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 data, and show that the conjugation rate estimates often depend strongly on the time of measurement, the initial population densities, or the initial ratio of donor to recipient populations. We derive a new ‘end-point’ measure to estimate conjugation rates, which extends the 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. All tools to estimate conjugation rates are available in an R package and Shiny app. The result is a set of guidelines for easy, accurate, and comparable measurement of conjugation rates and tools to verify these rates.