Abstract
We present the complete genome sequence for a novel Edwardsiella ictaluri-specific bacteriophage, PEi21, isolated from river water in Japan. An initial comparative genome analysis revealed that the phage was closely related to the previously reported Edwardsiella tarda phage MSW-3 isolated from a red sea bream farm in Japan.
GENOME ANNOUNCEMENT
Edwardsiella ictaluri, a Gram-negative bacterium, causes enteric septicemia of catfish (ESC), the most serious infectious disease in the channel catfish (Ictalurus punctatus) industry in the United States (1). E. ictaluri also infects other catfish species and is found in Southeast Asia (2–4). For a long time there had been no records of this bacterium in Japan. However, in 2007, E. ictaluri infections of wild ayu (Plecoglossus altivelis) were first found in some rivers of Japan (5, 6) and have been continuously observed since then (7).
Three E. ictaluri-specific bacteriophages (phages), eiAU, eiDWF, and eiMSLS, have been isolated from catfish aquaculture pounds in the United States and classified within the family Siphoviridae (8, 9). Recently, E. ictaluri-specific phages have also been isolated from rivers in Japan, in association with E. ictaluri infections of ayu (7). These phages exhibited the morphology of the family Myoviridae (7). To further characterize the E. ictaluri phages isolated from the Japanese rivers, we determined the complete genome sequence of the E. ictaluri-specific bacteriophage PEi21.
Whole-genome shotgun sequencing of PEi21 was performed using the Roche 454GS-FLX Titanium sequencing platform. De novo assembly of sequence reads was performed using Newbler 2.8. The complete genome sequence was annotated using the Rapid Annotations using Subsystems Technology (RAST) server (10) and BLASTP (11) against the viral sequence database (E value threshold of 1E−3).
The complete genome sequence of PEi21 was assembled as a circular contig. The circularly permutated genome showed a 43,378-bp length, with a GC content of 52.6%. The genome contained 71 predicted open reading frames (ORFs), of which 59 encode conserved hypothetical proteins or novel proteins and 12 have a predicted function. A phylogenetic analysis based on portal proteins revealed that PEi21 was closely related to dwarf myoviruses (12). The E. tarda phage MSW-3, which was isolated from a seawater sample obtained from a red sea bream (Pagrus major) farm in Japan (13), was the closest phage to PEi21, followed by Klebsiella phage JD001 (14), Iodobacteriophage φPLPE (15), Vibrio phages 138 and CP-T1 (12), and Pectobacterium phage ZF40 (12). CoreGenes3.5 (16) analysis (with the BLASTP threshold score set at 75) also confirmed these results, showing that PEi21 shared 54 homologous genes with MSW-3, while PEi21 has 40, 28, 31, and 20 homologous genes in common with Klebsiella phage JD001, Iodobacteriophage φPLPE, Vibrio phages 138 and CP-T1, and Pectobacterium phage ZF40, respectively. Thus, it will be interesting to investigate the function of the unique genes among these phage genomes in future studies, which will increase our understanding of the evolution of these phages and their host specificity. Furthermore, this E. ictaluri phage genome information provides a novel resource for detection of E. ictaluri in natural freshwater, for elucidating the transmission route of E. ictaluri (7), and for various applications of phages in the control of ESC and other E. ictaluri infections in aquaculture (17).
Nucleotide sequence accession number.
The complete genome sequence of the E. ictaluri phage PEi21 was submitted to DDBJ under the accession number AP013057.
ACKNOWLEDGMENTS
This study was supported by a Grant-in-Aid (Marine Metagenomics for Monitoring the Coastal Microbiota) from the Ministry of Agriculture, Forestry and Fisheries of Japan.
We thank Kristian von Schalburg (Centre for Biomedical Research, University of Victoria, Canada) for his help in preparing the manuscript. We also thank Ayako Kondo and Haruka Ito for support in genome sequencing.
Footnotes
Citation Yasuike M, Kai W, Nakamura Y, Fujiwara A, Kawato Y, Hassan ES, Mahmoud MM, Nagai S, Kobayashi T, Ototake M, Nakai T. 2014. Complete genome sequence of the Edwardsiella ictaluri-specific bacteriophage PEi21, isolated from river water in Japan. Genome Announc. 2(2):e00228-14. doi:10.1128/genomeA.00228-14.
REFERENCES
- 1. Hawke JP, McWhorter AC, Steigerwalt AG, Brenner DJ. 1981. Edwardsiella ictaluri sp. nov., the causative agent of enteric septicemia of catfish. Int. J. Syst. Bacteriol. 31:396–400. 10.1099/00207713-31-4-396 [DOI] [Google Scholar]
- 2. Kasornchandra J, Rogers WA, Plumb JA. 1987. Edwardsiella ictaluri from walking catfish, Clarias batrachus L., in Thailand. J. Fish Dis. 10:137–138. 10.1111/j.1365-2761.1987.tb00729.x [DOI] [Google Scholar]
- 3. Yuasa K, Kholidin EB, Panigoro N, Hatai K. 2003. First isolation of Edwardsiella ictaluri from cultured striped catfish Pangasius hypophthalmus in Indonesia. Fish Pathol. 38:181–183. 10.3147/jsfp.38.181 [DOI] [Google Scholar]
- 4. Crumlish M, Dung TT, Turnbull JF, Ngoc NTN, Ferguson HW. 2002. Identification of Edwardsiella ictaluri from diseased freshwater catfish, Pangasius hypophthalmus (Sauvage), cultured in the Mekong Delta, Vietnam. J. Fish Dis. 25:733–736. 10.1046/j.1365-2761.2002.00412.x [DOI] [Google Scholar]
- 5. Nagai T, Iwamoto E, Sakai T, Arima T, Tensha K, Iida Y, Iida T, Nakai T. 2008. Characterization of Edwardsiella ictaluri isolated from wild ayu Plecoglossus altivelis in Japan. Fish Pathol. 43:158–163. 10.3147/jsfp.43.158 [DOI] [Google Scholar]
- 6. Sakai T, Kamaishi T, Sano M, Tensha K, Arima T, Iida Y, Nagai T, Nakai T, Iida T. 2008. Outbreaks of Edwardsiella ictaluri infection in ayu Plecoglossus altivelis in Japanese rivers. Fish Pathol. 43:152–157. 10.3147/jsfp.43.152 [DOI] [Google Scholar]
- 7. Hassan ES, Mahmoud MM, Kawato Y, Nagai T, Kawaguchi O, Iida Y, Yuasa K, Nakai T. 2012. Subclinical Edwardsiella ictaluri infection of wild ayu Plecoglossus altivelis. Fish Pathol. 47:64–73. 10.3147/jsfp.47.64 [DOI] [Google Scholar]
- 8. Walakira JK, Carrias AA, Hossain MJ, Jones E, Terhune JS, Liles MR. 2008. Identification and characterization of bacteriophages specific to the catfish pathogen, Edwardsiella ictaluri. J. Appl. Microbiol. 105:2133–2142. 10.1111/j.1365-2672.2008.03933.x [DOI] [PubMed] [Google Scholar]
- 9. Carrias A, Welch TJ, Waldbieser GC, Mead DA, Terhune JS, Liles MR. 2011. Comparative genomic analysis of bacteriophages specific to the channel catfish pathogen Edwardsiella ictaluri. Virol. J. 8:6. 10.1186/1743-422X-8-6 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10. 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]
- 11. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403–410. 10.1016/S0022-2836(05)80360-2 [DOI] [PubMed] [Google Scholar]
- 12. Comeau AM, Tremblay D, Moineau S, Rattei T, Kushkina AI, Tovkach FI, Krisch HM, Ackermann HW. 2012. Phage morphology recapitulates phylogeny: the comparative genomics of a new group of myoviruses. PLoS One 7:e40102. 10.1371/journal.pone.0040102 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13. Yasuike M, Sugaya E, Nakamura Y, Shigenobu Y, Kawato Y, Kai W, Nagai S, Fujiwara A, Sano M, Kobayashi T, Nakai T. 2013. Complete genome sequence of a novel myovirus which infects atypical strains of Edwardsiella tarda. Genome Announc. 1(1):e00248-12. 10.1128/genomeA.00248-12 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 14. Cui Z, Shen W, Wang Z, Zhang H, Me R, Wang Y, Zeng L, Zhu Y, Qin J, He P, Guo X. 2012. Complete genome sequence of Klebsiella pneumoniae phage JD001. J. Virol. 86:13843. 10.1128/JVI.02435-12 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 15. Leblanc C, Caumont-Sarcos A, Comeau AM, Krisch HM. 2009. Isolation and genomic characterization of the first phage infecting Iodobacteria: φPLPE, a myovirus having a novel set of features. Environ. Microbiol. Rep 1:499–509. 10.1111/j.1758-2229.2009.00055.x [DOI] [PubMed] [Google Scholar]
- 16. 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 Res. Notes 6:140. 10.1186/1756-0500-6-140 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 17. Nakai T. 2010. Application of bacteriophages for control of infectious diseases in aquaculture, p 257–272 In Sabour PM, Griffiths MW. (ed), Bacteriophages in the control of food- and waterborne pathogens. ASM Press, Washington, DC [Google Scholar]