A guide to modeling plasmid co-infection dynamics

Mobile genetic elements like conjugative plasmids play a crucial role in shaping the genetic content and population dynamics of bacterial species. Bacterial populations often contain not one, but multiple co-circulating MGEs, which modify each other's population dynamics in a myriad of ways. Mathematical modeling is a powerful tool to gain intuition about the expected eco-evolutionary dynamics in a biological system with many interacting players. Here, we detail how to develop a mathematical model of plasmid co-infection, how to implement this computationally, and we give examples of what can be learned from such models.