Phenotypic and Genomic Comparison of Klebsiella pneumoniae Lytic Phages: vB_KpnM-VAC66 and vB_KpnM-VAC13

Abstract

Klebsiella pneumoniae is a human pathogen that worsens the prognosis of many immunocompromised patients. Here, we annotated and compared the genomes of two lytic phages that infect clinical strains of K. pneumoniae (vB_KpnM-VAC13 and vB_KpnM-VAC66) and phenotypically characterized vB_KpnM-VAC66 (time of adsorption of 12 min, burst size of 31.49 ± 0.61 PFU/infected cell, and a host range of 20.8% of the tested strains). Transmission electronic microscopy showed that vB_KpnM-VAC66 belongs to the Myoviridae family. The genomic analysis of the phage vB_KpnM-VAC66 revealed that its genome encoded 289 proteins. When compared to the genome of vB_KpnM-VAC13, they showed a nucleotide similarity of 97.56%, with a 93% of query cover, and the phylogenetic study performed with other Tevenvirinae phages showed a close common ancestor. However, there were 21 coding sequences which differed. Interestingly, the main differences were that vB_KpnM-VAC66 encoded 10 more homing endonucleases than vB_KpnM-VAC13, and that the nucleotidic and amino-acid sequences of the L-shaped tail fiber protein were highly dissimilar, leading to different three-dimensional protein predictions. Both phages differed significantly in their host range. These viruses may be useful in the development of alternative therapies to antibiotics or as a co-therapy increasing its antimicrobial potential, especially when addressing multidrug resistant (MDR) pathogens.

Molecular analysis of the interactions between phages and the bacterial host Klebsiella pneumoniae

“…In the Ackerviridae family, partial similarity between phages vB_KpnS-VAC35 and vB_KpnS-VAC51 (query: 93 %, identity: 95.37 %) was observed. Finally, in the Myoviridae family, the phage vB_KpnM-VAC36 was very different from the other two phages, vB_KpnM-VAC13 (query: 0 %, identity: 80.75 %) and vB_KpnM-VAC66 (query: 3 %, identity: 85.05 %), which are very similar (query: 95 %, identity: 97.56%), as previously demonstrated in a study carried out by our research group (38) (Figure 2).…”

“…It is worth mentioning that in the case of Autographiviridae , phage vB_KpnP-VAC1 was phylogenetically more similar to vB_KpnP-VAC71 than to B_KpnP-VAC25. Whereas, in the case of the Myoviridae , phage vB_KpnM-VAC36 was phylogenetically more distant than phages vB_KpnM-VAC13 and vB_KpnM-VAC66, which are very similar to each other, as demonstrated in a previous study conducted by our research group (38). (Figure 1A).…”

“…Most phages were found to have a typical organization of the genome in functional modules, as previously described (2, 51, 52). By contrast, members of the Myoviridae family, which are included in the “larger phages” (> 100 bp), did not present specific lysis blocks, and structural and morphogenesis-related proteins were repeated in several blocks throughout the genome (38, 53). The genomes of all phages had endolysins and holins, proteins that are responsible for degradation of the bacterial cell wall during the infection by the host to facilitate the exit of the phage progeny (54).…”

“…Ten new lytic phages isolated from sewage water samples and twelve lytic phages previously isolated by our research group (20, 37, 38) were used in this study. Briefly, 50 mL samples of water were collected near sewage plants and held at room temperature until processing in the laboratory.…”

Molecular characteristics of phages located in Carbapenemase-Producing Escherichia coli clinical isolates: New Phage-Like Plasmids

“…Other proteins identified were a large number of HNH homing endonucleases, which play a key role in DNA packaging and thus in the phage life cycle as previous studies described (19, 20). The endodeoxyribonuclease toxin RalR was also found in the prophages vB_EcoS-666R9, vB_EcoS-673R7 and vB_EcoS-683R6.…”