Genomic analysis of \(\textit{Aeromonas hydrophila}\) bacteriophages isolated in striped catfish farms in the Mekong delta, Vietnam


  • Tu Quang Vinh Ho Chi Minh City University of Technology, Ho Chi Minh City, Vietnam
  • Nguyen Le Hoai Nhan Ho Chi Minh City University of Technology, Ho Chi Minh City, Vietnam
  • Tran Thi Thanh Xuan Ho Chi Minh City University of Technology, Ho Chi Minh City, Vietnam
  • Le Phi Nga Ho Chi Minh City University of Technology, Ho Chi Minh City, Vietnam
  • Hoang Anh Hoang Ho Chi Minh City University of Technology, Ho Chi Minh City, Vietnam



Aeromonas hydrophila, bacteriophage, striped catfish, comparative genomic analysis.


Striped catfish or Vietnamese catfish mainly contributes to national aquaculture exports. However, bacterial diseases result in the decrease of striped catfish production efficiency and the most popular disease is hemorrhagic septicemia caused by Aeromonas hydrophila. Bacteriophages or bacterial viruses have been investigated as alternative biological agents to control pathogenic bacterial infections in aquaculture for many decades. A few genomes of striped catfish A. hydrophila bacteriophages have been analyzed, although many genomes of A. hydrophila bacteriophages in other fish have been investigated. In this study, the whole genome sequences of three new A. hydrophila bacteriophages such as PVN03, PVN04 and PVN05 were described. The morphological analysis by transmission electron microscopy indicated that these phages belonged to Myoviridae family. The genome sizes of the phages PVN03, PVN04 and PVN05 were 50,725 bp, 51,721 bp and 51,884 bp, respectively. PVN03 had 64 open reading frames (ORFs), while PVN04 and PVN05 had 65 ORFs and 66 ORFs, respectively. No tRNAs, rRNAs or sRNAs, antibiotic resistance genes, virulence factors, toxin genes and integrase genes were detected in three phage genomes. ANI analysis tool showed that Aeromonas hydrophila phages isolated in Vietnam formed a distinct group having a very low similarity with other Aeromonas hydrophila phages available on the database. In addition, phylogenetic tree analysis indicated that these phages formed a new genus in the Myrovidae family.


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Ackermann H. W., 2009a. Basic phage electron microscopy. In Bacteriophages, Humana Press, pp. 126.

Ackermann H. W., 2009b. Phage classification and characterization. In Bacteriophages, Humana Press, pp. 140.

Bin-Jang H., Bolduc B., Zablocki O., Kuhn J. H., Roux S., Adriaenssens E. M., Brister J. R., Kropinski A. M., Krupovic M., Lavigne R., Turner D., Sullivan M. B., 2019. Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks. Nat. Biotechnol., 37(6): 632–639.

Bolger A. M., Lohse M., Usadel B., 2014. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics, 30(15): 2114–2120.

Bortolaia V., Kaas R. S., Ruppe E., Roberts M. C., Schwarz S., Cattoir V., ..., Fagelhauer L., 2020. ResFinder 4.0 for predictions of phenotypes from genotypes. J. Antimicrob. Chemother., 75(12): 3491–3500.

Camacho C., Coulouris G., Avagyan V., Ma N., Papadopoulos J., Bealer K., Madden T. L., 2009. BLAST+: Architecture and applications. BMC Bioinformatics, 10: 1–9.

Clokie M. R., Millard A. D., Letarov A. V., Heaphy S., 2011. Phages in nature. Bacteriophage., 1(1): 31–45.

Contreras-Moreira B., Vinuesa P., 2013. GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis. Appl. Environ. Microbiol., 79(24): 7696–7701.

Culot A., Grosset N., Gautier M., 2019. Overcoming the challenges of phage therapy for industrial aquaculture: A review. Aquaculture, 513: 734423.

Dang T. H. O., Xuan T. T., Duyen L. T., Le N. P., Hoang H. A., 2021. Protective efficacy of phage PVN02 against haemorrhagic septicaemia in striped catfish Pangasianodon hypophthalmus via oral administration. J. Fish Dis.

De-Silva S. S., Phuong N. T., 2011. Striped catfish farming in the Mekong Delta, Vietnam: a tumultuous path to a global success. Rev. Aquaculture., 3: 45–73.

Doss J., Culbertson K., Hahn D., Camacho J., Barekzi N., 2017. A Review of Phage Therapy against Bacterial Pathogens of Aquatic and Terrestrial Organisms. Viruses 9(3), pp. 50.

Hatfull G. F., Hendrix, R. W., 2011. Bacteriophages and their genomes. Curr. Opin. Virol., 1(4): 298–303.

Hoang H. A., Tran T. T. X., Le P. N., Dang T. H. O., 2019. Selection of phages to control Aeromonas hydrophila - an infectious agent in striped catfish, Biocontrol. Sci., 24: 23–28.

Hoang H. A., Yen M. H., Ngoan V. T., Nga L. P., Oanh D. T. H., 2018. Virulent bacteriophage of Edwardsiella ictaluri isolated from kidney and liver of striped catfish Pangasianodon hypophthalmus in Vietnam. Dis. Aquat. Organ., 132(1): 49–56.

Hoang A. H., Abe M., Nakasaki, K., 2014. A novel colorimetric method for the detection of Escherichia coli using cytochrome c peroxidase-encoding bacteriophage. FEMS. Microbiol. Lett. 352: 97–103.

Johnson M., Zaretskaya I., Raytselis Y., Merezhuk Y., McGinnis S., Madden T. L., 2008. NCBI BLAST: a better web interface. Nucleic. Acids. Res., 36: W5–W9.

Liu B., Zheng D., Jin Q., Chen L., Yang J., 2019. VFDB 2019: A comparative pathogenomic platform with an interactive web interface. Nucleic. Acids. Res., 47(D1): D687–D692.

Katoh K., Standley D. M., 2013. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol. Biol. Evol., 30(4): 772–780.

Kowalska J. D., Kazimierczak J., Sowińska P. M., Wójcik E. A., Siwicki A. K., Dastych J., 2020. Growing trend of fighting infections in aquaculture environment opportunities and challenges of phage therapy. Antibiotics 9(6), pp. 301.

Le T. S., Nguyen T. H., Vo H. P., Doan V. C., Nguyen H. L., Tran M. T., Tran T. T., Southgate P. C., Kurtböke D.İ., 2018. Protective Effects of Bacteriophages against Aeromonas hydrophila Causing Motile Aeromonas Septicemia (MAS) in Striped Catfish. Antibiotics. 7(1): 15−16.

Le H. T., Truong Q. N., Nguyen H. G., Dang T. H. O., 2010. Study on application of multiplex PCR protocol for simultaneous detection of Edwardsiella ictaluri and Aeromonas hydrophila infection in kidney of striped catfish (Pangasianodon hypophthalmus). J. Sci. - Can Tho University, 16a: 129–135 (in Vietnamese with English summary).

Munro J., Oakey J., Bromage E., Owens L., 2003. Experimental bacteriophage-mediated virulence in strains of Vibrio harveyi. Dis. Aquat. Organ., 54(3): 187–194.

Nguyen L. T., Schmidt H. A., Von Haeseler A., Minh B. Q., 2015. IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol., 32(1): 268–274.

Oanh D. T. H., Nghia N. T., Tien T. V., Bondad-Reantaso M. G., 2018. Identification and characterization of vibrio bacteria isolated from shrimp infected with early mortality syndrome/acute hepatopancreatic necrosis syndrome (EMS/AHPNS) in Vietnam. Asian Fish. Sci, 31: 283–292.

Panangala V. S., Shoemaker C. A., Van S. V. L., Dybvig K., Klesius P. H., 2007. Multiplex-PCR for simultaneous detection of 3 bacterial fish pathogens, Flavobacterium columnare, Edwardsiella ictaluri, and Aeromonas hydrophila. Dis. Aquat. Organ., 74(3): 199–208.

Philipson C. W., Voegtly L. J., Lueder M. R., Long K. A., Rice G. K., Frey K. G., Biswajit B., Regina Z. C., Theron H., Bishop-Lilly K.A., 2018. Characterizing Phage Genomes for Therapeutic Applications. Viruses., 10(4): 187−188.

Quach V. C. T., Tu T. D., Dang P. H. H., 2014. The current status antimicrobial resistance in Edwardsiella ictaluri and Aeromonas hydrophila cause disease on the striped catfish farmed in the Mekong Delta. J. Sci. - Can Tho University, Special Issue: Aquaculture 2: 7–14 (in Vietnamese with English summary).

Ripp S., Jegier P., Johnson C. M., Brigati J. R., Sayler G. S., 2008. Bacteriophage-amplified bioluminescent sensing of Escherichia coli O157: H7. Anal. Bioanal. Chem., 391(2): 507–514.

Scanlan P. D., 2017. Bacteria–bacteriophage coevolution in the human gut: implications for microbial diversity and functionality. Trends. Microbiol., 25(8): 614–623.

Seemann T., 2014. Prokka: Rapid prokaryotic genome annotation. Bioinformatics, 30(14): 2068–2069.

Sullivan M. J., Petty N. K., Beatson S. A., 2011. Easyfig: a genome comparison visualizer. Bioinformatics (Oxford, England), 27(7): 1009–1010.

Tanji Y., Furukawa C., Na S. H., Hijikata T., Miyanaga, K., Unno H., 2004. Escherichia coli detection by GFP-labeled lysozyme-inactivated T4 bacteriophage. J. Biotechnol., 114(1–2): 11–20.

Tran L., Nunan L., Redman R. M., Mohney L. L., Pantoja C. R., Fitzsimmons K., Lightner D. V., 2013. Determination of the infectious nature of the agent of acute hepatopancreatic necrosis syndrome affecting penaeid shrimp. Dis. Aquat. Organ., 105(1): 45–55.

Tu V. Q., Nguyen T. T., Tran X. T., Millard A. D., Phan H. T., Le N. P., Hoang H. A., 2020. Complete genome sequence of a novel lytic phage infecting Aeromonas hydrophila, an infectious agent in striped catfish (Pangasianodon hypophthalmus). Arch. Virol. 165: 2973–2977.

VASEP, 2019. (access on December 18, 2020)

Walker B. J., Abeel T., Shea T., Priest M., Abouelliel A., Sakthikumar S., Cuomo C. A., Zeng Q., Wortman J., Young S. K., Earl A. M., 2014. Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE, 9(11).

Wick R. R., Judd L. M., Gorrie C. L., Holt K. E., 2017. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput. Biol., 13(6): 1–22.

Wu J. L., Lin H. M., Jan L., Hsu Y. L., Chang L. H., 1981. Biological control of fish acterial pathogen, Aeromonas hydrophila, by bacteriophage AH 1. Fish Pathol., 15: 271–276.




How to Cite

Vinh, T. Q., Nhan, N. L. H., Xuan, T. T. T., Nga, L. P., & Hoang, H. A. (2021). Genomic analysis of \(\textit{Aeromonas hydrophila}\) bacteriophages isolated in striped catfish farms in the Mekong delta, Vietnam. Academia Journal of Biology, 43(2), 55–71.