Comparative genomics of the fish pathogens Edwardsiella ictaluri 93-146 and Edwardsiella piscicida C07-087

Abstract

<i>Edwardsiella ictaluri</i> and <i>Edwardsiella piscicida</i> are important fish pathogens affecting cultured and wild fish worldwide. To investigate the genome-level differences and similarities between catfish-adapted strains in these two species, the complete <i>E. ictaluri</i> 93-146 and <i>E. piscicida</i> C07-087 genomes were evaluated by applying comparative genomics analysis. All available complete (10) and non-complete (19) genomes from five <i>Edwardsiella</i> species were also included in a systematic analysis. Average nucleotide identity and core-genome phylogenetic tree analyses indicated that the five <i>Edwardsiella</i> species were separated from each other. Pan-/core-genome analyses for the 29 strains from the five species showed that genus <i>Edwardsiella</i> members have 9474 genes in their pan genome, while the core genome consists of 1421 genes. Orthology cluster analysis showed that <i>E. ictaluri</i> and <i>E. piscicida</i> <i></i>genomes have the greatest number of shared clusters. However, <i>E. ictaluri</i> and <i>E. piscicida</i> also have unique features; for example, the <i>E. ictaluri</i> genome encodes urease enzymes and cytochrome o ubiquinol oxidase subunits, whereas <i>E. piscicida</i> genomes encode tetrathionate reductase operons, capsular polysaccharide synthesis enzymes and vibrioferrin-related genes. Additionally, we report for what is believed to be the first time that <i>E. ictaluri</i> 93-146 and three other <i>E. ictaluri</i> genomes encode a type IV secretion system (T4SS), whereas none of the <i>E. piscicida</i> genomes encode this system. Additionally, the <i>E. piscicida</i> C07-087 genome encodes two different type VI secretion systems. <i>E. ictaluri</i> genomes tend to encode more insertion elements, phage regions and genomic islands than <i>E. piscicida</i>. We speculate that the T4SS could contribute to the increased number of mobilome elements in <i>E. ictaluri</i> compared to <i>E. piscicida</i>. Two of the <i>E. piscicida</i> genomes encode full CRISPR-Cas regions, whereas none of the <i>E. ictaluri</i> genomes encode Cas proteins. Overall, comparison of the <i>E. ictaluri</i> and <i>E. piscicida</i> genomes reveals unique features and provides new insights on pathogenicity that may reflect the host adaptation of the two species.