References
Ackermann, H.-W. (2007). 5500 Phages examined in the electron microscope. Archives of Virology, 152 (2), 227-243. https://doi.org/10.1007/s00705-006-0849-1
Adams, M. H. (1959). Bacteriophages. Bacteriophages (pp. 443-522): Wiley Intersciences, New York
Afgan, E., Baker, D., Van den Beek, M., Blankenberg, D., Bouvier, D., Čech, M., . . . Eberhard, C. (2016). The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update.Nucleic Acids Research, 44 (W1), W3-W10. https://doi.org/10.1093/nar/gkw343
Akmal, M., Rahimi-Midani, A., Hafeez-ur-Rehman, M., Hussain, A., & Choi, T.-J. (2020). Isolation, characterization, and application of a bacteriophage infecting the fish pathogen Aeromonas hydrophila .Pathogens, 9 (3), 215. https://doi.org/10.3390/pathogens9030215
Anand, T., Vaid, R. K., Bera, B. C., Singh, J., Barua, S., Virmani, N., . . . Tripathi, B. (2016). Isolation of a lytic bacteriophage against virulent Aeromonas hydrophila from an organized equine farm.Journal of Basic Microbiology, 56 (4), 432-437. https://doi.org/10.1002/jobm.201500318
Arndt, D., Grant, J. R., Marcu, A., Sajed, T., Pon, A., Liang, Y., & Wishart, D. S. (2016). PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Research, 44 (W1), W16-W21. https://doi.org/10.1093/nar/gkw387
Cao, Y., Li, S., Han, S., Wang, D., Zhao, J., Xu, L., . . . Lu, T. (2020). Characterization and application of a novel Aeromonasbacteriophage as treatment for pathogenic Aeromonas hydrophilainfection in rainbow trout. Aquaculture, 523 , 735193. https://doi.org/10.1016/j.aquaculture.2020.735193
Cao, Y., Zhang, Y., Lan, W., & Sun, X. (2021). Characterization of vB_VpaP_MGD2, a newly isolated bacteriophage with biocontrol potential against multidrug-resistant Vibrio parahaemolyticus .Archives of Virology, 166 (2), 413-426. https://doi.org/10.1007/s00705-020-04887-x
Carver, T., Thomson, N., Bleasby, A., Berriman, M., & Parkhill, J. (2009). DNAPlotter: circular and linear interactive genome visualization. Bioinformatics, 25 (1), 119-120. https://doi.org/10.1093/bioinformatics/btn578
Chandrarathna, H., Nikapitiya, C., Dananjaya, S., De Silva, B., Heo, G.-J., De Zoysa, M., & Lee, J. (2020). Isolation and characterization of phage AHP-1 and its combined effect with chloramphenicol to controlAeromonas hydrophila . Brazilian Journal of Microbiology, 51 (1), 409-416. https://doi.org/10.1007/s42770-019-00178-z
Chen, S., Zhou, Y., Chen, Y., & Gu, J. (2018). fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics, 34 (17), i884-i890. https://doi.org/10.1093/bioinformatics/bty560
Cheng, Y., Gao, D., Xia, Y., Wang, Z., Bai, M., Luo, K., . . . Xiao, W. (2021). Characterization of novel bacteriophage AhyVDH1 and its lytic activity against Aeromonas hydrophila . Current Microbiology, 78 (1), 329-337. https://doi.org/10.1007/s00284-020-02279-7
Cui, H., Cong, C., Wang, L., Li, X., Li, J., Yang, H., . . . Xu, Y. (2021). Protective effectiveness of feeding phage cocktails in controlling Vibrio harveyi infection of turbot Scophthalmus maximus . Aquaculture, 535 , 736390. https://doi.org/10.1016/j.aquaculture.2021.736390
Culot, A., Grosset, N., & Gautier, M. (2019). Overcoming the challenges of phage therapy for industrial aquaculture: A review.Aquaculture, 513 , 734423. https://doi.org/10.1016/j.aquaculture.2019.734423
da Silva, B. C., Mouriño, J. L. P., Vieira, F. N., Jatobá, A., Seiffert, W. Q., & Martins, M. L. (2012). Haemorrhagic septicaemia in the hybrid surubim (Pseudoplatystoma corruscans × Pseudoplatystoma fasciatum ) caused by Aeromonas hydrophila . Aquaculture Research, 43 (6), 908-916. https://doi.org/10.1111/j.1365-2109.2011.02905.x
Dang, T. H. O., Xuan, T. T. T., Duyen, L. T. M., Le, N. P., & Hoang, H. A. (2021). Protective efficacy of phage PVN02 against haemorrhagic septicaemia in striped catfish Pangasianodon hypophthalmus via oral administration. Journal of Fish Diseases, n/a (n/a). https://doi.org/10.1111/jfd.13387
Dawood, M. A., Moustafa, E. M., Elbialy, Z. I., Farrag, F., Lolo, E. E., Abdel-Daim, H. A., . . . Van Doan, H. (2020). Lactobacillus plantarum L-137 and/or β-glucan impacted the histopathological, antioxidant, immune-related genes and resistance of Nile tilapia (Oreochromis niloticus ) against Aeromonas hydrophila .Research in Veterinary Science, 130 , 212-221. https://doi.org/10.1016/j.rvsc.2020.03.019
Dien, L. T., Vu Linh, N., Sangpo, P., Senapin, S., St-Hilaire, S., Rodkhum, C., & Dong, H. T. (2021). Ozone nanobubble treatments improve survivability of Nile tilapia (Oreochromis niloticus ) challenged with a pathogenic multidrug-resistant Aeromonas hydrophila .Journal of Fish Diseases, n/a (n/a). https://doi.org/ 10.1111/jfd.13451
Donati, V. L., Dalsgaard, I., Sundell, K., Castillo, D., Er-Rafik, M., Clark, J., . . . Madsen, L. (2021). Phage-mediated control ofFlavobacterium psychrophilum in Aquaculture: In vivoexperiments to compare delivery methods. Frontiers in Microbiology, 12 , 438. https://doi.org/10.3389/fmicb.2021.628309
Dong, H., Techatanakitarnan, C., Jindakittikul, P., Thaiprayoon, A., Taengphu, S., Charoensapsri, W., . . . Senapin, S. (2017).Aeromonas jandaei and Aeromonas veronii caused disease and mortality in Nile tilapia, Oreochromis niloticus (L.).Journal of Fish Diseases, 40 (10), 1395-1403. https://doi.org/10.1111/jfd.12617
Dong, H. T., Nguyen, V. V., Le, H. D., Sangsuriya, P., Jitrakorn, S., Saksmerprome, V., . . . Rodkhum, C. (2015). Naturally concurrent infections of bacterial and viral pathogens in disease outbreaks in cultured Nile tilapia (Oreochromis niloticus ) farms.Aquaculture, 448 , 427-435. https://doi.org/10.1016/j.aquaculture.2015.06.027
Dong, H. T., Nguyen, V. V., Phiwsaiya, K., Gangnonngiw, W., Withyachumnarnkul, B., Rodkhum, C., & Senapin, S. (2015). Concurrent infections of Flavobacterium columnare and Edwardsiella ictaluri in striped catfish, Pangasianodon hypophthalmus in Thailand. Aquaculture, 448 , 142-150. https://doi.org/10.1016/j.aquaculture.2015.05.046
Easwaran, M., Dananjaya, S., Park, S., Lee, J., Shin, H., & De Zoysa, M. (2017). Characterization of bacteriophage pAh-1 and its protective effects on experimental infection of Aeromonas hydrophila in Zebrafish (Danio rerio ). Journal Fish Diseases, 40 , 841-846. https://doi.org/10.1111/jfd.12536
Ellis, A. (1988). General principals of fish vaccination. Fish vaccination (pp. 1-19): Academic Press, New York
FAO. (2020). The State of World Fisheries and Aquaculture 2020 - Meeting the sustainable development goals. Fisheries and Aquaculture Department, Food and Agriculture Organization of the United Nations, Rome. https://doi.org/10.4060/ca9229en
Göker, M., García-Blázquez, G., Voglmayr, H., Tellería, M. T., & Martín, M. P. (2009). Molecular taxonomy of phytopathogenic fungi: a case study in Peronospora . PLoS One, 4 (7), e6319. https://dx.doi.org/10.1371%2Fjournal.pone.0006319
Guz, L., & Kozinska, A. (2004). Antibiotic susceptibility ofAeromonas hydrophila and A. sobria isolated from farmed carp (Cyprinus carpio L.). Bulletin of the Veterinary Institute in Pulawy, 48 , 391-395.
Hadfield, J., Croucher, N. J., Goater, R. J., Abudahab, K., Aanensen, D. M., & Harris, S. R. (2018). Phandango: an interactive viewer for bacterial population genomics. Bioinformatics, 34 (2), 292-293. http://dx.doi.org/10.1093/bioinformatics/btx610
Harrigan, W. F., & McCance, M. E. (2014). Laboratory Methods in Microbiology : Elsevier Science.
Hicks, C. C., Cohen, P. J., Graham, N. A., Nash, K. L., Allison, E. H., D’Lima, C., . . . Thorne-Lyman, A. L. (2019). Harnessing global fisheries to tackle micronutrient deficiencies. Nature, 574 (7776), 95-98. https://doi.org/10.1038/s41586-019-1592-6
Hoang, H. A., Xuan, T. T. T., Nga, L. R., & Oanh, D. T. H. (2019). Selection of phages to control Aeromonas hydrophila - An infectious agent in striped catfish. Biocontrol Science, 24 (1), 23-28. https://doi.org/10.4265/bio.24.23
Hoelzer, K., Bielke, L., Blake, D. P., Cox, E., Cutting, S. M., Devriendt, B., . . . Lemiere, S. (2018). Vaccines as alternatives to antibiotics for food producing animals. Part 1: challenges and needs.Veterinary Research, 49 (1), 64. https://doi.org/10.1186/s13567-018-0560-8
Hossain, M. J., Sun, D., McGarey, D. J., Wrenn, S., Alexander, L. M., Martino, M. E., . . . Liles, M. R. (2014). An Asian origin of virulentAeromonas hydrophila responsible for disease epidemics in United States-farmed catfish. MBio, 5 (3), e00848-00814. https://doi.org/10.1128/mBio.00848-14
Jhunkeaw, C., Khongcharoen, N., Rungrueng, N., Sangpo, P., Panphut, W., Thapinta, A., . . . Dong, H. T. (2021). Ozone nanobubble treatment in freshwater effectively reduced pathogenic fish bacteria and is safe for Nile tilapia (Oreochromis niloticus ). Aquaculture, 534 , 736286. https://doi.org/10.1016/j.aquaculture.2020.736286
Jun, J. W., Kim, H. J., Yun, S. K., Chai, J. Y., & Park, S. C. (2015). Genomic structure of the Aeromonas bacteriophage pAh6-C and its comparative genomic analysis. Archives of Virology, 160 (2), 561-564. https://doi.org/10.1007/s00705-014-2221-1
Jun, J. W., Kim, J. H., Shin, S. P., Han, J. E., Chai, J. Y., & Park, S. C. (2013). Protective effects of the Aeromonas phages pAh1-C and pAh6-C against mass mortality of the cyprinid loach (Misgurnus anguillicaudatus ) caused by Aeromonas hydrophila .Aquaculture, 416 , 289-295. https://doi.org/10.1016/j.aquaculture.2013.09.045
Kabwe, M., Brown, T., Speirs, L., Ku, H., Leach, M., Chan, H. T., . . . Tucci, J. (2020). Novel bacteriophages capable of disrupting biofilms from clinical strains of Aeromonas hydrophila . Frontiers in Microbiology, 11 , 194. https://doi.org/10.3389/fmicb.2020.00194
Katoh, K., & Standley, D. M. (2013). MAFFT multiple sequence alignment software version 7: improvements in performance and usability.Molecular Biology and Evolution, 30 (4), 772-780. https://doi.org/10.1093/molbev/mst010
Kuebutornye, F. K., Wang, Z., Lu, Y., Abarike, E. D., Sakyi, M. E., Li, Y., . . . Hlordzi, V. (2020). Effects of three host-associatedBacillus species on mucosal immunity and gut health of Nile tilapia, Oreochromis niloticus and its resistance againstAeromonas hydrophila infection. Fish & Shellfish Immunology, 97 , 83-95. https://doi.org/10.1016/j.fsi.2019.12.046
Kutateladze, M., & Adamia, R. (2010). Bacteriophages as potential new therapeutics to replace or supplement antibiotics. Trends in Biotechnology, 28 (12), 591-595. https://doi.org/10.1016/j.tibtech.2010.08.001
Langmead, B., & Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nature Methods, 9 (4), 357. https://doi.org/10.1038/nmeth.1923
Le, T. S., Nguyen, T. H., Vo, H. P., Doan, V. C., Nguyen, H. L., Tran, M. T., . . . Kurtboke, D. I. (2018). Protective fffects of bacteriophages against Aeromonas hydrophila species Causing Motile Aeromonas Septicemia (MAS) in striped catfish. Antibiotics (Basel), 7 (1). doi:10.3390/antibiotics7010016
Letunic, I., & Bork, P. (2019). Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Research, 47 (W1), W256-W259. https://doi.org/10.1093/nar/gkz239
Luo, X., Liao, G., Liu, C., Jiang, X., Lin, M., Zhao, C., . . . Huang, Z. (2018). Characterization of bacteriophage HN 48 and its protective effects in Nile tilapia Oreochromis niloticus againstStreptococcus agalactiae infections. Journal of Fish Diseases, 41 (10), 1477-1484. https://doi.org/10.1111/jfd.12838
Magiorakos, A.-P., Srinivasan, A., Carey, R., Carmeli, Y., Falagas, M., Giske, C., . . . Olsson-Liljequist, B. (2012). Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance. Clinical Microbiology and Infection, 18 (3), 268-281. https://doi.org/10.1111/j.1469-0691.2011.03570.x
Maulu, S., Hasimuna, O. J., Haambiya, L. H., Monde, C., Musuka, C. G., Makorwa, T. H., . . . Nsekanabo, J. D. (2021). Climate change effects on aquaculture production: sustainability implications, mitigation, and adaptations. Frontiers in Sustainable Food Systems, 5 , 70. https://doi.org/10.3389/fsufs.2021.609097
Meier-Kolthoff, J. P., & Göker, M. (2017). VICTOR: genome-based phylogeny and classification of prokaryotic viruses.Bioinformatics, 33 (21), 3396-3404. https://doi.org/10.1093/bioinformatics/btx440
Moriarty, D. (1973). The physiology of digestion of blue‐green algae in the cichlid fish, Tilapia nilotica . Journal of Zoology, 171 (1), 25-39. https://doi.org/10.1111/j.1469-7998.1973.tb07514.x
Naliato, R. F., Carvalho, P. L. P. F., Vicente, I. S. T., Xavier, W. d. S., Guimarães, M. G., Rodrigues, E. J. D., . . . Orsi, R. d. O. (2021). Ginger (Zingiber officinale ) powder improves growth performance and immune response but shows limited antioxidant capacity for Nile tilapia infected with Aeromonas hydrophila . Aquaculture Nutrition . https://doi.org/10.1111/anu.13229
Navarro, A., & Martínez‐Murcia, A. (2018). Phylogenetic analyses of the genus Aeromonas based on housekeeping gene sequencing and its influence on systematics. Journal of Applied Microbiology, 125 (3), 622-631. https://doi.org/10.1111/jam.13887
Naylor, R. L., Hardy, R. W., Buschmann, A. H., Bush, S. R., Cao, L., Klinger, D. H., . . . Troell, M. (2021). A 20-year retrospective review of global aquaculture. Nature, 591 (7851), 551-563. https://doi.org/10.1038/s41586-021-03308-6
Neamat-Allah, A. N., Mahmoud, E. A., & Mahsoub, Y. (2021). Effects of dietary white mulberry leaves on hemato-biochemical alterations, immunosuppression and oxidative stress induced by Aeromonas hydrophila in Oreochromis niloticus . Fish & Shellfish Immunology, 108 , 147-156. https://doi.org/10.1016/j.fsi.2020.11.028
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. Molecular Biology and Evolution, 32 (1), 268-274. https://doi.org/10.1093/molbev/msu300
Patil, H. J., Benet-Perelberg, A., Naor, A., Smirnov, M., Ofek, T., Nasser, A., . . . Cytryn, E. (2016). Evidence of increased antibiotic resistance in phylogenetically-diverse Aeromonas isolates from semi-intensive fish ponds treated with antibiotics. Frontiers in Microbiology, 7 , 1875. https://doi.org/10.3389/fmicb.2016.01875
Pérez-Sánchez, T., Mora-Sánchez, B., & Balcázar, J. L. (2018). Biological approaches for disease control in aquaculture: advantages, limitations and challenges. Trends in Microbiology, 26 (11), 896-903. https://doi.org/10.1016/j.tim.2018.05.002
Peterman, M. A., & Posadas, B. C. (2019). Direct economic impact of fish diseases on the East Mississippi catfish industry. North American Journal of Aquaculture, 81 (3), 222-229. https://doi.org/10.1002/naaq.10090
Pridgeon, J. W., & Klesius, P. H. (2012). Major bacterial diseases in aquaculture and their vaccine development. CAB Reviews, 7 , 1-16. http://dx.doi.org/10.1079/PAVSNNR20127048
Ross, A., Ward, S., & Hyman, P. (2016). More is better: selecting for broad host range bacteriophages. Frontiers in Microbiology, 7 , 1352. https://doi.org/10.3389/fmicb.2016.01352
Seemann, T. (2014). Prokka: rapid prokaryotic genome annotation.Bioinformatics, 30 (14), 2068-2069. https://doi.org/10.1093/bioinformatics/btu153
Seggel, A., & De Young, C. (2016). Climate change implications for fisheries and aquaculture: summary of the findings of the Intergovernmental Panel on Climate Change Fifth Assessment Report.FAO Fisheries and Aquaculture Circular (C1122), I.
Stentiford, G., Bateman, I., Hinchliffe, S., Bass, D., Hartnell, R., Santos, E., . . . Verner-Jeffreys, D. (2020). Sustainable aquaculture through the One Health lens. Nature Food, 1 (8), 468-474. https://doi.org/10.1038/s43016-020-0127-5
Stentiford, G. D., Sritunyalucksana, K., Flegel, T. W., Williams, B. A., Withyachumnarnkul, B., Itsathitphaisarn, O., & Bass, D. (2017). New paradigms to help solve the global aquaculture disease crisis.PLoS Pathogens, 13 (2), e1006160. https://doi.org/10.1371/journal.ppat.1006160
Stratev, D., & Odeyemi, O. A. (2016). Antimicrobial resistance ofAeromonas hydrophila isolated from different food sources: A mini-review. Journal of Infection and Public Health, 9 (5), 535-544. https://doi.org/10.1016/j.jiph.2015.10.006
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 ). Archives of Virology, 165 (12), 2973-2977. https://doi.org/10.1007/s00705-020-04793-2
Turner, D., Reynolds, D., Seto, D., & Mahadevan, P. (2013). CoreGenes3. 5: a webserver for the determination of core genes from sets of viral and small bacterial genomes. BMC Research Notes, 6 (1), 1-4. https://doi.org/10.1186/1756-0500-6-140
Van Twest, R., & Kropinski, A. M. (2009). Bacteriophage enrichment from water and soil. In Bacteriophages (pp. 15-21): Springer.
Walker, J., Clokie, M., & Kropinski, A. (2009). Bacteriophages: Methods and protocols, volume 1: Isolation, characterization, and interactions. In: Totowa, NJ: Humana Press.
Wang, J.-B., Lin, N.-T., Tseng, Y.-H., & Weng, S.-F. (2016). Genomic characterization of the novel Aeromonas hydrophila phage Ahp1 suggests the derivation of a new subgroup from phiKMV-like family.PLoS One, 11 (9), e0162060. https://doi.org/10.1371/journal.pone.0162060
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 Computational Biology, 13 (6), e1005595. https://doi.org/10.1371/journal.pcbi.1005595
Zhang, D., Gao, F., Jakovlić, I., Zou, H., Zhang, J., Li, W. X., & Wang, G. T. (2020). PhyloSuite: an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. Molecular Ecology Resources, 20 (1), 348-355. https://doi.org/10.1111/1755-0998.13096