ABSTRACT Mobile genetic elements (MGEs) drive genetic transfers between bacteria using mechanisms that are affected by the cell envelope composition, notably the capsule. Here, we show that capsules constrain phage-mediated gene flow between closely related serotypes in Klebsiella pneumoniae , a high-priority nosocomial enterobacteria. Serotype-specific phage pressure may also explain the inactivation of capsule genes, which occur frequently and recapitulate the capsule biosynthetic pathway. We show that plasmid conjugation is increased upon capsule inactivation and that capsule re-acquisition leaves long recombination tracts around the capsular locus. This suggests that capsule inactivation by phage pressure facilitates its subsequent re-acquisition by conjugation, a process re-wiring gene flow towards novel lineages whenever it leads to serotype swaps. These results reveal the basis of trade-offs between the evolution of virulence and multidrug resistance. They also caution that some alternatives to antibiotic therapy may select for capsule inactivation, thus decreasing virulence but facilitating antibiotic resistance genes acquisition.

Interplay between the cell envelope and mobile genetic elements shapes gene flow in populations of a nosocomial pathogen