Comparative genomics of Edwardsiella anguillarum and Edwardsiella piscicida isolated in Taiwan enables the identification of distinctive features and potential virulence factors using Oxford-Nanopore MinION® sequencing

Omkar Vijay Byadgi; Atiek Rahmawaty; Pei-Chi Wang; Shih-Chu Chen

doi:10.1111/jfd.13743

Comparative genomics of Edwardsiella anguillarum and Edwardsiella piscicida isolated in Taiwan enables the identification of distinctive features and potential virulence factors using Oxford-Nanopore MinION® sequencing

J Fish Dis. 2023 Apr;46(4):287-297. doi: 10.1111/jfd.13743. Epub 2022 Dec 26.

Authors

Omkar Vijay Byadgi¹, Atiek Rahmawaty¹, Pei-Chi Wang^{1

2

3}, Shih-Chu Chen^{1

2

3

4

5}

Affiliations

¹ International College, International Degree Program of Ornamental Fish Technology and Aquatic Animal Health, National Pingtung University of Science and Technology, Pingtung, Taiwan.
² Research Centre for Fish Vaccine and Diseases, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan.
³ Southern Taiwan Fish Diseases Research Centre, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan.
⁴ Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan.
⁵ Research Centre for Animal Biologics, National Pingtung University of Science and Technology, Pingtung, Taiwan.

PMID: 36571326
DOI: 10.1111/jfd.13743

Abstract

Edwardsiella tarda (ET) and Edwardsiella anguillarum (EA) are the most harmful bacterial fish pathogens in Taiwan. However, there is confusion regarding the genotypic identification of E. tarda and E. piscicida (EP). Therefore, we used a novel Nanopore MinION MK1C platform to sequence and compare the complete genomes of E. piscicida and E. anguillarum. The number of coding genes, rRNA, and tRNA recorded for E. anguillarum and E. piscicida were 8322, 25, and 98, and 5458, 25, and 98, respectively. Ribosomal multilocus sequence typing (rMLST) for E. piscicida indicated 35 rps. The shared clusters between E. anguillarum and E. piscicida indicated several unique clusters for the individual genomes. The phylogenetic tree analysis for all complete genomes indicated that E. anguillarum and E. piscicida were placed into two species-specific genotypes. Distribution of subsystems for annotated genomes found that genes related to virulence, defence, and disease for E. anguillarum were 103 and those for E. piscicida were 60 and pathogenic islands (PI) were 498 and 225, respectively. Vaccine candidates were identified in silico from the core genes using high antigenic, solubility, and secretion probabilities. Altogether, the genome data revealed distinctive features between E. anguillarum and E. piscicida, which suggest different pathogenicity and thus the need for separate preventive strategies.

Keywords: Edwardsiellosis; Oxford MinIon nanopore®; complete genome; species identification; vaccination; virulence factors.

MeSH terms

Animals
Edwardsiella*
Enterobacteriaceae Infections* / microbiology
Fish Diseases* / microbiology
Genomics
Nanopores*
Phylogeny
Taiwan
Virulence Factors / genetics

Substances

Virulence Factors

Supplementary concepts

Edwardsiella piscicida
Edwardsiella anguillarum

Grants and funding

National Pingtung University of Science and Technology