Whole-genome sequencing of Salmonella phage vB_SenS_TUMS_E15 for bio-control in the food chain
-
Narges torkashvand
,
Haniyeh Kamyab
,
Ahmad Reza Shahverdi
,
Mohammad Reza Khoshayand
,
Mohammad Amir Karimi Tarshizi
,
Zargham Sepehrizadeh
Abstract
Genome analysis of bacteriophages is crucial for their successful application in clinical and biocontrol settings. In this study, we isolated a new lytic phage, vB_SenS_TUMS-E15, from hospital sewage against Salmonella enteritidis and analyzed its genomic features. Complete genome analysis revealed that E15 had circularly permuted double-stranded DNA of 43,048 base pair (bp), with a G+C content of 49.7%. Sixty coding sequences (CDSs) were predicted in the genome, with 44 CDSs encoding known proteins in different modules, including the packaging, structure, replication and metabolism, and lysis modules, and there were no tRNA genes in the genome. Eight transcriptional promoter sequences and 37 rho-independent terminators were detected in the E15 genome. Phylogenetic analysis based on whole-genome sequences suggested that phage E15 should be included as a member of the Jersyvirus genus in the subfamily Guernseyvirinae. Also, no antibiotic-resistance genes, toxins, virulence factors, or lysogen-forming genes were observed in the genome. This indicates that E15 is a lytic phage, making it a promising candidate for clinical and biocontrol purposes.
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2. Kuźmińska-Bajor, M., P. Śliwka, M. Ugorski, P. Korzeniowski, A. Skaradzińska, M. Kuczkowski, et al., Genomic and functional characterization of five novel Salmonella-targeting bacteriophages. Virol. J., 2021. 18(1): p. 1-14.
3. Huh, H., S. Wong, J.S. Jean, and R. Slavcev, Bacteriophage interactions with mammalian tissue: Therapeutic applications. Adv. Drug Deliv. Rev., 2019. 145: p. 4-17.
4. Principi, N., E. Silvestri, and S. Esposito, Advantages and limitations of bacteriophages for the treatment of bacterial infections. Frontiers in pharmacology, 2019. 10: p. 513.
5. Venturini, C., A. Petrovic Fabijan, A. Fajardo Lubian, S. Barbirz, and J. Iredell, Biological foundations of successful bacteriophage therapy. EMBO Molecular Medicine, 2022. 14(7): p. e12435.
6. Lavilla, M., P. Domingo-Calap, S. Sevilla-Navarro, and A. Lasagabaster, Natural Killers: Opportunities and Challenges for the Use of Bacteriophages in Microbial Food Safety from the One Health Perspective. Foods, 2023. 12(3): p. 552.
7. Aziz, R.K., H.-W. Ackermann, N.K. Petty, and A.M. Kropinski, Essential steps in characterizing bacteriophages: biology, taxonomy, and genome analysis. Bacteriophages: Methods and Protocols, Volume 3, 2018: p. 197-215.
8. Kamyab, H., N. Torkashvand, A.R. Shahverdi, M.R. Khoshayand, M. Sharifzadeh, and Z. Sepehrizadeh, Isolation, characterization, and genomic analysis of vB_PaeP_TUMS_P121, a new lytic bacteriophage infecting Pseudomonas aeruginosa. Arch. Virol., 2023. 168(1): p. 8.
9. Philipson, C.W., L.J. Voegtly, M.R. Lueder, K.A. Long, G.K. Rice, K.G. Frey, et al., Characterizing phage genomes for therapeutic applications. Viruses, 2018. 10(4): p. 188.
10. Russell, D.A., Sequencing, assembling, and finishing complete bacteriophage genomes, in Bacteriophages. 2018, Springer. p. 109-125.
11. Shen, A. and A. Millard, Phage Genome Annotation: Where to Begin and End. PHAGE, 2021. 2(4): p. 183-193.
12. Kwon, J., S.G. Kim, H.J. Kim, S.S. Giri, S.W. Kim, S.B. Lee, et al., Isolation and characterization of Salmonella jumbo-phage pSal-SNUABM-04. Viruses, 2021. 13(1): p. 27.
13. Chan, P.P. and T.M. Lowe, tRNAscan-SE: searching for tRNA genes in genomic sequences, in Gene prediction. 2019, Springer. p. 1-14.
14. Moraru, C., A. Varsani, and A.M. Kropinski, VIRIDIC—A novel tool to calculate the intergenomic similarities of prokaryote-infecting viruses. Viruses, 2020. 12(11): p. 1268.
15. Torkashvand Narges, K.H., Shahverdi Ahmad Reza, Khoshayand Mohammad Reza Karimi Torshizi Mohammad Amir and Zargham Sepehrizadeh, Isolation, characterization, and genome analysis of a broad host range Salmonella phage vB_SenS_TUMS_E4: a candidate bacteriophage for biocontrol. Vet. Res. Commun., 2023.
16. Katoh, K., J. Rozewicki, and K.D. Yamada, MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Brief. Bioinformatics . 2019. 20(4): p. 1160-1166.
17. Maddison, W. and D. Maddison, Mesquite 2. A modular system for evolutionary analysis, 2007. 3.
18. Minh, B.Q., H.A. Schmidt, O. Chernomor, D. Schrempf, M.D. Woodhams, A. Von Haeseler, et al., IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol., 2020. 37(5): p. 1530-1534.
19. Grant, J.R., A.S. Arantes, and P. Stothard, Comparing thousands of circular genomes using the CGView Comparison Tool. BMC Genom., 2012. 13(1): p. 1-8.
20. Clokie, M.R., A.M. Kropinski, and R. Lavigne, Bacteriophages. Vol. 501. 2009: Springer.
21. Casjens, S., D.A. Winn-Stapley, E.B. Gilcrease, R. Morona, C. Kühlewein, J.E. Chua, et al., The chromosome of Shigella flexneri bacteriophage Sf6: complete nucleotide sequence, genetic mosaicism, and DNA packaging. J. Mol. Biol., 2004. 339(2): p. 379-394.
22. Jia, B., A.R. Raphenya, B. Alcock, N. Waglechner, P. Guo, K.K. Tsang, et al., CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res, 2016: p. gkw1004.
23. Zankari, E., H. Hasman, S. Cosentino, M. Vestergaard, S. Rasmussen, O. Lund, et al., Identification of acquired antimicrobial resistance genes. J. Antimicrob. Chemother., 2012. 67(11): p. 2640-2644.
24. Gupta, S.K., B.R. Padmanabhan, S.M. Diene, R. Lopez-Rojas, M. Kempf, L. Landraud, et al., ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes. J. Antimicrob.Chemother., 2014. 58(1): p. 212-220.
25. Chen, L., D. Zheng, B. Liu, J. Yang, and Q. Jin, VFDB 2016: hierarchical and refined dataset for big data analysis—10 years on. Nucleic Acids Res., 2016. 44(D1): p. D694-D697.
26. Carattoli, A., E. Zankari, A. García-Fernández, M. Voldby Larsen, O. Lund, L. Villa, et al., In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob. Agents Chemother., 2014. 58(7): p. 3895-3903.
27. Seemann, T. ABRicate: mass screening of contigs for antiobiotic resistance genes. 2016; Available from: https://github.com/tseemann/abricate.
28. Turner, D., M.E. Wand, Y. Briers, R. Lavigne, J.M. Sutton, and D.M. Reynolds, Characterisation and genome sequence of the lytic Acinetobacter baumannii bacteriophage vB_AbaS_Loki. PLoS One, 2017. 12(2): p. e0172303.
29. Rambaut, A., FigTree v1. 3.1. http://tree. bio. ed. ac. uk/software/figtree/, 2009.
30. Adriaenssens, E. and J.R. Brister, How to name and classify your phage: an informal guide. Viruses, 2017. 9(4): p. 70.
| Files | ||
| Issue | Vol 2 No 1 (2024) | |
| Section | Original Articles | |
| DOI | https://doi.org/10.18502/abi.v2i1.16245 | |
| Keywords | ||
| Bacteriophage Salmonella enteritidis Jersyvirus Guernseyvirinae Biocontrol. | ||
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How to Cite
1.
torkashvand N, Kamyab H, Shahverdi AR, Khoshayand MR, Karimi Tarshizi MA, Sepehrizadeh Z. Whole-genome sequencing of Salmonella phage vB_SenS_TUMS_E15 for bio-control in the food chain. ABI. 2024;2(1):31-35.
