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. 2023 Mar 1;4(1):46-50.
doi: 10.1089/phage.2022.0037. Epub 2023 Mar 17.

Whole Genome Sequence of a Novel Bacteriophage APT65 Infecting Aeromonas hydrophila

Ayşe Cebeci  1 , Mustafa Türe  1 , Melike Alemdağ  1 , Ilhan Altinok  2
Affiliations

Whole Genome Sequence of a Novel Bacteriophage APT65 Infecting Aeromonas hydrophila

Ayşe Cebeci et al. Phage (New Rochelle). .

Abstract

Background: Aeromonas hydrophila is a prevalent pathogenic bacterium in aquaculture that causes economic loss around the world. Antimicrobials are used to control and prevent the incidence of bacterial pathogens in aquaculture. However, they lead to the emergence of antimicrobial resistance strains and the accumulation of antibiotic residues in fish tissue. To address these issues, bacteriophages may be promising alternatives to many antibiotics in combating bacterial infections in aquaculture.

Materials and methods: The phage specific to A. hydrophila was isolated from domestic wastewater. The morphology of phages was analyzed using transmission electron microscopy. The genomic DNA of the Aeromonas phage T65 strain (APT65) phage was sequenced with a paired-end read length of 2 × 150 bp. The genome sequence was assembled and annotated. The tRNAs were predicted, and antimicrobial resistance and virulence genes were screened. A representation of the APT65 genome was constructed.

Results: The genome of APT65 is linear double-stranded DNA with 85188 base pairs having 116 open reading frames (ORFs) and a G + C content of 39.41%. The 32 ORFs were predicted to encode proteins with known phage functions. No virulence factors, antibiotic resistance genes, or temperate lifestyle genes were found. The phage is icosahedral and measures 60 nm in diameter. Based on the whole genome sequence, APT65 belongs to Lahexavirus.

Conclusions: The taxonomic analysis of the phage with a genome length of 85,188 bp revealed that it is a new species of the genus Lahexavirus. We announce the whole genome sequence of APT65, which should be named Lahexavirus APT65, as well as the absence of antimicrobial resistance and virulence factors from its genome. Based on our results, the Lahexavirus APT65 phage may have potential as a therapeutic agent to tackle antimicrobial resistance in aquaculture.

Keywords: Aeromonas hydrophila phage; Lahexavirus; NGS; bacteriophage.

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Conflict of interest statement

No competing financial interests exist.

Figures

FIG. 1.
FIG. 1.
ORF map of the genome of Aeromonas phage, APT65. The genomic map was prepared by the CGView Server. The outer lane and the next lane display genes on the forward and reverse strands, respectively. APT65, Aeromonas phage T65 strain; ORF, open reading frame.
FIG. 2.
FIG. 2.
The clustering of viral bacteriophage proteins into two different levels. Proteins are first grouped into PCs based on their reciprocal BLASTP similarities; these PCs are then grouped into protein superclusters based on their HMM similarities. HMM, hidden Markov model; PCs, protein clusters.
FIG. 3.
FIG. 3.
Distance Heatmap among bacteriophage genomes.
FIG. 4.
FIG. 4.
ANI value of the APT65 phage in comparison with related and unrelated bacteriophages. ANI, average nucleotide identity.
FIG. 5.
FIG. 5.
Transmission electron microscopy image of APT65 phage.
See this image and copyright information in PMC

References

    1. Ture M, Altinok I, Alp H. Effects of cage farming on antimicrobial and heavy metal resistance of Escherichia coli, Enterococcus faecium, and Lactococcus garvieae. Microb Drug Resist 2018;24:1422–1430. - PubMed
    1. Larsen JL, Jensen NJ. An Aeromonas species implicated in ulcer-disease of the cod (Gadus morhua). Nord Vet Med 1977;29(4–5):199–211. - PubMed
    1. Ozturk RC, Altinok I. Bacterial and viral fish diseases in Turkey. Turkish J Fish Aquat Sci 2014;14(1):275–297.
    1. Peterman MA, Posadas BC. Direct economic impact of fish diseases on the east Mississippi catfish industry. N Am J Aquac 2019;81(3):222–229.
    1. Janda JM, Abbott SL. The genus Aeromonas: Taxonomy, pathogenicity, and infection. Clin Microbiol Rev 2010(1):35–73. - PMC - PubMed

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