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

“…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 . In total, 9886 prophages were identified in the genomes, with their 16,319 gene families accounting for 19.5% of the species pan-genome (Figure 1B).…”

“…Instead, phages infecting bacteria with related serotypes might carry capsule depolymerases, which are known to act on di-or tri-saccharides 30-32 similar across these serotypes. 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 phage-mediated gene flow between very distinct serotypes.…”

“…The large size of the Kpn capsule locus is difficult to accommodate in the phage genome and the tendency of phages to be serotype-specific makes them unlikely vectors of novel capsular loci. Also, the recombination tracts observed in Figure 2C are too large to be transduced by most temperate phages of Kpn, whose prophages average 46 kb 26 . Since Kpn is not naturally transformable, we hypothesized that conjugation is the major driver of capsule acquisition.…”

“…Whether these swaps implicate a direct serotype replacement, or an intermediate non-capsulated state, is not sufficiently known. Several processes are known to select for capsule loss in some bacteria, including growth in rich medium 36 , phage-pressure, and immune response 26,27,44,45 (Figure 7B). Because of the physiological effects of these losses, and their impact on the rates and types of HGT, it’s important to quantify the frequency of inactivated (or silent) capsular loci and the mechanisms favouring it.…”

Prophage elements function as reservoir for antibiotic resistance and virulence genes in nosocomial pathogens

“…In the lytic cycle, the prophage is induced to produce progeny phages in response to chemical or physical stressors (4,5). Lysogenic phages or prophages are known to drive horizontal gene transfer (HGT) through transduction, but they also play an important role in increasing the genetic diversity of the host (6)(7)(8)(9)(10). Furthermore, defective prophages, also known as prophage-like elements, are stable in the host genome despite deleting most of the phage genes (6) and are known to increase host survival by conferring resistance against various stresses (11)(12)(13).…”