Comparative genomics of Edwardsiella ictaluri revealed four distinct host-specific genotypes and thirteen potential vaccine candidates

Edwardsiella ictaluri has been considered an important threat for catfish aquaculture industry for more than 4 decades and an emerging pathogen of farmed tilapia but only 9 sequenced genomes were publicly available. We hereby report two new complete genomes of E. ictaluri originated from diseased hybrid red tilapia (Oreochromis sp.) and striped catfish (Pangasianodon hypophthalmus) in Southeast Asia. E. ictaluri species has an open pangenome consisting of 2615 core genes and 5592 pan genes. Phylogenetic analysis using core genome MLST (cgMLST) and ANI values consistently placed E. ictaluri isolates into 4 host-specific genotypes. Presence of unique genes and absence of certain genes from each genotype provided potential biomarkers for further development of genotyping scheme. Vaccine candidates with high antigenic, solubility and secretion probabilities were identified in silico from the core genes. Microevolution within the species is brought about by bacteriophages and insertion elements and possibly drive host adaptation.

Automated summary

E. ictaluri has been recognized as a major threat to catfish aquaculture for over 40 years, with only 9 publicly available sequenced genomes. Our study reports two new complete genomes of E. ictaluri isolated from diseased hybrid red tilapia and striped catfish in Southeast Asia. Through core genome MLST (cgMLST) and ANI values, E. ictaluri isolates were consistently grouped into 4 host-specific genotypes, offering potential biomarkers for further genotyping scheme development. High antigenic, solubility, and secretion probabilities of vaccine candidates were identified in silico from the core genes.