Extended Data Fig. 10: Increasing growth rate at carrying capacity to model inflammation, or running simulations on a finer parameter grid, does not affect overall simulation trends.
From: Salmonella persisters promote the spread of antibiotic resistance plasmids in the gut
a, b, Simulations were run with identical parameters to Fig. 3c, d, but an increased birth and death rate at carrying capacity to simulate cases in which inflammation is present (Supplementary Information). The trends of the simulations remain the same as in Fig. 3c, d. a, Likelihood of the model as a function of the donor re-seeding (including donor-to-recipient conjugation) rate, and the rate of transconjugant-to-recipient plasmid transfer. All other parameter values are given in the Supplementary Information. The most-likely set of parameters is shown in red (η = 1 × 10−9 events per recipient per day; γ = 3.16 × 10−8 events per recipient per CFU per gram of faeces per day). b, The fraction of simulations with plasmid re-seeding (defined as a final transconjugant population size above 5 × 108 CFU per gram of faeces) is shown as a function of η. Here, γ is fixed at its most-likely value of 3.16 × 10−8 events per recipient per CFU per gram of faeces per day. The black vertical dotted line at η = 1 × 10−9 events per recipient per day indicates the estimated most-likely value from a. The red vertical dotted line at η = 1 × 10–11 events per recipient per day indicates a hypothetical 100-fold decrease of η (shown by a red arrow) (as might be caused, for example, by vaccination). c–f, Running simulations on a finer parameter grid does not affect the overall simulation trends. Supplementary Table 4 provides details of the differences between specific simulation results. c, d, Simulations were run on a grid of η = 10−12 to 10−6 and γ = 10−10 to 10−1 with 0.25-log increments, instead of the η = 10−12 to 10−1 and γ = 10−12 to 10−1 with 0.5-log increments used in Fig. 3c, d. e, f, Simulations were run with parameters identical to a, b, but on a grid of η = 10−12 to 10−6 and γ = 10−10 to 10−1 with 0.25-log increments, instead of η = 10−12 to 10−1 and γ = 10−12 to 10−1 with 0.5-log increments. c, e, Likelihood of the model as a function of the donor re-seeding (including donor-to-recipient conjugation) rate, and the rate of transconjugant-to-recipient plasmid transfer. All other parameter values are given in the Supplementary Information. The most-likely set of parameters is shown in red. d, f, The fraction of simulations with plasmid re-seeding (defined as a final transconjugant population size above 5 × 108 CFU per gram of faeces) is shown as a function of η. Here γ is fixed at its most likely value. The black vertical dotted line indicates the estimated most-likely value (from c or e). The red vertical dotted line indicates a hypothetical 100-fold decrease of η (shown by a red arrow) (as might be caused, for example, by vaccination).
