Abstract
We present the genome of a clinical isolate, Aeromonas hydrophila SNUFPC-A8, from a moribund cherry salmon. The completed draft genome of this strain shows high sequence homology to the reference strain A. hydrophila ATCC 7966 (NC008570.1) and known plasmids pAsa2 and pAAk1 from other Aeromonas species (NC004925.1 and NC019014.1).
GENOME ANNOUNCEMENT
In aquatic environments, fish are predisposed to Aeromonas infections because of the widespread distribution of these pathogens and the stress induced by intensive culture (1). In humans, motile Aeromonas species have received increasing attention as emergent agents of food-borne gastrointestinal disease. Recently, Aeromonas was reported as the cause of necrotizing fasciitis, better known as flesh-eating bacteria, especially in patients with immunosuppression who underwent an aquatic wetting (2).
The complete genome of A. hydrophila ATCC 7966 (NC008570.1), a well-characterized type strain isolated from a tin of milk, was sequenced previously (3). However, there are no genome sequences available for A. hydrophila strains isolated from clinical samples.
The A. hydrophila strain SNUFPC-A8 isolated from a kidney of a moribund cherry salmon (Oncorhynchus masou masou) (4) was used for draft-genome sequencing. Genomic DNA was extracted (5) and sequenced using the Roche/454 GS FLX titanium pyrosequencing method with 37.5× coverage (Macrogen, South Korea). Putative open reading frames (ORFs) were predicted by using Glimmer 3.0 software (6), and the putative functions of the ORFs were determined using the BLAST program in GenBank (7).
The sequence data consisted of a total of 185,951,609 bp and 303,268 reads with an average read length of 613.16 bp. Furthermore, the data include 295,118 assembled reads and 3,418 partially assembled reads. Using de novo software (v. 2.6), the reads were assembled into 59 contigs, which included 41 contigs that were longer than 500 bp. The average contig size was 13,019 bp, and the data include 300 singletons. The draft genome of A. hydrophila SNUFPC-A8 was 4,969,090 bp in length, and a total of 4,779 ORFs were discovered.
Gene ontology (GO) searches were performed using all predicted ORFs, and the results revealed that 35%, 33%, and 11% of the sequences included genes related to biological processes, molecular functions, and cellular components, respectively. Of the GO categories related to biological processes, metabolic processes represented the most dominant category, which contained 32% of genes. In the cellular component category, 45% of the genes were unclassified. Based on molecular functions characterized by GO terms, 40% of the genes were associated with catalytic activities.
The strain SNUFPC-A8 shows high nucleotide sequence similarity to the reference strain A. hydrophila ATCC 7966 (NC008570.1), and 217,553 reads of SNUFPC-A8 were fully aligned. Additionally, SNUFPC-A8 shows sequence homology with the known plasmids A. salmonicida A449 and A. aquariorum AAK1 (NC004925.1 and NC019014.1) The sequence data generated in this study will contribute to the understanding of genome diversity of A. hydrophila and other Aeromonas species.
Nucleotide sequence accession number.
The nucleotide sequence for the draft genome was deposited in GenBank under accession number AMQA00000000.
ACKNOWLEDGMENTS
This study was financially supported by the Basic Science Research Program (2010-0016748) through the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science and Technology through a Korea Research Foundation grant (KRF-2008-331-E00385).
Footnotes
Citation Han JE, Kim JH, Choresca C, Shin SP, Jun JW, Park SC. 2013. Draft genome sequence of a clinical isolate, Aeromonas hydrophila SNUFPC-A8, from a moribund cherry salmon (Oncorhynchus masou masou). Genome Announc. 1(1):e00133-12. doi:10.1128/genomeA.00133-12.
REFERENCES
- 1. Saavedra MJ, Guedes-Novais S, Alves A, Rema P, Tacao M, Correia A, Martinez-Murcia AJ. 2004. Resistance to β-lactam antibiotics in Aeromonas hydrophila isolated from rainbow trout (Oncorhynchus mykiss). Int. Microbiol. 7:201–211 [PubMed] [Google Scholar]
- 2. Abuhammour W, Hasan RA, Rodgers D. 2006. Necrotizing fasciitis caused by Aeromonas hydrophila in an immunocompetent child. Pediatr. Emerg. Care 22:48–51 [DOI] [PubMed] [Google Scholar]
- 3. Seshadri R, Joseph SW, Chopra AK, Sha J, Shaw J, Graf J, Haft D, Wu M, Ren Q, Rosovitz MJ, Madupu R, Tallon L, Kim M, Jin S, Vuong H, Stine OC, Ali A, Horneman AJ, Heidelberg JF. 2006. Genome sequence of Aeromonas hydrophila ATCC 7966T: jack of all trades. J. Bacteriol. 188:8272–8282 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4. Han JE, Kim JH, Choresca CH, Jr, Shin SP, Jun JW, Chai JY, Han SY, Park SC. 2012. First description of the qnrS-like (qnrS5) gene and analysis of quinolone resistance-determining regions in motile Aeromonas spp. From diseased fish and water. Res. Microbiol. 163:73–79 [DOI] [PubMed] [Google Scholar]
- 5. Sambrook J, Fritsch EF, Maniatis T. 1989. Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY [Google Scholar]
- 6. Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with glimmer. Bioinformatics 23:673–679 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389–3402 [DOI] [PMC free article] [PubMed] [Google Scholar]