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

Abstract

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.

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

“…This fits our previous studies on the infection networks of Kpn prophages 26 and suggests that a population of cells encoding and expressing a given serotype has more frequent phage-mediated genetic exchanges with bacteria of identical or similar serotypes ( Figure 6A). In this context, phages carrying multiple capsule depolymerases have broader host range and may have a key role in phagemediated gene flow between very distinct serotypes.…”

“…for the transfer of temperate phages from one bacterial genome to another. We found that 97% of the strains were lysogens, with 86% being poly-lysogens, in line with our previous results in a much smaller dataset 26 .…”

“…capsule for initial adherence before attaching to the primary cell receptor. Hence, instead of being hampered by the capsule, many Kpn phages have become dependent on it 26,27 . This means that the capsule may affect the rates of HGT positively or negatively depending on how it enables or blocks phage infection.…”

“…Furthermore, intense phage predation may select for capsule swap or inactivation, because this renders bacteria resistant to serotype-specific phages. While such serotype swaps may allow cells to escape phages to which they were previously sensitive, albeit exposing them to new infectious phages, capsule inactivation can confer pan-resistance to capsule-dependent phages 26 . In contrast, very little is known on the effect of capsules on conjugation, except that it is less efficient between a few different serotypes of Haemophilus influenzae 28 .…”

Selection for the bacterial capsule in the absence of biotic and abiotic aggressions depends on growth conditions

“…Capsule extraction and quantification. The bacterial capsule was extracted as described in (Domenico et al 1989) and quantified by using the uronic acid method (Blumenkrantz and Asboe-Hansen 1973). Briefly, 500 μL of an overnight culture was mixed with 100 μL of 1%…”