Biology subjects

de Visser, J. A. G. M.

Publications and source records attributed to de Visser, J. A. G. M..

4 recordsLinked to original sources

bioRxiv2024

Collective β-lactam resistance in Escherichia coli due to β-lactamase release upon cell death

Collective antibiotic resistance occurs when populations of bacteria survive antibiotic treatments that are lethal to individual bacteria, which affects the efficacy of drug therapies. An important mechanism of collective resistance against widely used {beta}-lactams is the production of drug-degrading {beta}-lactamases. Here, we integrate experiments with mathematical modeling to understand the collective survival of Escherichia coli challenged with cefotaxime. At near-lethal cefotaxime concentrations, we observe complex dynamics, involving initial biomass growth due to filamentation, followed by death, and subsequently growth recovery. We show that production of AmpC, a chromosomal {beta}-lactamase, is responsible for cefotaxime degradation, allowing the resumption of cell division in surviving filaments. The detoxification of the environment proceeds through CTX hydrolysis by AmpC in the periplasm of intact cells, as well as extracellularly after cell lysis. Our model predicts the recovery time from molecular parameters, and quantifies the relative roles of periplasmic and extracellular degradation for two strains of E. coli that differ in the degree of privatization of AmpC hydrolysis. Our findings suggest that {beta}-lactam survival of bacterial infections depends on a combination of intra- and extracellular {beta}-lactamase activity, which will likely vary among isolates.

microbiology↗

bioRxiv2021

Population size mediates the contribution of high-rate and large-benefit mutations to parallel evolution

Both mutations with large benefits and mutations occurring at high rates may cause parallel evolution, but their contribution is expected to depend on population size. We show that small and large bacterial populations adapt to a novel antibiotic using similar numbers, but different types of mutations. Small populations repeatedly substitute similar high-rate structural variants, including the deletion of a nonfunctional {beta}-lactamase, and evolve modest resistance levels. Hundred-fold larger populations more frequently use the same low-rate, large-benefit point mutations, including those activating the {beta}-lactamase, and reach 50-fold higher resistance levels. Our results demonstrate a key role of clonal interference in mediating the contribution of high-rate and large-benefit mutations in populations of different size, facilitated by a tradeoff between rates and fitness effects of different mutation classes.

evolutionary biology↗

bioRxiv2020

Estimating the rate of plasmid transfer in liquid mating cultures

Plasmids are important vectors for the spread of genes among diverse populations of bacteria. However, there is no standard method to determine the rate at which they spread horizontally via conjugation. Here, we compare commonly used methods on simulated and experimental data, and show that the resulting conjugation rate estimates often depend strongly on the time of measurement, the initial population densities, or the initial ratio of donor to recipient populations. Differences in growth rate, e.g. induced by sub-lethal antibiotic concentrations or temperature, can also significantly bias conjugation rate estimates. We derive a new end-point measure to estimate conjugation rates, which extends the well-known Simonsen method to include the effects of differences in population growth and conjugation rates from donors and transconjugants. We further derive analytical expressions for the parameter range in which these approximations remain valid. We present an easy to use R package and web interface which implement both new and previously existing methods to estimate conjugation rates. The result is a set of tools and guidelines for accurate and comparable measurement of plasmid conjugation rates. HighlightsO_LIWe present an R package and Shiny app to estimate conjugation rates from experimental data C_LIO_LIWe highlight the diversity of existing measures used to estimate conjugation rates C_LIO_LIWe show these measures are biased for populations with differing growth and conjugation rates from donors or transconjugants C_LIO_LIWe develop a new end-point measure which accounts for such differences in growth and conjugation rates C_LI

microbiology↗

bioRxiv2017

Mutation supply and the repeatability of selection for antibiotic resistance

Whether evolution can be predicted is a key question in evolutionary biology. Here we set out to better understand the repeatability of evolution, which is a necessary condition for predictability. We explored experimentally the effect of mutation supply and the strength of selective pressure on the repeatability of selection from standing genetic variation. Different sizes of mutant libraries of an antibiotic resistance gene, TEM-1 {beta}-lactamase in Escherichia coli, were subjected to different antibiotic concentrations. We determined whether populations went extinct or survived, and sequenced the TEM gene of the surviving populations. The distribution of mutations per allele in our mutant libraries--generated by error-prone PCR--followed a Poisson distribution. Extinction patterns could be explained by a simple stochastic model that assumed the sampling of beneficial mutations was key for survival. In most surviving populations, alleles containing at least one known large-effect beneficial mutation were present. These genotype data also support a model which only invokes sampling effects to describe the occurrence of alleles containing large-effect driver mutations. Hence, evolution is largely predictable given cursory knowledge of mutational fitness effects, the mutation rate and population size. There were no clear trends in the repeatability of selected mutants when we considered all mutations present. However, when only known large-effect mutations were considered, the outcome of selection is less repeatable for large libraries, in contrast to expectations. Furthermore, we show experimentally that alleles carrying multiple mutations selected from large libraries confer higher resistance levels relative to alleles with only a known large-effect mutation, suggesting that the scarcity of high-resistance alleles carrying multiple mutations may contribute to the decrease in repeatability at large library sizes.

evolutionary biology↗