ARS | Publication request: Comparative genomic analysis of bacteriophages specific to the channel catfish pathogen Edwardsiella ictaluri

Submitted to: Virology Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 7, 2011
Publication Date: January 7, 2011
Citation: Carrias, A., Welch, T.J., Waldbieser, G.C., Mead, D.A., Terhune, J.S., Liles, M.R. 2011. Comparative genomic analysis of bacteriophages specific to the channel catfish pathogen Edwardsiella ictaluri. Virology Journal. 8:6. DOI: 10.1186/1743-422X-8-6.

Interpretive Summary: Infectious diseases are a major impediment to the U.S. Catfish aquaculture industry. While traditional chemical antibacterials provide a powerful means for the control of pathogens their use causes serious environmental and human health concerns. Furthermore, antibiotics are of low specificity and can cause disruptions of the beneficial bacteria present in the treated animal thus causing additional problems. Pathogen-specific antibiotics could control disease without these negative consequences. One possibility is the use of bacteriophages (or phage), which are naturally occurring, highly specific viruses that infect, replicate in and kill bacteria. In theory these infectious agents have great potential as highly specific and self-replicating antimicrobials that offer an alternative to traditional chemical antibiotics. However, before using a specific bacteriophage for disease control a careful investigation of the physiology and genetics of the bacteriophage must be undertaken to assess the safety of its use. This manuscript describes the genome sequences of three Edwardsiella ictaluri-specific bacteriophages that are candidates for use as biocontrol agents for this important catfish pathogen. The three Edwardsiella ictaluri-specific bacteriophages characterized were from geographically distinct catfish ponds and were greater than 98 % identical to each other at the nucleotide level showing that they were highly related phage isolates. Additionally all three phages had a genome organization similar to members of a well characterized bacteriophage family. Differences between the phages were primarily observed in regions that did not code for proteins and in regions encoding the proteins that form the phage structure. Genomic analysis of these phages generally supported their safe use as biocontrol agents.

Technical Abstract: Background: The bacterial pathogen Edwardsiella ictaluri is a primary cause of mortality in channel catfish raised commercially in aquaculture farms. Additional treatment and diagnostic regimes are needed for this enteric pathogen, motivating the discovery and characterization of bacteriophages specific to E. ictaluri. Results:The genomes of three Edwardsiella ictaluri-specific bacteriophages isolated from geographically distant aquaculture ponds, at different times, were sequenced and analyzed. The genomes for phages eiAU, eiDWF, and eiMSLS are 42.80 kbp, 42.12 kbp, and 42.69 kbp, respectively, and are greater than 98 % identical to each other at the nucleotide level. Nucleotide differences were mostly observed in non-coding regions and in structural proteins, with significant variability in the sequences of putative tail fiber proteins. The genome organization of these phages exhibit a pattern shared by other Siphoviridae. Conclusions:These E. ictaluri-specific phage genomes reveal considerable conservation of genomic architecture and sequence identity, even with considerable temporal and spatial divergence in their isolation. Their genomic homogeneity is similarly observed among E. ictaluri bacterial isolates. The genomic analysis of these phage supports the conclusion that these are virulent phage, lacking the capacity for lysogeny or expression of virulence genes. This study contributes to our knowledge of phage genomic diversity and facilitates studies on the diagnostic and therapeutic applications of these phages.