Modular prophage interactions driven by capsule serotype select for capsule loss under phage predation

Klebsiella species are able to colonize a wide range of
environments and include worrisome nosocomial pathogens. Here, we sought
to determine the abundance and infectivity of prophages
of Klebsiella to understand how the interactions between
induced prophages and bacteria affect population dynamics and evolution.
We identified many prophages in the species, placing these taxa among the
top 5% of the most polylysogenic bacteria. We selected 35 representative
strains of the Klebsiella pneumoniae species complex to
establish a network of induced phage–bacteria interactions. This revealed
that many prophages are able to enter the lytic cycle, and subsequently
kill or lysogenize closely related Klebsiella strains.
Although 60% of the tested strains could produce phages that infect at
least one other strain, the interaction network of all pairwise
cross-infections is very sparse and mostly organized in modules
corresponding to the strains’ capsule serotypes. Accordingly, capsule
mutants remain uninfected showing that the capsule is a key factor for
successful infections. Surprisingly, experiments in which bacteria are
predated by their own prophages result in accelerated loss of the capsule.
Our results show that phage infectiousness defines interaction modules
between small subsets of phages and bacteria in function of capsule
serotype. This limits the role of prophages as competitive weapons because
they can infect very few strains of the species complex. This should also
restrict phage-driven gene flow across the species. Finally, the
accelerated loss of the capsule in bacteria being predated by their own
phages, suggests that phages drive serotype switch in nature.