ABSTRACT
Edwardsiella piscicida is a Gram-negative bacteria belonging to the Hafniaceae family which affects several species of marine and freshwater fish. We present the complete genome of E. piscicida strain BEP80 recovered from the Brazilian catfish named Surubim (Pseudoplatystoma corruscans), consisting a chromosome of 3,883,256 bp and no plasmids.
ANNOUNCEMENT
The first description of the bacterial Edwardsiella genus occurred in 1960, with a characterization of the biochemical reactions for the species Edwardsiella tarda in in vitro tests (1). Retrospectively, the species Edwardsiella hoshinae and Edwardsiella ictaluri were also included at genus (2, 3). In recent years, the species E. tarda was found to comprise three phenotypically similar but genetically different taxa/genotypes, E. tarda, E. anguillarum, and E. piscicida, the last being more virulent for catfish than the others (4, 5). Until then, there had been no reports of Edwardsiella piscicida from fish in Brazil, so this is the first report of the strain deposited for this pathogen.
Edwardsiella piscicida strain BEP80, classified as a member of the Gammaproteobacteria of the order Enterobacterales, family Hafniaceae, and the genus Edwardsiella, was isolated at a farm with high mortality in Brazil and identified by seeding a cranial kidney fragment of a Surubim (Pseudoplatystoma corruscans) on a plate containing Mueller-Hinton agar (Kasvi, São José dos Pinhais, Brazil) enriched with 5% defibrinated sheep blood. After incubation at 29°C for 48 h, the colony was isolated and screening tests were executed (Gram stain, oxidase, and biochemical tests) to identify the bacterial genus. A single CFU was subjected to extraction of genomic DNA by use of a PureLink genomic DNA mini kit (Invotrogen, USA), according to the manufacturer's instructions. A multiplex PCR (mPCR) assay was performed to identify the bacterial species, which was characterized as Edwardsiella piscicida (6). For sequencing, the DNA was prepared using a NEBNext fast DNA fragmentation and library preparation kit (New England Biolabs, Inc.) sequenced on an Illumina HiSeq 2500 platform (2 × 150 bp), and FastQC v0.11.9 (7) was used to verify the sequencing quality (https://www.bioinformatics.babraham.ac.uk/projects/fastqc).
A total of 6,289,711 reads and coverage of 282× were generated. The genome assembly was performed using Unicycler v0.4.8 (8), which generated 119 contigs. Contigs smaller than 1,000 bp were removed, and the remaining contigs were submitted to CONTIGuator v2.7.4 software (9) to assemble the scaffold. E. piscicida strain CZ12001 was used as a reference (GenBank accession number CP090962.1), resulting in an initial scaffold. The genome was compared with other genomes of the same species, and gaps were curated with recursive rounds of short reads mapped using the Qiagen CLC Genomics Workbench v.22.1 (https://digitalinsights.qiagen.com/). The complete genome was annotated by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) and Rapid Annotation using System Technology v2.0 (RAST) (10) submitted to the GenBank database. The average nucleotide identity (ANI) (11) and digital DNA-DNA hybridization (dDDH) (12) estimations were determined using the Type (Strain) Genome Server (http://ggdc.dsmz.de/distcalc2.php).
The BEP80 genome consists of one circular chromosome of 3,883,256 bp with a G+C content of 59.7% and no plasmid. The circularization of the genome was accomplished based on the site of origin, using Ori-Finder 3 v1.0.1 software (13) (http://tubic.tju.edu.cn/Ori-Finder3/public/index.php). The absence of plasmids was confirmed using PlasmidFinder (14) (https://cge.cbs.dtu.dk/services/PlasmidFinder/). RAST annotation predicted 3,806 genes: 3,684 coding DNA sequences (CDS), 25 rRNA genes, and 97 tRNA genes. E. piscicida strain BEP80 shares ANIs of 99.45% (dDDH, 96.3%) with E. piscicida CZ12001 (CP090962.1), 94.92% (dDDH, 59.4%) with E. anguillarum ET080813 (CP006664.1), 92.45% (dDDH, 48.2%) with E. ictaluri MS-17-156 (CP028813.1), 83.54% (dDDH, 24.7%) with E. hoshinae FDAARGOS 940 (CP065626.1), and 83.93% (dDDH, 25.4%) with E. tarda Kc-Pc-HB1 (CP023706.1).
Data availability.
The complete genome sequence of Edwardsiella piscicida BEP80 has been deposited in GenBank under accession number CP101126.1, BioProject identifier PRJNA856875, BioSample identifier SAMN29594514, and Sequence Read Archive (SRA) identifier SRR21788775.
ACKNOWLEDGMENTS
We are grateful to the Postgraduate Program in Animal Science at the State University of Londrina (UEL, Brazil) for the financial support provided to N.A.F. by the Coordination for the Improvement of Higher Education Personnel (CAPES, Brazil) and to J.V.G.T. by UEL. We are also grateful to the Department of Molecular Biology of Livestock at the University of Göttingen (UG, Germany) for funding the genome sequencing and to the collaborators at the Omic Science Network (RECOM).
Contributor Information
Ulisses de P. Pereira, Email: upaduapereira@uel.br.
Frank J. Stewart, Montana State University
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Associated Data
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Data Availability Statement
The complete genome sequence of Edwardsiella piscicida BEP80 has been deposited in GenBank under accession number CP101126.1, BioProject identifier PRJNA856875, BioSample identifier SAMN29594514, and Sequence Read Archive (SRA) identifier SRR21788775.