Characterization of Klebsiella Phages Isolated Against a Clinical Host with High Genome and Proteome Identity but Variable Tail Fibers

The rate at which bacteria are gaining resistance to antibiotics is outpacing the discovery of new drugs. The rise of superbugs such as Carbapenem-resistant and Extended-Spectrum Beta-Lactamase Producing Enterobacteriaceae are leading to infections that are resistant to our last lines of defense. One of the most prolific genera of these bacteria is Klebsiella, which causes one third of Gram-negative infections. The need for alternative and companion treatments has never been greater. Bacteriophages are bacteria-infecting viruses with high specificity to their host. They show great promise as a potential treatment for antibiotic-resistant infections. Here, we describe the characterization of five closely related bacteriophages (ValerieMcCarty01–05) isolated against an antibiotic-resistant clinical strain of Klebsiella oxytoca, which is an emerging antimicrobial-resistant threat within the Klebsiella genus. These phages demonstrate high similarity at both the genomic and proteomic levels and share homology with other T4-like Enterobacterales phage. Two phages were further characterized through a mass spectrometry analysis of purified virions, identifying peptide spectrum matches for 40 proteins which appear to be virion proteins. In addition, the peptide spectrum matches for 39 hypothetical proteins suggest they are indeed proteins. Amino acid alignment revealed that the tail fibers display more variability than most of their genome, suggesting possible adaptive tail fiber gene shuffling. Despite this variability, these phages maintained broad but high specificity for Klebsiella species in this paper, including K. oxytoca, K. pneumoniae and K. aerogenes and several clinical Klebsiella isolates, with infectivity differences seen only in efficiency. This specificity for Klebsiella is consistent with the genus to which they belong (the Jiaodavirus, which contains only Klebsiella phages) and suggests they may be involved in the evolution of Klebsiella and be useful therapeutics.