Biology subjects

Reding Roman, R. C.

Publications and source records attributed to Reding Roman, R. C..

3 recordsLinked to original sources

bioRxiv2019

Hotspot Dosages of Most Rapid Antibiotic Resistance Evolution

We treated Escherichia coli with the antibiotic erythromycin from zero to high dosages to determine how the evolutionary dynamics of antibiotic resistant phenotypes and genotypes depend on dose. The most rapid increase in resistance was observed just below erythromycins minimal inhibitory concentration (MIC) and genotype-phenotype correlations determined from whole genome sequencing revealed the molecular basis of this: simultaneous selection for copy number variation in 3 resistance mechanisms which shared an inverted-U pattern of dose-dependent selection with several insertion sequences and an integron. Many genes did not conform to this pattern, however, because of changes in selection as dose increased: media adaptation at zero-to-low dosages gave way to drug target (ribosomal RNA operon) amplification at mid dosages whereas prophage-mediated drug efflux dominated at higher dosages where population densities were lowest. All dosages saw E. coli amplify the efflux operons acr and emrE at rates that correlated strongly with changes in population density that exhibited an inverted-U geometry too. However, we show by example that inverted-U geometries are not a universal feature of dose-resistance relationships.

evolutionary biology↗

bioRxiv2019

Metabolic trade-offs hide unforeseen benefits of plasmids carriage

The link between fitness and reproduction rate is a central tenet in microbiology, and indeed evolutionary biology: Mutants reproducing faster than the dominant wild-type are favoured by selection, but otherwise the mutation is lost. This link was given by Ronald Fisher in 1930 under the assumption that fitness can only change through mutations that boost or hinder growth rate, whence the use of logarithms on growth data by experimentalists. Here I show that logarithms are highly sensitive to sampling times, resulting in fitness estimates that are not constant over the growth of bacterial cultures. This variability invalidates typical selection measurements, and unfit mutants can be co-maintained if they reach their equilibrium. And this is what I observed in competition assays between two Escherichia coli constructs, one of which harbours a non-transmissible plasmid that protects against tetracycline (pGW155B), without using the antibiotic. Despite growing 40% slower than its drug-sensitive counterpart, the construct harbouring the plasmid persisted throughout the competition. And, perhaps more importantly, maintained the plasmid. My study suggests that reliance on growth rate masks that selection on plasmid carriage may be stronger than previously thought--explaining the seemingly-paradoxical abundance of plasmids in nature.

evolutionary biology↗

bioRxiv2019

Fluorescence photography of patterns and waves of bacterial adaptation at high antibiotic doses

Fisher suggested advantageous genes would spread through populations as a wave so we sought genetic waves in evolving populations, as follows. By fusing a fluorescent marker to a drug efflux protein (AcrB) whose expression provides Escherichia coli with resistance to some antibiotics, we quantified the evolution and spread of drug-resistant E. coli through spacetime using image analysis and quantitative PCR. As is done in hospitals routinely, we exposed the bacterium to a gradient of antibiotic in a disk diffusion drug susceptibility test that we videoed. The videos show complex spatio-genomic patterns redolent of, yet more complex than, Fishers predictions whereby a decelerating wave front of advantageous genes colonises towards the antibiotic source, forming bullseye patterns en route and leaving a wave back of bacterial sub-populations expressing AcrB at decreasing levels away from the drug source. qPCR data show that E. coli sited at rapidly-adapting spatial hotspots gain 2 additional copies of acr, the operon that encodes AcrB, within 24h and imaging data show resistant sub-populations thrive most near the antibiotic source due to non-monotone relationships between inhibition due to antibiotic and distance from the source. In the spirit of Fisher, we provide an explicitly spatial nonlinear diffusion equation that exhibits these properties too. Finally, linear diffusion theory quantifies how the spatial extent of bacterial killing scales with increases in antibiotic dosage, predicting that microbes can survive chemotherapies that have been escalated to 250x the clinical dosage if the antibiotic is diffusion-limited.

evolutionary biology↗