Draft genome for Flavobacterium psychrophilum isolates from diseased coho salmon (Oncorhynchus kisutch) in Chile

TL;DR

This paper presents the draft genomes of six bacteria isolated from sick coho salmon in Chile, offering new insights into this fish pathogen.

Contribution

The study provides the first genomic insights into Flavobacterium psychrophilum from coho salmon in Chile.

Findings

Draft genome sequences of six Flavobacterium psychrophilum isolates were generated.

The isolates were recovered from diseased coho salmon in Chile.

This is the first genomic study of this pathogen in this host and region.

Abstract

We present the draft genome sequences of six Flavobacterium psychrophilum isolates recovered from diseased coho salmon (Oncorhynchus kisutch) cultured by two farms in Chile. This study provides the first detailed insights into the genomic characteristics of this fish pathogen recovered from a host with limited information and cultured in Chile.

Tables

TABLE 1. Listing of Flavobacterium psychrophilum isolate genomes released to NCBI

Strain/library	Sampling tissue	SRA	Assembly	WGS	Total lengtha	Genome coverage	No. readsb	Contigsc	%GCb	N50 kbb	Genesa	Protein-codinga	tRNAa
Flp-133/S74	Kidney	SRR28673983	GCF_038405635.1	JBCARS01	2,694,494	100×	1,408,614	50	32.5	119.3	2,427	2,363	41
Flp-134/S78	External lesions	SRR28673979	GCF_038405535.1	JBCARW01	2,736,257	100×	1,693,310	117	32.5	55.3	2,472	2,408	39
Flp-138/S75	Kidney	SRR28673982	GCF_038405615.1	JBCART01	2,733,480	100×	1,466,238	119	32.5	55.3	2,471	2,407	39
Flp-142/S76	Kidney	SRR28673981	GCF_038405595.1	JBCARU01	2,694,456	100×	1,520,966	54	32.5	119.4	2,430	2,367	40
Flp-143/S77	Spleen	SRR28673980	GCF_038405575.1	JBCARV01	2,696,331	100×	2,048,008	52	32.5	119.3	2,431	2,369	39
Flp-146/S215	Spine	SRR28673984	GCF_038405655.1	JBCARR01	2,694,356	100×	4,004,454	61	32.5	98	2,433	2,371	39

Full text

ANNOUNCEMENT

Flavobacterium psychrophilum, a Gram-negative, filamentous, psychotropic bacterium, causes bacterial cold-water disease and rainbow trout fry syndrome in salmonids worldwide (1). Genetic studies suggest some specific genotypes for certain fish species, especially coho salmon (Oncorhynchus kisutch) (2, 3). To date, analyzed isolates from this fish species are limited, and none are from Chile. Herein, we present the draft genome sequences of six isolates recovered from diseased coho salmon cultured by two farms in Los Lagos Region (Chile).

Samples for bacterial isolation were taken from external lesions, the spine, the kidney, and the spleen of each coho salmon and streaked onto the tryptone yeast extract salts (TYES) medium (4). Colonies were recovered after incubation at 15°C for 7 days and streaked onto fresh TYES plates to isolate pure cultures. Six isolates were confirmed as F. psychrophilum via PCR analysis, following the protocol by Urdaci et al. (5), with genomic DNA extraction using the InstaGene matrix (Bio-Rad). All F. psychrophilum cultured underwent no more than two rounds of culturing and were stored at −80°C in CryoBank vials (Mast Diagnostica, Reinfield, Germany).

For genomic sequencing, three pure colonies of each F. psychrophilum were subjected to DNA extraction and were sent for genome sequencing to SeqCenter (Pennsylvania). Libraries were prepared using the Illumina DNA Prep Kit and IDT 10 bp UDI indices and sequenced on Illumina NextSeq 2000, producing 2 × 151-bp reads. Before de novo genome assembly, raw Illumina sequence data were quality-checked with FastQC v.0.12.1 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Next-generation sequencing reads were pre-processed with Geneious Prime v.2024.0.7 (www.geneious.com) with the following workflow: (i) pairing reads using the “set paired reads” function (insert size = 350  bp); (ii) trimming poor-quality bases from read ends using the BBDuk Trimmer plugin version 38.84 (6) (reads of <20 bp, and those with a quality score <20 were removed), with paired-read overlaps trimmed to ensure complete adapter removal; (iii) normalizing coverage by down-sampling reads in high-depth genome areas with the “error correct” and “normalize reads” functions using BBNorm version 38.84 (6); and (iv) removing duplicate reads using the Dedupe plugin. For the assembling process, Spades v3.13.0 was used (7), evaluating the quality and completeness of the final assemblies using CheckM v1.2.2 (8), and quality was checked by QUAST v.5.2.0 (9). The assembled genomes were then annotated using the RAST server v.2.0 (10). Default parameters were used for all software. Statistics of assembled genomes are shown in Table 1.

Genome assemblies ranged from 50 to 119 contigs and 2,694,356 to 2,736,257 bp with a G+C content of 32.5% (Table 1). To trace any plasmid, the filtered reads were mapped using SOAP (https://ccb-microbe.cs.uni-saarland.de/plsdb/) to the bacterial plasmid database (11). Only F. psychrophilum Flp-134 presented a 2,191-bp contig matching a plasmid (JBCARW000000000.1).

The in silico genome analysis discovered genes associated with secretion systems, including the type I and type IX secretion systems (T1SS and T9SS, respectively), as detected by the TXSScan:MascSyFinder-based detection of protein secretion systems (12). Genes associated with antibiotic resistance were not found in the Resistance Gene Identifier incorporated with the Comprehensive Antibiotic Resistance Database (https://card.mcmaster.ca/analyze/rgi). The present study provides initial comprehensive insights into the genomic characteristics of F. psychrophilum isolates from coho salmon farmed in Chile, with further details on virulence potential slated for future publication.