Genomic characteristics of vB_PpaP_PP74, a T7-like Autographivirinae bacteriophage infecting a potato pathogen of the newly proposed species Pectobacterium parmentieri

Kabanova, Anastasia P.; Shneider, Mikhail M.; Bugaeva, Eugenia N; Ha, Vo Thi Ngoc; Miroshnikov, Kirill K.; Korzhenkov, Aleksei A.; Kulikov, Eugene E.; Toschakov, Stepan V; Игнатов, А. Н.; Miroshnikov, Konstantin A.

doi:10.1007/s00705-018-3766-1

Cited by 9 publications

(11 citation statements)

References 25 publications

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“…The closest match in the database is an as yet unpublished D. solani phage Ninurta (Genbank reference: MH059639) isolated from organic waste in Denmark that shares 95% DNA identity with JA10. The closest published phage is the Pectobacterium parmentieri phage PP74 isolated from potato washing waste water in Russia in 2015 (Kabanova et al, 2018 ), which shares less than 14% nucleotide identity. It shares no DNA sequence identity with the other sequenced Dickeya -infecting Podoviridae family member BF25/12 (Alič et al, 2017b ).…”

Section: Resultsmentioning

confidence: 99%

Jumbo Bacteriophages Are Represented Within an Increasing Diversity of Environmental Viruses Infecting the Emerging Phytopathogen, Dickeya solani

2018

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Dickeya species are economically important phytopathogens widespread in mainland Europe that can reduce crop yields by 25%. There are no effective environmentally-acceptable chemical systems available for diseases caused by Dickeya. Bacteriophages have been suggested for use in biocontrol of these pathogens in the field, and limited field trials have been conducted. To date the majority of bacteriophages capable of infecting Dickeya solani, one of the more aggressive species, are from the same family, the Ackermannviridae, many representatives of which have been shown to be unsuitable for use in the field due to their capacity for generalized transduction. Members of this family are also only capable of forming individual plaques on D. solani. Here we describe novel bacteriophages from environmental sources isolated on D. solani, including members of two other viral families; Myoviridae and Podoviridae, most of which are capable of forming plaques on multiple Dickeya species. Full genomic sequencing revealed that the Myoviridae family members form two novel clusters of jumbo bacteriophages with genomes over 250 kbp, with one cluster containing phages of another phytopathogen Erwinia amylovora. Transduction experiments showed that the majority of the new environmental bacteriophages are also capable of facilitating efficient horizontal gene transfer, however the single Podoviridae family member is not. This particular phage therefore has potential for use as a biocontrol agent against multiple species of Dickeya.

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Section: Resultsmentioning

confidence: 99%

Jumbo Bacteriophages Are Represented Within an Increasing Diversity of Environmental Viruses Infecting the Emerging Phytopathogen, Dickeya solani

2018

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“…The highest similarity throughout the whole vB_ShiP-A7 genome was observed with 15 phages (coverage 74%-88%, identity 86%-93%), including Escherichia phage P483 (Chen et al, 2016), Escherichia phage P694 (Chen et al, 2016), Enterobacteria phage BA14 (Mertens and Hausmann, 1982), Escherichia phage vB EcoP S523, Enterobacteria phage 285P,Pectobacterium phage PP74 (Kabanova et al, 2018), Kluyvera phage Kvp1 (Lingohr et al, 2008), Erwinia phage FE44 (Faidiuk and Tovkach, 2014), Salmonella phage BSP161, Salmonella phage BP12A, Yersinia phage PYPS50, Yersinia phage Yepe2,Yersinia phage YpP-G (Rashid et al, 2012), Yersinia phage Berlin and Yersinia phage Yep-phi (Zhao et al, 2011) (Figure 4). Except for Escherichia phage vB EcoP S523, Salmonella phage BSP161, Salmonella phage BP12A, and Yersinia phage PYPS50, all the other 11 related phages are known T7-like phages.…”

Section: Comparative Genome Analysis Of Vb_ship-a7 With Its Related Phagesmentioning

confidence: 99%

Molecular Characteristics of Novel Phage vB_ShiP-A7 Infecting Multidrug-Resistant Shigella flexneri and Escherichia coli, and Its Bactericidal Effect in vitro and in vivo

Zhang

et al. 2021

Front. Microbiol.

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In recent years, increasing evidence has shown that bacteriophages (phages) can inhibit infection caused by multidrug-resistant (MDR) bacteria. Here, we isolated a new phage, named vB_ShiP-A7, using MDR Shigella flexneri as the host. vB_ShiP-A7 is a novel member of Podoviridae, with a latency period of approximately 35 min and a burst size of approximately 100 phage particles/cell. The adsorption rate constant of phage vB_ShiP-A7 to its host S. flexneri was 1.405 × 10–8 mL/min. The vB_ShiP-A7 genome is a linear double-stranded DNA composed of 40,058 bp with 177 bp terminal repeats, encoding 43 putative open reading frames. Comparative genomic analysis demonstrated that the genome sequence of vB_ShiP-A7 is closely related to 15 different phages, which can infect different strains. Mass spectrometry analysis revealed that 12 known proteins and 6 hypothetical proteins exist in the particles of phage vB_ShiP-A7. Our results confirmed that the genome of vB_ShiP-A7 is free of lysogen-related genes, bacterial virulence genes, and antibiotic resistance genes. vB_ShiP-A7 can significantly disrupt the growth of some MDR clinical strains of S. flexneri and Escherichia coli in liquid culture and biofilms in vitro. In addition, vB_ShiP-A7 can reduce the load of S. flexneri by approximately 3–10 folds in an infection model of mice. Therefore, vB_ShiP-A7 is a stable novel phage with the potential to treat infections caused by MDR strains of S. flexneri and E. coli.

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“…Based on the result of BLAST analyses, vB_ShiP-A7's genome sequence is related to 15 different phages (coverage 74-88%, identity 86-93%), including Escherichia phage P483 [32], Escherichia phage P694 [32], Enterobacteria phage BA14 [33], Escherichia phage vB EcoP S523, Enterobacteria phage 285P, Pectobacterium phage PP74 [34], Kluyvera phage Kvp1 [35], Erwinia phage FE44 [36], Salmonella phage BSP161, Salmonella phage BP12A, Yersinia phage PYPS50, Yersinia phage Yepe2, Yersinia phage YpP-G [37], Yersinia phage Berlin and Yersinia phage Yep-phi [38] (Fig. 4).…”

Section: Comparative Genome Analysis Of Vb_ship-a7 With Its Related Pmentioning

confidence: 99%

Molecular Characterization and Genomic Analysis of Novel Phage vB_ ShiP-A7 Infecting Multidrug-Resistant Shiglla Fexneri and Escherichia Coli

Xu¹,

Gu²,

Yu³

et al. 2020

Preprint

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BackgroundPhage therapy has regained more attention due to the rise of multidrug-resistant (MDR) bacteria. Several case reports demonstrated clinical application of phage in resolving infections caused by MDR bacteria in recent years. ResultsWe isolated a new phage, vB_ShiP-A7, and then investigated its characteristics. Phage vB_ShiP-A7 is a member of Podoviridae that has an icosahedral spherical head and a short tail. vB_ShiP-A7 has large burst size and short replication time. vB_ShiP-A7’s genome is linear double stranded DNA composed of 40058 bp, encoding forty-three putative open reading frames. Comparative genome analysis demonstrated vB_ShiP-A7’s genome sequence is closely related to fifteen different phages (coverage 74-88%, identity 86-93%). Mass Spectrometry analysis revealed that twelve known proteins and six hypothetical proteins exist in particles of vB_ShiP-A7. Genome and proteome analyses confirmed the absence of lysogen-related proteins and toxic proteins in this phage. In addition, phage vB_ShiP-A7 can significantly reduce the growth of clinical MDR stains of Shigella ﬂexneri and Escherichia coli in liquid culture. Furthermore, vB_ShiP-A7 can disrupt biofilms formed by Shigella ﬂexneri or Escherichia coli in vitro. ConclusionPhage vB_ShiP-A7 is a stable novel phage, which has a strong application potential to inhibit MDR stains of Shigella ﬂexneri and Escherichia coli. Comparing the genomes between vB_ShiP-A7 and other closely-related phages will help us better understand the evolutionary mechanism of phages.

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Genomic characteristics of vB_PpaP_PP74, a T7-like Autographivirinae bacteriophage infecting a potato pathogen of the newly proposed species Pectobacterium parmentieri

Cited by 9 publications

References 25 publications

Jumbo Bacteriophages Are Represented Within an Increasing Diversity of Environmental Viruses Infecting the Emerging Phytopathogen, Dickeya solani

Jumbo Bacteriophages Are Represented Within an Increasing Diversity of Environmental Viruses Infecting the Emerging Phytopathogen, Dickeya solani

Molecular Characteristics of Novel Phage vB_ShiP-A7 Infecting Multidrug-Resistant Shigella flexneri and Escherichia coli, and Its Bactericidal Effect in vitro and in vivo

Molecular Characterization and Genomic Analysis of Novel Phage vB_ ShiP-A7 Infecting Multidrug-Resistant Shiglla Fexneri and Escherichia Coli

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