Abstract
Aeromonas hydrophila AL09-71 was isolated from diseased channel catfish in west Alabama during a 2009 disease outbreak. The full genome of A. hydrophila AL09-71 is 5,023,861 bp. The availability of this genome will allow comparative genomics to identify genes involved in pathogenesis or immunogens for the purpose of vaccine development.
GENOME ANNOUNCEMENT
Gram-negative bacterium Aeromonas hydrophila is the causative agent of motile aeromonad septicemia (MAS) (1) or epizootic ulcerative syndrome (2) in fish. Red sores, necrosis, ulceration, and hemorrhagic septicemia are typical symptoms of MAS (3). MAS disease outbreaks in channel catfish have led to an estimated loss of more than $3 million in 2009 in west Alabama (4–8). The complete genome of one of the virulent epidemic isolates (A. hydrophila ML09-119) from west Alabama has been recently published (8). Lateral genetic transfer has been implicated as the molecular basis of the emergence of an A. hydrophila epidemic outbreak (9). Another strain A. hydrophila AL09-71 was also collected from channel catfish in west Alabama during the 2009 disease outbreak (5, 6). Virulence studies revealed that A. hydrophila AL09-71 was highly virulent to channel catfish (5, 6). Through mass spectrometry, 23 proteins were identified in toxic fractions of the extracellular products of A. hydrophila AL09-71 (10). However, it was unknown how many virulence related genes existed in the genome of A. hydrophila AL09-71. Whole genome sequencing will enable the revelation of the complete list of potential virulence factors in A. hydrophila (11). Therefore, the complete genome sequence of A. hydrophila AL09-71 was determined in this study.
The genome of A. hydrophila AL09-71 was sequenced using an Illumina 1500 Hiseq platform. BioNumerics (Applied Maths) was used to assemble a total of 24,036,568 sequence reads with an average length of 100.24 bp (estimated 479×coverage). Using the west Alabama epidemic isolate A. hydrophila ML09-119 genome (accession no. CP005966) as reference, the assembled genome of A. hydrophila AL09-71 is 5,023,861 bp with a G+C content of 60.8%. RNAmmer (12) predicted 11, 10, and 10 copies of 5S RNA, 16S RNA, and 23S RNA, respectively, in the genome of A. hydrophila AL09-71, similar to that in the genome of A. hydrophila ML09-119 (8). A Vista comparative genomics tool (13) revealed 99.5% conserved intervals between the two genomes, with 17 intervals (a total of 4,938,481 bp) sharing 100% identities. The RAST server (14) predicted 4,489 coding sequences belonging to 533 subsystems, including 84 involved in virulence, disease, and defense. In addition, the RAST server identified the following subsystems: 192 in cell wall or capsule, 22 as phages, prophages, transposable elements, or plasmids, 183 in membrane transport, 56 in iron acquisition and metabolism, 127 in motility and chemotaxis, 295 as cofactors, vitamins, prosthetic groups, or pigments, 38 in potassium metabolism, 123 in DNA metabolism, 224 in RNA metabolism, 240 in protein metabolism, 45 in nitrogen metabolism, 37 in sulfur metabolism, 44 in phosphorus metabolism, 127 in nucleosides and nucleotides, 44 in cell division and cell cycle, 100 in regulation and cell signaling, 6 in secondary metabolism, 9 regulons, 136 in fatty acids, lipids, and isoprenoids, 3 in dormancy and sporulation, 171 in respiration, 159 in stress response, 437 in amino acids and derivatives, and 466 in the carbohydrates subsystem.
Nucleotide sequence accession number.
The complete genome sequence of A. hydrophila AL09-71 was deposited at DDBJ/EMBL/GenBank under the accession no. CP007566.
ACKNOWLEDGMENTS
This study was supported by the USDA/ARS CRIS project 6420-32000-024-00D. The use of trade, firm, or corporate names in this publication is for the information and convenience of the reader. Such use does not constitute an official endorsement or approval by the United States Department of Agriculture or the Agricultural Research Service of any product or service to the exclusion of others that may be suitable.
We thank Dr. Victor Panangala (USDA-ARS) and Dr. Mark Liles (Auburn University) for critical reviews of the manuscript. We thank William Hemstreet (Alabama Fish Farming Center, Department of Fisheries, Auburn University) for providing the isolate and Beth Peterman (USDA-ARS) for her technical support.
Footnotes
Citation Pridgeon JW, Zhang D, Zhang L. 2014. Complete genome sequence of the highly virulent Aeromonas hydrophila AL09-71 isolated from diseased channel catfish in west Alabama. Genome Announc. 2(3):e00450-14. doi:10.1128/genomeA.00450-14.
REFERENCES
- 1. Harikrishnan R, Rani MN, Balasundaram C. 2003. Hematological and biochemical parameters in common carp, Cyprinus carpio, following herbal treatment for Aeromonas hydrophila infection. Aquaculture 221:41–50. 10.1016/S0044-8486(03)00023-1 [DOI] [Google Scholar]
- 2. Mastan SA, Qureshi TA. 2001. Role of bacteria in the epizootic ulcerative syndrome (EUS) of fishes. J. Environ. Biol. 22:187–192 [PubMed] [Google Scholar]
- 3. Karunasagar I, Rosalind GM, Karunasagar I, Gopal Rao K. 1989. Aeromonas hydrophila septicaemia of Indian major carps in some commercial fish farms of West Godavari District, Andhra Pradesh. Curr. Sci. 58:1044–1045 [Google Scholar]
- 4. Hemstreet B. 2010. An update on Aeromonas hydrophila from a fish health specialist for summer 2010. Catfish J. 24:4 [Google Scholar]
- 5. Pridgeon JW, Klesius PH. 2011. Molecular identification and virulence of three Aeromonas hydrophila isolates cultured from infected channel catfish during a disease outbreak in west Alabama (USA) in 2009. Dis. Aquat. Organ. 94:249–253. 10.3354/dao02332 [DOI] [PubMed] [Google Scholar]
- 6. Pridgeon JW, Klesius PH. 2011. Virulence of Aeromonas hydrophila to channel catfish Ictaluras punctatus fingerlings in the presence and absence of bacterial extracellular products. Dis. Aquat. Organ. 95:209–215. 10.3354/dao02357 [DOI] [PubMed] [Google Scholar]
- 7. Griffin MJ, Goodwin AE, Merry GE, Liles MR, Williams MA, Ware C, Waldbieser GC. 2013. Rapid quantitative detection of Aeromonas hydrophila strains associated with disease outbreaks in catfish aquaculture. J. Vet. Diagn. Invest. 25:473–481. 10.1177/1040638713494210 [DOI] [PubMed] [Google Scholar]
- 8. Tekedar HC, Waldbieser GC, Karsi A, Liles MR, Griffin MJ, Vamenta S, Sonstegard T, Hossain M, Schroeder SG, Khoo L, Lawrence ML. 2013. Complete genome sequence of a channel catfish epidemic isolate, Aeromonas hydrophila strain ML09-119. Genome Announc. 1(5):e00755-13. 10.1128/genomeA.00755-13 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9. Hossain MJ, Waldbieser GC, Sun D, Capps NK, Hemstreet WB, Carlisle K, Griffin MJ, Khoo L, Goodwin AE, Sonstegard TS, Schroeder S, Hayden K, Newton JC, Terhune JS, Liles MR. 2013. Implication of lateral genetic transfer in the emergence of Aeromonas hydrophila isolates of epidemic outbreaks in channel catfish. PLoS One 8:e80943. 10.1371/journal.pone.0080943 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10. Pridgeon JW, Klesius PH, Song L, Zhang D, Kojima K, Mobley JA. 2013. Identification, virulence, and mass spectrometry of toxic ECP fractions of west Alabama isolates of Aeromonas hydrophila obtained from a 2010 disease outbreak. Vet. Microbiol. 164:336–343. 10.1016/j.vetmic.2013.02.020 [DOI] [PubMed] [Google Scholar]
- 11. Grim CJ, Kozlova EV, Sha J, Fitts EC, van Lier CJ, Kirtley ML, Joseph SJ, Read TD, Burd EM, Tall BD, Joseph SW, Horneman AJ, Chopra AK, Shak JR. 2013. Characterization of Aeromonas hydrophila wound pathotypes by comparative genomic and functional analyses of virulence genes. mBio 4(2):e00064-13. 10.1128/mBio.00064-13 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, Ussery DW. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35:3100–3108. 10.1093/nar/gkm160 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13. Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I. 2004. VISTA: computational tools for comparative genomics. Nucleic Acids Res. 32:W273–W279. 10.1093/nar/gkh053 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 14. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST Server: Rapid Annotations using Subsystems Technology. BMC Genomics 9:75. 10.1186/1471-2164-9-75 [DOI] [PMC free article] [PubMed] [Google Scholar]