Data from: Clinical antibiotic-resistance plasmids have small effects on biofilm formation and population growth in Escherichia coli in vitro
Data files
Oct 06, 2023 version files 87.48 KB
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bf_growth_sum.csv
17.58 KB
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bf_replicates.csv
47.59 KB
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growth_replicates.csv
18.89 KB
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README.md
3.42 KB
Abstract
Antimicrobial resistance (AR) mechanisms encoded on plasmids can affect other phenotypic traits in bacteria, including biofilm formation. These effects may be important contributors to the spread of AR and the evolutionary success of plasmids, but it is not yet clear how common such effects are for clinical plasmids/bacteria, and how they vary among different plasmids and host strains. Here, we used a combinatorial approach to test the effects of clinical AR plasmids on biofilm formation and population growth in clinical and laboratory Escherichia coli strains. In most of the 25 plasmid-bacterium combinations tested, we observed no significant change in biofilm formation upon plasmid introduction, contrary to the notion that plasmids frequently alter biofilm formation. In a few cases we detected altered biofilm formation, and these effects were specific to particular plasmid-bacterium combinations. By contrast, we found a relatively strong effect of a chromosomal streptomycin-resistance mutation (in rpsL) on biofilm formation. Further supporting weak and host-strain- dependent effects of clinical plasmids on bacterial phenotypes in the combinations we tested, we found growth costs associated with plasmid carriage (measured in the absence of antibiotics) were moderate and varied among bacterial strains. These findings suggest some key clinical resistance plasmids cause only mild phenotypic disruption to their host bacteria, which may contribute to the persistence of plasmids in the absence of antibiotics.
README: Clinical antibiotic-resistance plasmids have small effects on biofilm formation and population growth in Escherichia coli in vitro
https://doi.org/10.5061/dryad.612jm6497
This folder contains the data for the article:
Brülisauer, L., Leon-Sampedro, R., Hall, A. R. (2023). Clinical antibiotic-resistance plasmids have small effects on biofilm formation and population growth in Escherichia coli in vitro. Plasmid.
Comments and requests should be addressed to Laura Brülisauer: laura.bruelisauer@env.ethz.ch. The data is free of use, but I would appreciate being told, and this dataset and the matching article cited if appropriate.
We used a combinatorial approach to test the effects of clinical antibiotic resistance plasmids on biofilm formation and population growth in clinical and laboratory Escherichia coli strains. This dataset contains biofilm and growth data for each of the 25 plasmid-host combinations and the 5 plasmid-free host strains.
Description of the data and file structure
The file "bf_replicates.csv" contains all biofilm data collected for 9 replicates of each strain in both LB medium and M9 Minimal medium. We measured biofilm formation using a crystal violet assay in three 96-well microplates. Briefly, we distributed 9 replicates of each strain randomly on the three microplates and incubated them for 24 hours. After incubation, we measured culture optical density (OD) before staining the attached cells with crystal violet (OD_culture). We determined absolute biofilm formation for each replicate by measuring OD of the dissolved crystal violet (OD_abs) and calculated a normalised biofilm formation score by dividing the absolute biofilm formation by the culture density before staining (OD_norm). To assess the effect of plasmid introduction on biofilm formation, we calculated relative biofilm formation by dividing the normalised biofilm score of each plasmid-host combination by the mean of the normalised biofilm formation score of the respective plasmid-free host strain (OD_norm.rel).
The file "growth_replicates.csv" contains growth parameter data for 3 replicates of each strain in LB and M9 Minimal medium. We measured culture OD of each replicate every 15 min for 24 h. Using the growthrates (Petzoldt, 2017) and flux (Jurasinski et al., 2022) packages in R, version 0.8.2, we determined the maximum growth rate (mumax), maximum optical density (ODmax) and area under the curve (auc). We calculated relative mumax, ODmax and auc for each replicate by dividing the value of the plasmid-host combination by the mean of the respective parameter of the plasmid-free host strain.
The file "bf_growth_sum.csv" contains summarised data used for the figures in the article calculated using the data in "bf_replicates.csv" and "growth_replicates.csv", specifically the mean / median values and error measures. The columns are named using the prefixes in the biofilm and growth files with the following suffixes:
- .rel: relative to the plasmid-free recipient
- .mean: mean
- .median: median
- .se: standard error
- .errorpro: propagated standard error using the formula from Silva et al. (2011). Pervasive Sign Epistatis between Conjugative Plasmids and Drug-Resistance Chromosomal Mutations. PLoS Genet.
In all data sets, for plasmid-free host strains, the value in the "plasmid" column is NA.