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Rehman MNU, Dawar FU, Zeng J, Fan L, Feng W, Wang M, Yang N, Guo G, Zheng J. Complete genome sequence analysis of Edwardsiella tarda SC002 from hatchlings of Siamese crocodile. Front Vet Sci 2023; 10:1140655. [PMID: 36968469 PMCID: PMC10034365 DOI: 10.3389/fvets.2023.1140655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/08/2023] [Indexed: 03/11/2023] Open
Abstract
Edwardsiella tarda is a Gram-negative, facultative anaerobic rod-shaped bacterium and the causative agent of the systemic disease “Edwardsiellosis”. It is commonly prevalent in aquatic organisms with subsequent economic loss and hence has attracted increasing attention from researchers. In this study, we investigated the complete genome sequence of a highly virulent isolate Edwardsiella tarda SC002 isolated from hatchlings of the Siamese crocodile. The genome of SC002 consisted of one circular chromosome of length 3,662,469 bp with a 57.29% G+C content and four novel plasmids. A total of 3,734 protein-coding genes, 12 genomic islands (GIs), 7 prophages, 48 interspersed repeat sequences, 248 tandem repeat sequences, a CRISPR component with a total length of 175 bp, and 171 ncRNAs (tRNA = 106, sRNA = 37, and rRNA = 28) were predicted. In addition, the coding genes of assembled genome were successfully annotated against eight general databases (NR = 3,618/3,734, COG = 2,947/3,734, KEGG = 3,485/3,734, SWISS-PROT = 2,787/3,734, GO = 2,648/3,734, Pfam = 2,648/3,734, CAZy = 130/3,734, and TCDB = 637/3,734) and four pathogenicity-related databases (ARDB = 11/3,734, CARD = 142/3,734, PHI = 538/3,734, and VFDB = 315/3,734). Pan-genome and comparative genome analyses of the complete sequenced genomes confirmed their evolutionary relationships. The present study confirmed that E. tarda SC002 is a potential pathogen bearing a bulk amount of antibiotic resistance, virulence, and pathogenic genes and its open pan-genome may enhance its host range in the future.
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Affiliation(s)
- Muhammad Nafees Ur Rehman
- Laboratory of Microbiological Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, China
| | - Farman Ullah Dawar
- Department of Zoology, Kohat University of Science and Technology, Kohat, Pakistan
| | - Jifeng Zeng
- Laboratory of Microbiological Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, China
- One Health Institute, Hainan University, Haikou, China
| | - Lixia Fan
- Laboratory of Microbiological Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, China
| | - Wei Feng
- Laboratory of Microbiological Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, China
| | - Mengqi Wang
- Laboratory of Microbiological Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, China
| | - Nuo Yang
- Laboratory of Microbiological Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, China
| | - Guiying Guo
- Laboratory of Microbiological Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, China
| | - Jiping Zheng
- Laboratory of Microbiological Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, China
- One Health Institute, Hainan University, Haikou, China
- *Correspondence: Jiping Zheng
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Comparative genomics of Edwardsiellaictaluri revealed four distinct host-specific genotypes and thirteen potential vaccine candidates. Genomics 2021; 113:1976-1987. [PMID: 33848586 DOI: 10.1016/j.ygeno.2021.04.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 12/31/2020] [Accepted: 04/05/2021] [Indexed: 02/02/2023]
Abstract
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 pan-genome 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.
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Tekedar HC, Blom J, Kalindamar S, Nho S, Karsi A, Lawrence ML. Comparative genomics of the fish pathogens Edwardsiella ictaluri 93-146 and Edwardsiella piscicida C07-087. Microb Genom 2020; 6. [PMID: 32108566 PMCID: PMC7067208 DOI: 10.1099/mgen.0.000322] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
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.
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Affiliation(s)
- Hasan C Tekedar
- College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, 35392 Giessen, Hesse, Germany
| | - Safak Kalindamar
- College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
| | - Seongwon Nho
- Division of Microbiology, National Center for Toxicological Research/FDA, Jefferson, AR, USA
| | - Attila Karsi
- College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
| | - Mark L Lawrence
- College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
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