Complete Nucleotide Sequence of Klebsiella pneumoniae Bacteriophage vB_KpnM_KpV477

Komisarova, Ekaterina V.; Kislichkina, Angelina A.; Krasilnikova, Valentina M.; Богун, А. Г.; Fursova, Nadezhda K.; Volozhantsev, Nikolay V.

doi:10.1128/genomea.00694-17

Cited by 5 publications

(2 citation statements)

References 14 publications

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“…Globally, K. pneumoniae phages have been isolated from various sources, including sewage [ 18 ], ponds [ 19 ], rivers [ 20 ], seas [ 21 ], farm wastewater [ 22 ], water troughs [ 23 ], animal feces [ 24 ], and clinical samples [ 25 , 26 ], with sewage from hospitals being the most common source [ 27 – 33 ]. The majority of the isolated phages of K. pneumoniae are members of the class Caudoviricetes , which is characterized by being naked (non-enveloped), dsDNA and tailed [ 34 ].…”

Section: Introductionmentioning

confidence: 99%

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

Fayez

Hakim

Zaki

et al. 2023

Virol J

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Background 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). Methods 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. Results 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.

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Section: Introductionmentioning

confidence: 99%

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

Fayez

Hakim

Zaki

et al. 2023

Virol J

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“…KP1 exhibits a close relation with Klebsiella phages JD18, KP179, KPV15, Mineola, PKO111, and vB_KpnM_KpV477 which formed a cluster that belongs to Jiaodavirus genus ( Tevenvirinae subfamily, Myoviridae family; Komisarova et al, 2017 ), suggesting the grouping of KP1 to the sublineage shared by these phages. Since Jiaodavrius phages encode a Hoc-like protein which is highly immunogenic ( Townsend et al, 2021 ), it would be insightful to investigate the immunogenicity of KP1.…”

Section: Discussionmentioning

confidence: 98%

Characterization of Klebsiella pneumoniae bacteriophages, KP1 and KP12, with deep learning-based structure prediction

et al. 2023

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Concerns over Klebsiella pneumoniae resistance to the last-line antibiotic treatment have prompted a reconsideration of bacteriophage therapy in public health. Biotechnological application of phages and their gene products as an alternative to antibiotics necessitates the understanding of their genomic context. This study sequenced, annotated, characterized, and compared two Klebsiella phages, KP1 and KP12. Physiological validations identified KP1 and KP12 as members of Myoviridae family. Both phages showed that their activities were stable in a wide range of pH and temperature. They exhibit a host specificity toward K. pneumoniae with a broad intraspecies host range. General features of genome size, coding density, percentage GC content, and phylogenetic analyses revealed that these bacteriophages are distantly related. Phage lytic proteins (endolysin, anti-/holin, spanin) identified by the local alignment against different databases, were subjected to further bioinformatic analyses including three-dimensional (3D) structure prediction by AlphaFold. AlphaFold models of phage lysis proteins were consistent with the published X-ray crystal structures, suggesting the presence of T4-like and P1/P2-like bacteriophage lysis proteins in KP1 and KP12, respectively. By providing the primary sequence information, this study contributes novel bacteriophages for research and development pipelines of phage therapy that ultimately, cater to the unmet clinical and industrial needs against K. pneumoniae pathogens.

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Suggestion for a new bacteriophage genus for the Klebsiella pneumoniae phage vB_KpnS-Carvaje

et al. 2022

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Complete Nucleotide Sequence of Klebsiella pneumoniae Bacteriophage vB_KpnM_KpV477

Cited by 5 publications

References 14 publications

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

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

Characterization of Klebsiella pneumoniae bacteriophages, KP1 and KP12, with deep learning-based structure prediction

Suggestion for a new bacteriophage genus for the Klebsiella pneumoniae phage vB_KpnS-Carvaje

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