Abstract
This work describes the newly isolated Klebsiella pneumoniae phage vB_KpnS-Carvaje that presents unique features in relation to other phages reported to date. These findings provide new insights into the diversity and evolutionary pathways of Klebsiella phages. The genome characterization of the Carvaje phage revealed that its genome length is approximately 57 kb with 99 open reading frames (ORFs), 33 of which have assigned functions while 66 are unknown. This phage differs from other sequenced Klebsiella phages, showing the closest resemblance (up to 65.32%) with Salmonella phages belonging to the Nonanavirus and Sashavirus genera. Comparisons at the amino acid level and phylogeny analysis among homologous genomes indicate that the Klebsiella Carvaje phage forms a novel sister taxon within the node of the Nonanaviruses and Sashaviruses cluster. Due to the unique features of the Carvaje phage, we propose the constitution of a new genus within the Caudoviricetes class. Further studies include the exploitation of this phage and its identified proteins for the control of Klebsiella infections and as recognition molecules in diagnostic methods.
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Phage infectivity, one-step growth curves, genome assembly and annotation, whole-genome alignment with closest relatives, phylogenetic analysis of vB_KpnS-Carvaje’s whole and partial (Open Reading Frames) genome, detailed bioinformatic analysis of most relevant phage proteins. vB_KpnS-Carvaje whole-genome is deposited in Genbank under the Accession number: OL604152. Further relevant data are within the paper and its Supporting Information file.
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Acknowledgements
The authors would like to thank the Clinical Academic Center of Braga (2CA-Braga) for establishing the ethical agreement between the Hospital of Braga and our research group, which led to the provision of the clinical isolates.
Funding
This study was supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the project “Phages‐on‐chip” PTDC/BTM‐SAL/32442/2017 (POCI‐01‐0145‐FEDER‐032442) and the strategic funding of the research unit INESC MN (UID/05367/2020) through pluriannual BASE and PROGRAMATICO financing. JCS acknowledges financial support from FCT through the grant SFRH/BD/144992/2019. SS acknowledges funding by FCT through the individual scientific employment program contract (2020.03171.CEECIND).
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CMC: conceived and coordinated the study. JCS: performed the laboratory experiments and curated raw sequencing data. JCS, SS and CMC: performed and analyzed whole and partial genome alignments and phylogenetics. AF isolated and characterized the hospital clinical isolates. JCS: wrote the original draft. SS and CC: performed the writing review and editing. All the authors reviewed and approved the final version of the manuscript.
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Sousa, J.C., Sillankorva, S., Faustino, A. et al. Suggestion for a new bacteriophage genus for the Klebsiella pneumoniae phage vB_KpnS-Carvaje. Curr Genet 68, 393–406 (2022). https://doi.org/10.1007/s00294-022-01242-2
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DOI: https://doi.org/10.1007/s00294-022-01242-2