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

Edwardsiella ictaluri   and   Edwardsiella piscicida   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   E. ictaluri   93-146 and   E. piscicida   C07-087 genomes were evaluated by applying comparative genomics analysis. All available complete (10) and non-complete (19) genomes from five   Edwardsiella   species were also included in a systematic analysis. Average nucleotide identity and core-genome phylogenetic tree analyses indicated that the five   Edwardsiella   species were separated from each other. Pan-/core-genome analyses for the 29 strains from the five species showed that genus   Edwardsiella   members have 9474 genes in their pan genome, while the core genome consists of 1421 genes. Orthology cluster analysis showed that   E. ictaluri   and   E. piscicida   genomes have the greatest number of shared clusters. However,   E. ictaluri   and   E. piscicida   also have unique features; for example, the   E. ictaluri   genome encodes urease enzymes and cytochrome o ubiquinol oxidase subunits, whereas   E. piscicida   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   E. ictaluri   93-146 and three other   E. ictaluri   genomes encode a type IV secretion system (T4SS), whereas none of the   E. piscicida   genomes encode this system. Additionally, the   E. piscicida   C07-087 genome encodes two different type VI secretion systems.   E. ictaluri   genomes tend to encode more insertion elements, phage regions and genomic islands than   E. piscicida   . We speculate that the T4SS could contribute to the increased number of mobilome elements in   E. ictaluri   compared to   E. piscicida   . Two of the   E. piscicida   genomes encode full CRISPR-Cas regions, whereas none of the   E. ictaluri   genomes encode Cas proteins. Overall, comparison of the   E. ictaluri   and   E. piscicida   genomes reveals unique features and provides new insights on pathogenicity that may reflect the host adaptation of the two species.