Implication of lateral genetic transfer in the emergence of Aeromonas hydrophila isolates of epidemic outbreaks in channel catfish

Authors: HOSSAIN, MOHAMMAD - Auburn University; Waldbieser, Geoffrey - Geoff; SUN, DAWEI - Auburn University; CAPPS, NANCY - Auburn University; HEMSTREET, WILLIAM - Auburn University; GRIFFIN, MATT - Mississippi State University; KHOO, LESTER - Mississippi State University; GOODWIN, ANDREW - University Of Arkansas; Sonstegard, Tad; Schroeder, Steven - Steve; HAYDEN, KARL - Auburn University; TERHUNE, JEFFERY - Auburn University; LIES, MARK - Auburn University

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/8/2013
Publication Date: 11/20/2013
Citation: Hossain, M., Waldbieser, G.C., Sun, D., Capps, N., Hemstreet, W., Griffin, M.J., Khoo, L., Goodwin, A., Sonstegard, T.S., Schroeder, S.G., Hayden, K., Terhune, J.S., Lies, M.R. 2013. Implication of lateral genetic transfer in the emergence of Aeromonas hydrophila isolates of epidemic outbreaks in channel catfish. PLoS One. 8:e80943.

Interpretive Summary: A new strain of the bacteria Aeromonas hydrophila has recently been implicated in severe disease outbreaks in commercial catfish culture, leading to rapid and substantial losses of large catfish in affected ponds. This bacteria is commonly found in catfish ponds in a less virulent form. A team of scientists from Mississippi State University, the University of Arkansas-Pine Bluff, Auburn University, and the USDA-ARS-Catfish Genetics Research Unit used comparative genomics to identify differences in DNA sequence between common A. hydrophila and the new epidemic strain.

Technical Abstract: Background: A recent epidemic outbreak of motile Aeromonas septicemia of catfish caused by highly virulent Aeromonas hydrophila is a major threat to the catfish industry in the southeastern United States. The lack of a complete genome sequence for this newly emerged A. hydrophila genotype hampers efforts to control the spread and understand the emergence of this pathogen. Methods: A total of 11 A. hydrophila isolates including six recent epidemic isolates and five reference isolates were sequenced at > 150-fold coverage using an Illumina HiSeq 2000. Genome-wide comparisons were carried out to identify epidemic-associated genomic regions responsible for enhanced virulence. In addition to putative virulence genes, A. hydrophila genomes were examined for the presence of genomic islands, prophage elements, and other functions that could contribute to their ability to infect and replicate within a catfish. Results: Comparative genomics revealed that recent epidemic A. hydrophila isolates are highly clonal whereas reference isolates are greatly diverse. These epidemic isolates share 58 unique genetic regions comprising 341 kb in total with 311 predicted genes that putatively encode prophage elements, virulence factors, and clusters of genes predicted to be involved in pilus biogenesis and myo-inositol utilization, along with many predicted genes with unknown functions. An in vitro growth assay revealed that epidemic isolates were able to use myo-inositol as a sole carbon source and that this phenotype could be used to test field isolates for detection of epidemic strains. Four different novel O-antigen biosynthesis gene clusters were identified within the genome of 11 A. hydrophila isolates, and all epidemic strains shared a single type of O-antigen biosynthesis cluster. Conclusions: Most of the unique genomic regions associated with epidemic A. hydrophila strains were within genomic islands, suggesting that these epidemic strains have acquired a large number of genes by lateral transfer. Our comparative genomic study reveals new insights into the evolutionary changes that have occurred in A. hydrophila strains associated with epidemic outbreaks in channel catfish and provides a foundation for studying the specific molecular determinants of virulence in this emerging pathogen.