Morphological, biological, and genomic characterization of Klebsiella pneumoniae phage vB_Kpn_ZC2

• Published in: Virology journal 2023-05, Vol.20 (1), p.86-16, Article 86
• Main Authors: Fayez, Mohamed S, Hakim, Toka A, Zaki, Bishoy Maher, Makky, Salsabil, Abdelmoteleb, Mohamed, Essam, Kareem, Safwat, Anan, Abdelsattar, Abdallah S, El-Shibiny, Ayman
• Format: Article
• Language: English
• Subjects: Analysis; Anti-Bacterial Agents - pharmacology; Antibacterial activity; Antibacterial agents; Antibiotic resistance; Antibiotics; Antimicrobial agents; Bacteria; Bacterial infections; Bacterial pneumonia; Bacteriophage; Bacteriophages; DNA sequencing; Drug resistance; Drug resistance in microorganisms; Ethylenediaminetetraacetic acid; Gel electrophoresis; Genes; Genetic aspects; Genome, Viral; Genomes; Genomics; Gram negative; Health aspects; Holins; Identification and classification; Klebsiella; Klebsiella pneumoniae; Klebsiella pneumoniae - genetics; Lysogeny; Lytic enzymes; Medical research; Medicine, Experimental; Molecular weight; Multi-drug resistance (MDR); Multidrug resistance; Nosocomial infections; Nucleotide sequencing; Opportunist infection; Pathogens; Phage therapy; Phages; Physiological aspects; Pneumonia; Public health; Sewage; Siphovirus; Transmembrane domains; Transmission electron microscopy; Virulence; Virulence (Microbiology); Whole genome sequencing
• ISSN: 1743-422X; 1743-422X
• DOI: 10.1186/s12985-023-02034-x

Bacteriophages (phages) are one of the most promising alternatives to traditional antibiotic therapies, especially against multidrug-resistant bacteria. Klebsiella pneumoniae is considered to be an opportunistic pathogen that can cause life-threatening infections. Thus, this study aims at the characterization of a novel isolated phage vB_Kpn_ZC2 (ZCKP2, for short). The phage ZCKP2 was isolated from sewage water by using the clinical isolate KP/08 as a host strain. The isolated bacteriophage was purified and amplified, followed by testing of its molecular weight using Pulse-Field Gel Electrophoresis (PFGE), transmission electron microscopy, antibacterial activity against a panel of other Klebsiella pneumoniae hosts, stability studies, and whole genome sequencing. Phage ZCKP2 belongs morphologically to siphoviruses as indicated from the Transmission Electron Microscopy microgram. The Pulsed Field Gel Electrophoresis and the phage sequencing estimated the phage genome size of 48.2 kbp. Moreover, the absence of lysogeny-related genes, antibiotic resistance genes, and virulence genes in the annotated genome suggests that phage ZCKP2 is safe for therapeutic use. Genome-based taxonomic analysis indicates that phage ZCKP2 represents a new family that has not been formally rated yet. In addition, phage ZCKP2 preserved high stability at different temperatures and pH values (-20 - 70 °C and pH 4 - 9). For the antibacterial activity, phage ZCKP2 maintained consistent clear zones on KP/08 bacteria along with other hosts, in addition to effective bacterial killing over time at different MOIs (0.1, 1, and 10). Also, the genome annotation predicted antibacterial lytic enzymes. Furthermore, the topology of class II holins was predicted in some putative proteins with dual transmembrane domains that contribute significantly to antibacterial activity. Phage ZCKP2 characterization demonstrates safety and efficiency against multidrug-resistant K. pneumoniae, hence ZCKP2 is a good candidate for further in vivo and phage therapy clinical applications.