Raoultella bacteriophage RP180, a new member of the genus Kagunavirus, subfamily Guernseyvirinae

Fofanov, Mikhail V; Morozova, Vera; Kozlova, Yuliya; Tikunov, Artem; Бабкин, И. В.; Poletaeva, Yuliya; Ryabchikova, E. I.; Tikunova, Nina

doi:10.1007/s00705-019-04349-z

Cited by 5 publications

(4 citation statements)

References 21 publications

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“…oxytoca (0/1). To the best of our knowledge, ISF3 and ISF6 [23] and RP180 [24] are the only three Raoultella phages recorded in the literature. They were isolated against Raoultella ornithinolytica and Raoultella spp., respectively.…”

Section: Introductionmentioning

confidence: 99%

Extended genomic analyses of the broad-host-range phages vB_KmiM-2Di and vB_KmiM-4Dii reveal slopekviruses have highly conserved genomes

et al. 2022

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High levels of antimicrobial resistance among members of the Klebsiella oxytoca complex (KoC) have led to renewed interest in the use of bacteriophage (phage) therapy to tackle infections caused by these bacteria. In this study we characterized two lytic phages, vB_KmiM-2Di and vB_KmiM-4Dii, that were isolated from sewage water against two GES-5-positive Klebsiella michiganensis strains (PS_Koxy2 and PS_Koxy4, respectively). ViPTree analysis showed both phages belonged to the genus Slopekvirus. rpoB gene-based sequence analysis of 108 presumptive K. oxytoca isolates (n=59 clinical, n=49 veterinary) found K. michiganensis to be more prevalent (46 % clinical and 43 % veterinary, respectively) than K. oxytoca (40 % clinical and 6 % veterinary, respectively). Host range analysis against these 108 isolates found both vB_KmiM-2Di and vB_KmiM-4Dii showed broad lytic activity against KoC species. Several hypothetical homing endonuclease genes were encoded within the genomes of both phages, which may contribute to their broad host range. Differences in the tail fibre protein may explain the non-identical host range of the two phages. Pangenome analysis of 24 slopekviruses found that genomes within this genus are highly conserved, with more than 50 % of all predicted coding sequences representing core genes at ≥95 % identity and ≥70 % coverage. Given their broad host ranges, our results suggest vB_KmiM-2Di and vB_KmiM-4Dii represent attractive potential therapeutics. In addition, current recommendations for phage-based pangenome analyses may require revision.

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Section: Introductionmentioning

confidence: 99%

Extended genomic analyses of the broad-host-range phages vB_KmiM-2Di and vB_KmiM-4Dii reveal slopekviruses have highly conserved genomes

et al. 2022

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“…Gp68, Gp69, and Gp70 share 79, 98, and 95% identity, respectively, with their counterparts in Raoultella phage RP180. Furthermore, the lysis gene organization in the fBC-Eco01 genome is similar to that of Raoultella phage RP180 (NC_048181) [ 16 ].…”

Section: Resultsmentioning

confidence: 99%

Characterization and genome analysis of Escherichia phage fBC-Eco01, isolated from wastewater in Tunisia

et al. 2023

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The rise of antibiotic resistance in bacterial strains has led to vigorous exploration for alternative treatments. To this end, phage therapy has been revisited, and it is gaining increasing attention, as it may represent an efficient alternative for treating multiresistant pathogenic bacteria. Phage therapy is considered safe, and phages do not infect eukaryotic cells. There have been many studies investigating phage-host bacteria interactions and the ability of phages to target specific hosts. Escherichia coli is the causative agent of a multitude of infections, ranging from urinary tract infections to sepsis, with growing antibiotic resistance. In this study, we characterized the Escherichia phage fBC-Eco01, which was isolated from a water sample collected at Oued, Tunis. Electron microscopy showed that fBC-Eco01 phage particles have siphovirus morphology, with an icosahedral head of 61 ± 3 nm in diameter and a non-contractile tail of 94 ± 2 nm in length and 12 ± 0.9 nm in width. The genome of fBC-Eco01 is a linear double-stranded DNA of 43.466 bp with a GC content of 50.4%. Comparison to databases allowed annotation of the functions to 39 of the 78 predicted gene products. A single-step growth curve revealed that fBC-Eco01 has a latent period of 30 minutes and a burst size of 175 plaque-forming units (PFU) per infected cell. Genomic analysis indicated that fBC-Eco01 is a member of the subfamily Guernseyvirinae. It is most closely related to a group of phages of the genus Kagunavirus that infect Enterobacter, Raoultella, and Escherichia strains.

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“…The Thermo Scientific™ Gene JET PCR Purification Kit was used to clean PCR products. Purified samples were checked for DNA concentration and purity using a NanoDrop™ 2000 spectrophotometer (24). Samples were then adjusted to 10 ng/µL and sent for sequencing (Source BioScience) using the MLST forward primer (5'-GTTTTCCCAGTCACGACGTTGTA-3') (25).…”

Section: Growth Media and Culture Conditionsmentioning

confidence: 99%

“…KMI8 was lytic against 3/5 K. michiganensis strains but not K. pneumoniae (0/5) or K. oxytoca (0/1). To the best of our knowledge, ISF3 and ISF6 (23) and RP180 (24) are the only three Raoultella phages recorded in the literature. They were isolated against Raoultella ornithinolytica and Raoultella spp., respectively.…”

Section: Introductionmentioning

confidence: 99%

Extended genomic analyses of the broad-host-range phages vB_KmiM-2Di and vB_KmiM-4Dii reveal slopekviruses have highly conserved genomes

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et al. 2022

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High levels of antimicrobial resistance among members of the Klebsiella oxytoca complex (KoC) have led to renewed interest in the use of bacteriophage (phage) therapy to tackle infections caused by these bacteria. In this study we characterized two lytic phages, vB_KmiM-2Di and vB_KmiM-4Dii, that were isolated from sewage water against two GES-5-positive Klebsiella michiganensis strains (PS_Koxy2 and PS_Koxy4, respectively). ViPTree analysis showed both phages belonged to the genus Slopekvirus. rpoB gene-based sequence analysis of 108 presumptive K. oxytoca isolates (n=59 clinical, n=49 veterinary) found K. michiganensis to be more prevalent (46 % clinical and 43 % veterinary, respectively) than K. oxytoca (40 % clinical and 6 % veterinary, respectively). Host range analysis against these 108 isolates found both vB_KmiM-2Di and vB_KmiM-4Dii showed broad lytic activity against KoC species. Several putative homing endonuclease genes were encoded within the genomes of both phages, which may contribute to their broad host range. Pangenome analysis of 24 slopekviruses found that genomes within this genus are highly conserved, with more than 50 % of all predicted coding sequences representing core genes at ≥95 % identity and ≥70 % coverage. Given their broad host ranges, our results suggest vB_KmiM-2Di and vB_KmiM-4Dii represent attractive potential therapeutics. In addition, current recommendations for phage-based pangenome analyses may require revision.

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Raoultella bacteriophage RP180, a new member of the genus Kagunavirus, subfamily Guernseyvirinae

Cited by 5 publications

References 21 publications

Extended genomic analyses of the broad-host-range phages vB_KmiM-2Di and vB_KmiM-4Dii reveal slopekviruses have highly conserved genomes

Extended genomic analyses of the broad-host-range phages vB_KmiM-2Di and vB_KmiM-4Dii reveal slopekviruses have highly conserved genomes

Characterization and genome analysis of Escherichia phage fBC-Eco01, isolated from wastewater in Tunisia

Extended genomic analyses of the broad-host-range phages vB_KmiM-2Di and vB_KmiM-4Dii reveal slopekviruses have highly conserved genomes

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