Alain Hartmann

Abstract Plasmids carrying antibiotic resistance genes (ARG) are the main mechanism of resistance dissemination in Enterobacterales. However, the fitness-resistance trade-off may result in their elimination. Chromosomal integration of ARGs preserves resistance advantage while relieving the selective pressure for keeping costly plasmids. In some bacterial lineages, such as carbapenemase producing sequence type ST38 Escherichia coli, most ARGs are chromosomally integrated.

1. Introduction Antimicrobial resistance (AMR) currently exists at higher than natural levels due to antibiotics use and misuse in human and animal medicine and livestock production (Davies and Davies, 2010). Wastes from these origins contain pathogens and associated antibiotic resistance genes (ARGs), which can be dispersed via runoff into rivers in the environment (Amarasiri et al., 2019).