A Frameshift Mutation in wcaJ Associated with Phage Resistance in Klebsiella pneumoniae

Abstract

Phage therapy is a potential and promising avenue for controlling the emergence and spread of multidrug-resistant (MDR) Klebsiella pneumoniae, however, the rapid development of anti-phage resistance has been identified as an obstacle to the development of phage therapy. Little is known about the mechanism employed by MDR K. pneumoniae strains and how they protect themselves from lytic phage predation in vitro and in vivo. In this study, comparative genomic analysis shows undecaprenyl-phosphate glucose-1-phosphate transferase (WcaJ), the initial enzyme catalyzing the biosynthesis of colanic acid, is necessary for the adsorption of phage 117 (Podoviridae) to the host strain Kp36 to complete its lytic life cycle. In-frame deletion of wcaJ alone was sufficient to provide phage 117 resistance in the Kp36 wild-type strain. Complementation assays demonstrated the susceptibility of phage 117, and the mucoid phenotype could be restored in the resistant strain Kp36-117R by expressing the wild-type version of wcaJ. Remarkably, we found that bacterial mobile genetic elements (insA and insB) block phage 117 infections by disrupting the coding region of wcaJ, thus preventing phage adsorption to its phage receptor. Further, we revealed that the wcaJ mutation likely occurred spontaneously rather than adapted by phage 117 predation under unfavorable environments. Taken together, our results address a crucial evolutionary question around the mechanisms of phage–host interactions, increasing our current understandings of anti-phage defense mechanisms in this important MDR pathogen.

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

“…In contrast, our results show that the capsule is often required for infection by Klebsiella induced prophages. This is in agreement with a recent study where inactivation of wcaJ, a gene essential for capsule synthesis, rendered the strain resistance to phage infection by a virulent phage (Tan et al 2020). Specific interactions between the phage and the capsule could be caused by the latter stabilizing viral adsorption, allowing more time for efficient DNA injection (Bertozzi Silva et al 2016).…”

“…However, the results above show that induced prophages tend to infect strains of similar CLT, and capsule mutants of the strain Kp36 were previously shown to become resistant to the virulent phage 117 (Tan et al 2020). Hence, we wondered if strains lacking a capsule would also be immune to temperate phages,, and so we tested whether isogenic capsule mutants from different CLTs (KL2, KL30 and KL1) were sensitive to phages present in the lysates.…”

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

“…Given that non-capsulated mutants are resistant to phages (as shown above and also observed in other studies [ 60 ]), we hypothesized that phages that infect a particular strain could drive the loss of its capsule. To test this, we performed a short-term evolution experiment (ten days, ca 70 generations).…”

“…It is often mentioned in the literature that capsules protect against phages [ 39 ]. However, the results above show that induced prophages tend to infect strains of similar CLT, and capsule mutants of the strain Kp36 were previously shown to become resistant to the virulent phage 117 [ 60 ]. Hence, we wondered if strains lacking a capsule would also be immune to temperate phages, and so we tested whether isogenic capsule mutants from different CLTs (KL2, KL30, and KL1) were sensitive to phages present in the lysates.…”

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

“…These predictions have an impact in the evolution of virulence and antimicrobial therapy. Some alternatives to antibiotics -phage therapy, depolymerases associated with antibiotics, pyocins, capsular polysaccharide vaccines -may select for the inactivation of the capsule26,44,55 . Such non-capsulated variants have often been associated with better disease outcomes56 , lower antibiotics tolerance22 and reduced virulence21 .…”