Estimating plasmid conjugation rates: A new computational tool and a critical comparison of methods
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Date
2022-05
Publication Type
Journal Article
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yes
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Abstract
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.
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Publication status
published
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Book title
Journal / series
Volume
121
Pages / Article No.
102627
Publisher
Elsevier
Event
Edition / version
Methods
Software
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Date collected
Date created
Subject
Plasmid; Horizontal gene transfer; Conjugation rate; Simonsen method; Liquid mating culture
Organisational unit
09497 - Hall, Alex / Hall, Alex
03584 - Bonhoeffer, Sebastian / Bonhoeffer, Sebastian
Notes
Funding
167121 - Towards quantification of the contribution of plasmids to the spread of antibiotic resistance (SNF)