high-throughput laboratory evolution of Escherichia coli under the addition of 95 antibacterial chemicals and quantified the transcriptome, resistance, and genomic profiles for the evolved strains. Using interpretable machine learning techniques, we analyzed the phenotype-genotype data and identified low dimensional phenotypic states among the evolved strains. Further analysis revealed the underlying biological processes responsible for these distinct states, leading to the identification of novel trade-off relationships associated with drug resistance. We also report a novel constraint that leads to decelerated evolution. These findings bridge the genotypic, gene expression, and drug resistance space and lead to a better understanding of evolutionary constraints for antibiotic resistance.

Identification of drivers of mycobacterial resistance to peptidoglycan synthesis inhibitors

“…The detection of a mutation in Rv2864c in the meropenem-resistant Mtb isolates in our study is in accordance with these observations and further supported by reports of increased cefotaxime sensitivity in a Mtb mutant generated through Rv2864c disruption and by CRISPR interference studies on Mycobacterium abscessus orthologue gene MAB_3167c (Wivagg et al, 2016;Akusobi et al, 2022). Maeda et al (2021) additionally report in their meropenemselected mutants a non-synonymous mutation in the coding sequence of MSMEG_6319 and an intergenic variant upstream MSMEG_6406 (AT701_RS31385), orthologue of Rv3811 and which encodes a putative N-acetylmuramoyl-l-alanine amidase. We did not observe the two latter features, but two of our meropenem-exposed mutants alternatively displayed a mutation 11 bp upstream the TSS of MSMEG_6317, adjacent to MSMEG_6319.…”

“…In conclusion, our study outputs imply that mycobacterial resistance to beta-lactams may not be as simplistic as once thought. Confirmation of mutations in Rv2864c and upstream MSMEG_6319 in mutants isolated with meropenem, corroborated previous descriptions of the involvement of the Msm gene in resistance to this carbapenem (Maeda et al, 2021). This is also in 10.…”

“…Rv2864c is a putative high-molecular-mass PBP with a lipoprotein motif, recently shown to be relatively resistant to all beta-lactam subclasses when compared to other well-known PBPs (Kumar et al, 2022). The mutation in the putative promoter region of MSMEG_6319 (AT701_RS30910) has been previously described in meropenem-resistant Msm mutants (Maeda et al, 2021). The detection of a mutation in Rv2864c in the meropenem-resistant Mtb isolates in our study is in accordance with these observations and further supported by reports of increased cefotaxime sensitivity in a Mtb mutant generated through Rv2864c disruption and by CRISPR interference studies on Mycobacterium abscessus orthologue gene MAB_3167c (Wivagg et al, 2016;Akusobi et al, 2022).…”

Genetic and Chemical Screening in Human Blood Serum Reveals Unique Antibacterial Targets and Compounds against Klebsiella pneumoniae

“…Several mutations that sensitized K. pneumoniae to ruthenium red, such as uvrD and recCG, have been shown to render bacteria more susceptible to DNA-damaging antibiotics such as ciprofloxacin (Tamae et al, 2008), suggesting that ruthenium red treatment leads to damaged DNA. Indeed, ruthenium red has been shown to bind DNA in vitro (Karpel et al, 1981), and a recent report showed that recA mutants of E. coli were more susceptible to this compound (Maeda et al, 2019). Ruthenium red has also been shown to modulate the polymerization of FtsZ in vitro, which plays an important role in cell division and interacts with FtsK (Grenga et al, 2008;Santra et al, 2004).…”

mbtD and celA1 association with ethambutol resistance in Mycobacterium tuberculosis: A multiomics analysis

“…In contrast to the method of agar-based selection for laboratory evolution against antibiotics (Maeda et al, 2021) or induced by high-concentration drugs (Zhao et al, 2014), the strategy of a continuous drug concentration gradient can better simulate the accumulation of drugs in the human body. Determination of the MIC value of 14 anti-TB drugs showed that laboratory-induced mono-EMB drug-resistant strains were successfully obtained (Supplementary Table S2).…”