Genomic Characterization of 30 Lytic Klebsiella pneumoniae Bacteriophages

The emergence and spread of Gram-negative pathogens that are resistant to multiple antibiotic classes pose a global risk to public health. Among such pathogens, carbapenem-resistant strains of Klebsiella pneumoniae (CR-KP) are of concern due to their resistance to treatment by most antibiotics and the mobility of their drug resistance determinants. Bacteriophages that target K. pneumoniae are a promising alternative antimicrobial option. Here, we characterize 30 lytic bacteriophages from various environmental sources using whole-genome sequencing, bioinformatic analysis, virulence assays, and assessment of the effects of media on phage sensitivity. Bioinformatic analysis revealed a diverse collection of phages that span 9 ICTV Caudoviricetes families and 13 genera with genome sizes ranging from 39 kbp to 349 kbp, representing all three tailed phage morphotypes. The phages were all found to be strictly lytic and able to inhibit bacterial growth, and no virulence or antibiotic resistance genes were detected within the phage genomes. Host range testing showed that the culture medium used for plating can have a significant effect on observed susceptibility of some isolates to phages, and phages infecting multiple strains showed greater variation between media. Analysis of phage tail fiber proteins indicated that phages in the collection are predicted to encode from one to nine receptor-binding proteins, with 17/30 phages encoding at least one tail spike with predicted capsular depolymerase activity. The lack of detectable depolymerase domains in 13/30 phages suggests a large portion of the phage collection may recognize non-capsule receptors. This study describes a collection of candidate phages for further development as potential antimicrobial agents against CR-KP and the complexity in understanding phage–host dynamics of phages that recognize non-capsule receptors in K. pneumoniae.