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. 2024 Oct 3;12(10):e0025424.
doi: 10.1128/spectrum.00254-24. Epub 2024 Aug 28.

Targeted phage hunting to specific Klebsiella pneumoniae clinical isolates is an efficient antibiotic resistance and infection control strategy

Affiliations

Targeted phage hunting to specific Klebsiella pneumoniae clinical isolates is an efficient antibiotic resistance and infection control strategy

Celia Ferriol-González et al. Microbiol Spectr. .

Abstract

Klebsiella pneumoniae is one of the most threatening multi-drug-resistant pathogens today, with phage therapy being a promising alternative for personalized treatments. However, the intrinsic capsule diversity in Klebsiella spp. poses a substantial barrier to the phage host range, complicating the development of broad-spectrum phage-based treatments. Here, we have isolated and genomically characterized phages capable of infecting each of the acquired 77 reference serotypes of Klebsiella spp., including capsular types widespread among high-risk K. pneumoniae clones causing nosocomial infections. We demonstrated the possibility of isolating phages for all capsular types in the collection, revealing high capsular specificity among taxonomically related phages, in contrast to a few phages that exhibited broad-spectrum infection capabilities. To decipher the determinants of the specificity of these phages, we focused on their receptor-binding proteins, with particular attention to depolymerases. We also explored the possibility of designing a broad-spectrum phage cocktail based on phages isolated in reference capsular-type strains and determining the ability to lyse relevant clinical isolates. A combination of 12 phages capable of infecting 55% of the reference Klebsiella spp. serotypes was tested on a panel of carbapenem-resistant K. pneumoniae clinical isolates. Thirty-one percent of isolates were susceptible to the phage cocktail. However, our results suggest that in a highly variable encapsulated bacterial host, phage hunting must be directed to the specific Klebsiella isolates. This work is a step forward in the understanding of the complexity of phage-host interactions and highlights the importance of implementing precise and phage-specific strategies to treat K. pneumoniae infections worldwide.IMPORTANCEThe emergence of resistant bacteria is a serious global health problem. In the absence of effective treatments, phages are a personalized and effective therapeutic alternative. However, little is still known about phage-host interactions, which are key to implementing effective strategies. Here, we focus on the study of Klebsiella pneumoniae, a highly pathogenic encapsulated bacterium. The complexity and variability of the capsule, where in most cases phage receptors are found, make it difficult for phage-based treatments. Here, we isolated a large collection of Klebsiella phages against all the reference strains and in a cohort of clinical isolates. Our results suggest that clinical isolates represent a challenge, especially high-risk clones. Thus, we propose targeted phage hunting as an effective strategy to implement phage-derived therapies. Our results are a step forward for new phage-based strategies to control K. pneumoniae infections, highlighting the importance of understanding phage-host interactions to design personalized treatments against Klebsiella spp.

Keywords: Klebsiella pneumoniae; bacterial capsule; depolymerase; host range; phage cocktail; phage hunting; phage therapy; receptor-binding protein.

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Conflict of interest statement

P.D.-C. is a co-founder of Evolving Therapeutics SL and a member of its scientific advisory board.

Figures

Fig 1
Fig 1
Viral cluster network including 76 isolated and characterized Klebsiella phages. The network analysis has been performed on protein profiles encoded by phages using the vConTACT2 software. Each of the Klebsiella phages isolated here is represented as red nodes. Previous phages belonging to the same VC are represented with specific color nodes. The gray nodes correspond to other phages that were used as references for our analysis. The graph was visualized using a force-directed layout through Cytoscape software (42). NaN, non-available name.
Fig 2
Fig 2
Intergenomic similarity between the isolated and characterized Klebsiella phages taxonomically classified. The viral clusters obtained after the vContact2 process were organized into family or subfamily and genus. The intergenomic similarities were computed using blastn (46). The arrows, oriented along the coding strand, represent the identified opening reading frames. Each color is related to a functional group, as defined in the PHROG database (43). Correspondence between the name of the phages and the alias is available in supplementary material.
Fig 3
Fig 3
Count of the receptor-binding proteins (RBP) in the isolated and characterized Klebsiella phages arranged by viral cluster. The chart plot represents in the vertical axis each of the phages classified in their viral clusters. The horizontal axis indicates the total RBP count. The count of tail fibers is represented in blue and the count of depolymerases in gold.
Fig 4
Fig 4
Host range of the 86 isolated Klebsiella phages against 77 Klebsiella reference serotypes. (A) Modular distribution of the cross-infection matrix representing the host range of the 86 isolated Klebsiella phages in each column over the 77 Klebsiella spp. reference strains in each row. Positive interactions are represented in blue, and negative interactions are represented in white. The 17 modules detected are squared in red [modularity value Q = 0.604 (P-value = 2.2 × 10−16)]. (B) General properties of cross-infection matrix, including host interactions and phage interactions. (C) Graphic representation of the number of phages among the 86 isolated with different host ranges. The horizontal axis represents the phage host range (number of susceptible reference strains), while the vertical axis represents the amount of Klebsiella phages for each group.
Fig 5
Fig 5
Association between KL, ST, and susceptibility to the phage cocktail in a panel of 58 carbapenem-resistant K. pneumoniae clinical isolates. (A) Association between KL and ST. The inner circle represented the different STs of the isolates proportionally to the number of isolates with each ST. The outer circle represented the different KLs of the isolates with each ST, also proportionally to the number of isolates with each KL. Colors represent the different KLs. STs colored in gray are not associated with a single KL. The number of strains with each KL type is indicated between parentheses in the legend. (B) Association between KL and susceptibility to the phage cocktail. The inner circle represents the proportion of susceptible and resistant isolates, represented in light gray and dark gray, respectively. The outer circle represented the different KLs of the strains susceptible and resistant to the cocktail. Some KLs are present in both categories because there are both resistant and susceptible isolates with these particular KLs. Portions are proportional to the number of isolates resistant or susceptible to each particular KL. Reference KL types are represented in orange and non-reference in blue. 77.8% of susceptible isolates have a reference KL type, while only 22.2% have a non-reference KL type. In contrast, 42.5% of resistant isolates had a reference KL type, while 57.5% had a non-reference KL type.
Fig 6
Fig 6
Host range of 21 Klebsiella phages and 11 isolates with KL-type 64. (A) Cross-infection matrix between 21 Klebsiella phages and 10 KL-type 64 clinical isolates and the K64 reference strain (represented in bold). Twenty of the phages were directly isolated in clinical isolates and one in the K64 reference strain (represented in bold). (B) General properties of the phage–bacteria cross-infection matrix host interactions and phage interactions.

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