Note: This sample program estimates the number of surviving antibiotic-resistant gene copies that undergo base editor-driven mutation over a specified number of generations. It assumes constant mutation and repair rates per generation, with equal segregation of gene copies into each daughter cell.

When using base editors to inactivate antibiotic resistance genes, tracking the number of remaining resistant bacteria across generations under continuous antibiotic selection is critical for evaluating the stability of the edited population. This program supports such analysis by allowing users to input the base editor efficiency (as the mutation rate), the back-mutation rate (as the repair rate), and the generation time.

Simulation results are visualized as a histogram showing the number of surviving cells as a function of generation number, with the mode highlighted in red. This helps evaluate the distribution of residual antibiotic-resistant bacteria across successive generations. Surviving cell counts are normalized to an initial population of one cell. Cells that lose antibiotic resistance due to base editor-mediated gene inactivation become sensitive and are gradually eliminated from the population under antibiotic pressure.

How to simulate Antibiotic Survival

This program simulates the accumulation of base editor-induced inactivation of antibiotic resistance genes in a population of gene copies across successive generations under continuous antibiotic exposure. It assumes that each resistance gene on the plasmid is equally likely to be inherited by daughter cells, and that mutation and repair occur at specified constant rates per generation.

User Inputs Required:

1. Target Antibiotic-Resistant Gene Copy Number

   • Definition: The initial number of resistance gene copies present on the plasmid in the system.

2. Mutation Rate

   • Definition: The probability that an antibiotic resistance gene copy undergoes base editor-mediated inactivation during a single generation.

   • Note: This corresponds to the base editor's efficiency in introducing a termination codon in the gene's coding sequence.

3. Repair Rate

   • Definition: The probability that an inactivated (mutated) gene reverts to its original, functional form in a single generation.

   • Note: This represents the rate of reversion or repair per generation.

4. Generation Time

   • Definition: The number of generations over which the simulation of mutation and repair is performed.