Abstract
Aeromonas veronii strain B565 was isolated from aquaculture pond sediment in China. We present here the complete genome sequence of B565 and compare it with 2 published genome sequences of pathogenic strains in the Aeromonas genus. The result represents an independent stepwise acquisition of virulence factors of pathogenic strains in this genus.
GENOME ANNOUNCEMENT
Aeromonas veronii is a Gram-negative, rod-shaped bacterium, commonly isolated from clinical, environmental, and food samples (1). It can cause wound infections, diarrhea, or septicaemia in immunocompromised patients (4, 6, 10). A. veronii is also the causative agent of bacterial hemorrhagic septicemia in fish and is becoming a major economic problem in the fish-farming industry (2). A. veronii strain B565, isolated from aquaculture pond sediment in Tianjin, China, was found to have the ability to produce chitinase to control fungal or Myxozoa-related diseases in a separate study.
Whole-genome sequencing of A. veronii B565 was performed with a combined strategy involving Roche/454 (8) and Solexa paired-end sequencing technology (3). Genomic libraries containing 5.8-kb inserts were constructed, and 225,134 paired-end reads were generated using the GS FLX system, giving 18.8-fold coverage of the genome. A total of 94.65% of the reads were assembled into 3 large scaffolds, including 62 nonredundant contigs, using a 454 Newbler assembler (454 Life Science, Branford, CT). A total of 4,340,032 reads (2-kb insert) were generated to reach a depth of 95-fold coverage with an Illumina Solexa GA IIx and mapped to the scaffolds using a Burrows-Wheeler alignment (BWA) tool (7). The interscaffold and intrascaffold gaps were filled by local assembly of Roche and Solexa reads around or sequencing PCR products using an ABI 3730 capillary sequencer. The analysis of the genome was performed as described previously (5, 13).
The complete genome sequence of B565 contains a circular 4,551,783-bp chromosome, with a GC content of 58.72%. There are 4,057 protein-coding genes, 10 rRNA operons, and 102 tRNA genes in its genome. B565 encodes some putative virulence factors, such as hemolysins, RTX protein, adhesion factor, flagella, and mannose-sensitive hemagglutinin (MSHA) (12), all of which were shared with at least one of the sequenced genomes for Aeromonas hydrophila ATCC 7966 (11) and A. salmonicida A449 (9). There are 5 genes encoding chitinase in B565, and all could be found in ATCC 7966 and A449, indicating an important role for these conserved chitinases in Aeromonas.
There are fewer virulence genes in B565 than in ATCC 7966 and A449, suggesting a less virulent or nonvirulent character. There are 346 genes shared by ATCC 7966 and A449 but absent in B565. Some of these genes encode putative virulence factors such as hemolysins and the type III secretion protein. There are 329 and 666 unique genes in ATCC 7966 and A449, respectively, some of which are virulence genes and often form large clusters, such as the rtx cluster in ATCC 7966 and the flagellar gene cluster in A449, or are related to mobile elements such as phages and transposons, illuminating their lateral transfer history.
The comparison represents a two-stepwise process during the acquisition of virulence in these pathogenic Aeromonas species: some weapons were acquired a long time ago and inherited from their common ancestors, while others can be obtained quickly by lateral transfer.
Nucleotide sequence accession number.
The sequence and annotation of the A. veronii B565 are available in GenBank under accession number CP002607.
Acknowledgments
This work was supported by the Conversion of Agricultural Science and Technology Achievement (Ministry of Science and Technology of China) (grant no. 2010GB23260591), the Agricultural Science and Technology Achievement Transformation and Promotion in Tianjin (grant no. 201004040), the Chinese National Science Fund for Distinguished Young Scholars (grant no. 30788001), the National 863 Program (grant no. 2010AA10A203), the National 973 program of China (grant no. 2009CB522603), the NSFC Key Program (grant no. 31030002), and the National Key Programs for Infectious Diseases of China (grant no. 2009ZX10004-108).
Footnotes
Published ahead of print on 6 May 2011.
REFERENCES
- 1. Ashbolt N. J. 2004. Microbial contamination of drinking water and disease outcomes in developing regions. Toxicology 198:229–238 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2. Austin B., Austin D. A. 1999. Bacterial fish pathogens: disease in farmed and wild fish, 3rd ed. Springer Verlag, New York, NY [Google Scholar]
- 3. Bentley D. R., et al. 2008. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53–59 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4. Cui H., Hao S., Arous E. 2007. A distinct cause of necrotizing fasciitis: Aeromonas veronii biovar sobria. Surg. Infect. (Larchmt.) 8:523–528 [DOI] [PubMed] [Google Scholar]
- 5. Ferenci T., et al. 2009. Genomic sequencing reveals regulatory mutations and recombinational events in the widely used MC4100 lineage of Escherichia coli K-12. J. Bacteriol. 191:4025–4029 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6. Grobner S., et al. 2007. Severe diarrhoea caused by Aeromonas veronii biovar sobria in a patient with metastasised GIST. Pol. J. Microbiol. 56:277–279 [PubMed] [Google Scholar]
- 7. Li H., Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26:589–595 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8. Margulies M., et al. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9. Reith M. E., et al. 2008. The genome of Aeromonas salmonicida subsp. salmonicida A449: insights into the evolution of a fish pathogen. BMC Genomics 9:427. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10. Sanchez-Cespedes J., et al. 2009. Development of imipenem resistance in an Aeromonas veronii biovar sobria clinical isolate recovered from a patient with cholangitis. J. Med. Microbiol. 58:451–455 [DOI] [PubMed] [Google Scholar]
- 11. Seshadri R., et al. 2006. Genome sequence of Aeromonas hydrophila ATCC 7966T: jack of all trades. J. Bacteriol. 188:8272–8282 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12. Watnick P. I., Fullner K. J., Kolter R. 1999. A role for the mannose-sensitive hemagglutinin in biofilm formation by Vibrio cholerae El Tor. J. Bacteriol. 181:3606–3609 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13. Zhou Z., et al. Derivation of Escherichia coli O157:H7 from its O55:H7 precursor. PLoS One 5:e8700. [DOI] [PMC free article] [PubMed] [Google Scholar]