Characterization of Dev-CD-23823 and Dev-CT57, new Autographivirinae bacteriophages infecting Cronobacter spp.

Kajsik, Michal; Bugala, Juraj; Kadličeková, Veronika; Szemes, Tomáš; Turňa, Ján; Drahovská, Hana

doi:10.1007/s00705-019-04202-3

Cited by 12 publications

(11 citation statements)

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“…BLASTN analysis revealed the highest sequence identity of 98 with 97% coverage (total identity of 93.2%, as determined by the EMBOSS stretcher alignment tool) to another Yersinia phage fHe-Yen3-01 that we recently isolated in Finland (Jun et al, 2018), followed by Pectobacterium phage MA13 (75,5%) and Cronobacter sakazakii phage vB_CskP_GAP227 (73,5%) ( Table 1). Whole-genome phylogenetic tree (Figure 2) places f80-18 in well-defined clade, which was defined as Gap227virus (Kajsík et al, 2019) or broader as Ahp1-like subgroup (Wang et al, 2016). This significant phylogenetic association is supported by a tree inferred using single marker, RNA polymerase (RNAP) (Figure 3).…”

Section: Phylogenetic Analysis Of φ80-18mentioning

confidence: 85%

“…Only one rho-independent terminator was detected by the FindTerm program, located inside the g37 gene encoding the phage RNA polymerase. While in general, the genomes of many podoviruses can be divided into three regions comprising early, middle and late genes for virus-host interactions, DNA metabolism and (Wang et al, 2016) and Gap227virus genus (Kajsík et al, 2019) are proposed, yet not recognized by ICTV taxonomy (2018b Release). Here, both groups are extended beyond the range of taxa proposed in the original publications to cover the full cluster.…”

Section: Promotersmentioning

confidence: 99%

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The Podovirus ϕ80-18 Targets the Pathogenic American Biotype 1B Strains of Yersinia enterocolitica

et al. 2020

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We report here the complete genome sequence and characterization of Yersinia bacteriophage vB_YenP_φ80-18. φ80-18 was isolated in 1991 using a Y. enterocolitica serotype O:8 strain 8081 as a host from a sewage sample in Turku, Finland, and based on its morphological and genomic features is classified as a podovirus. The genome is 42 kb in size and has 325 bp direct terminal repeats characteristic for podoviruses. The genome contains 57 predicted genes, all encoded in the forward strand, of which 29 showed no similarity to any known genes. Phage particle proteome analysis identified altogether 24 phage particle-associated proteins (PPAPs) including those identified as structural proteins such as major capsid, scaffolding and tail component proteins. In addition, also the DNA helicase, DNA ligase, DNA polymerase, 5-exonuclease, and the lytic glycosylase proteins were identified as PPAPs, suggesting that they might be injected together with the phage genome into the host cell to facilitate the takeover of the host metabolism. The phage-encoded RNA-polymerase and DNA-primase were not among the PPAPs. Promoter search predicted the presence of four phage and eleven host RNA polymerase-specific promoters in the genome, suggesting that early transcription of the phage is host RNA-polymerase dependent and that the phage RNA polymerase takes over later. The phage tolerates pH values between 2 and 12, and is stable at 50 • C but is inactivated at 60 • C. It grows slowly with a 50 min latent period and has apparently a low burst size. Electron microscopy revealed that the phage has a head diameter of about 60 nm, and a short tail of 20 nm. Whole-genome phylogenetic analysis confirmed that φ80-18 belongs to the Autographivirinae subfamily of the Podoviridae family, that it is 93.2% identical to Yersinia phage fHe-Yen3-01. Host range analysis showed that φ80-18 can infect in addition to Y. enterocolitica serotype O:8 strains

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Section: Phylogenetic Analysis Of φ80-18mentioning

confidence: 85%

Section: Promotersmentioning

confidence: 99%

The Podovirus ϕ80-18 Targets the Pathogenic American Biotype 1B Strains of Yersinia enterocolitica

et al. 2020

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“…By comparison, latent period and burst size of kayfunavirus Escherichia virus ZG49 are 9 min and 150 PFU/cell [ 24 ]. The latent period of the putative cronosvirus Kc318 (40 min) was much longer than that for Cronobacter Dev-CD-23823 and Cronobacter Dev-CT57 cronosviruses, which are 15 and 20 min, respectively, and also the burst size of Kc318 (90 particles) was smaller than those for the Cronobacter viruses (111 and 180 particles, respectively) [ 25 ]. The latent period of putative sortsneviruses Kc166B and Kc237 was 40 min, and burst size 100 PFU/cell.…”

Section: Resultsmentioning

confidence: 99%

Novel Viruses That Lyse Plant and Human Strains of Kosakonia cowanii

Petrzik

Brázdová

Krawczyk

2021

Viruses

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Kosakonia cowanii (syn. Enterobacter cowanii) is a highly competitive bacterium that lives with plant, insect, fish, bird, and human organisms. It is pathogenic on some plants and an opportunistic pathogen of human. Nine novel viruses that lyse plant pathogenic strains and/or human strains of K. cowanii were isolated, sequenced, and characterized. Kc166A is a novel kayfunavirus, Kc261 is a novel bonnellvirus, and Kc318 is a new cronosvirus (all Autographiviridae). Kc237 is a new sortsnevirus, but Kc166B and Kc283 are members of new genera within Podoviridae. Kc304 is a new winklervirus, and Kc263 and Kc305 are new myoviruses. The viruses differ in host specificity, plaque phenotype, and lysis kinetics. Some of them should be suitable also as pathogen control agents.

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“…It is also possible to identify bacteriophages that infect noncultivable bacteria, the so-called "bacterial dark matter". Our studies have been previously focused on the identification of specific bacteriophages capable of infecting foodborne pathogens [62,63].…”

Section: Discussionmentioning

confidence: 99%

PHERI - Phage Host Exploration pipeline

Baláž

Kajsik

Budiš

et al. 2020

Preprint

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Antibiotic resistance is becoming a common problem in health care, veterinary medicine, agriculture or food industry. Multi-resistant bacterial strains occur in all regions of the world. One of the possible future solutions is the use of bacteriophages in therapy.Bacteriophages are the most abundant form of life in the biosphere, so it is highly likely that we can purify a specific phage against each target bacterium. A standard identification and consistent characterization of individual bacteriophages include host-specificity of viruses.Unfortunately, these routine methods are also considerably time consuming. With the advent of new modern sequencing methods, scientists are able to obtain multiple phage sequences from samples and identify more phages. However there appeared a problem with unknown host specificity of identified phages. The solution to this problem may be to use a bioinformatic approach in the form of prediction software capable to determine a bacterial host based on the phage whole-genome sequence. The result of our research is the machine learning algorithm based tool called PHERI. PHERI predicts suitable bacterial host genus for purification of individual viruses from different samples. In addition, the tool can identify and highlight protein sequences that are important for host selection.

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Characterization of Dev-CD-23823 and Dev-CT57, new Autographivirinae bacteriophages infecting Cronobacter spp.

Cited by 12 publications

References 40 publications

The Podovirus ϕ80-18 Targets the Pathogenic American Biotype 1B Strains of Yersinia enterocolitica

The Podovirus ϕ80-18 Targets the Pathogenic American Biotype 1B Strains of Yersinia enterocolitica

Novel Viruses That Lyse Plant and Human Strains of Kosakonia cowanii

PHERI - Phage Host Exploration pipeline

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