Draft Whole-Genome Sequences of 18 Flavobacterium spp.

We report here the draft whole-genome sequences for 18 Flavobacterium species type strains that have historically been associated with fish gill disease.

GENOME ANNOUNCEMENT

Bacterial gill disease (BGD) is an important disease of cultured fish worldwide. Flavobacterium branchiophilum has been identified as the causative agent of BGD (1); however, other bacteria are reported to be involved in Flavobacteriaceae-associated and nontypical bacterial gill disease (2–4). We sequenced the species in this report based on their prior association with gill disease (3) in order to facilitate investigation of the etiologic agents of bacterial gill disease in the United States.

Flavobacterium species type strains were obtained from the following repositories: the American Type Culture Collection, USA (ATCC); the Culture Collection, University of Göteborg, Sweden (CCUG); and the Leibniz Institute–German Collection of Microorganisms and Cell Cultures (DSM). DNA was extracted from Flavobacterium spp. using an UltraClean microbial DNA isolation kit (Mo Bio Laboratories, Inc., Carlsbad, CA, USA) according to the manufacturer’s recommendations. Whole-genome sequencing (WGS) was performed using V3 chemistry with paired-end 2 × 300-bp reads on the MiSeq platform (Illumina, San Diego, CA, USA). Sequencing libraries were prepared according to the Illumina Nextera XT sample preparation guide.

WGS data were imported into CLC Genomics Workbench, and a de novo assembly was performed using default CLC Genomics Workbench version 8.0 assembly parameters (Qiagen, Valencia, CA, USA). Contigs of less than 300 bp were removed from analysis. The genomes were annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP version 4) (https://www.ncbi.nlm.nih.gov/genome/annotation_prok). Assemblies had between 20 and 241 contigs, between 2,638,051 and 6,041,815 bases, between 30.5% and 35.7% G+C contents, and between 2,438 and 5,164 total coding sequences (CDSs). WGS assembly data are shown in Table 1. The publicly available resistance gene database ResFinder was used for identification of antimicrobial resistance genes, using a 90% sequence identity and 60% length minimum to identify resistance genes (5). Only 2 of the 18 Flavobacterium spp. carried acquired resistance genes. The tetracycline resistance gene (tetX; 91% sequence identity) was identified in F. plurextorum (WGS0045). F. johnsoniae (CVM 41394) was found to carry blaJOHN, a class B beta-lactamase gene. None of the remaining Flavobacterium spp. were positive for any acquired resistance genes.

TABLE 1 

Summary of analyses of type strains of Flavobacterium spp. associated with fish disease

Sample no.	Strain	Species	No. of contigs	Assembly size (bp)	G+C content (%)	Coverage (×)	No. of genes (total)	No. of CDSs (total)	No. of CDSs (coding)	No. of genes (RNA)	WGS accession no.
WGS0040	ATCC 49418	F. psychrophilum	83	2,638,051	32.44	106	2,393	2,348	2,301	45	MUHE00000000
WGS0041	ATCC 23463	F. columnare	193	3,116,347	31.36	71	2,838	2,776	2,702	62	PCMX00000000
CVM 41392	ATCC 11947	F. aquatile	20	3,490,044	32.23	104	3,204	3,161	3,140	43	MUGQ00000000
WGS0042	ATCC 35035	F. branchiophilum	241	3,580,395	32.75	23	3,236	3,190	3,130	46	MUGT00000000
CVM 43445	CCUG 59446	F. oncorhynchi	54	4,732,158	33.28	50	4,063	4,006	3,970	57	MUHA00000000
WGS0044	CCUG 60100	F. tructae	101	4,952,969	35.68	56	4,133	4,070	4,046	63	MUHH00000000
WGS0045	CCUG 60112	F. plurextorum	65	5,062,246	33.1	55	4,297	4,239	4,213	58	MUHD00000000
CVM 43415	DSM 18292	F. hercynium	101	5,260,169	33.78	65	4,540	4,484	4,450	56	MUGW00000000
CVM 43443	ATCC 51468	F. hibernum	65	5,305,016	33.15	63	4,530	4,470	4,432	60	MUGX00000000
CVM 43414	DSM 15937	F. frigidimaris	72	5,423,080	33.95	69	4,607	4,548	4,497	59	MUGV00000000
CVM 43441	ATCC BAA-2541	F. spartansii	60	5,354,799	35.67	74	4,464	4,400	4,358	64	MUHG00000000
CVM 43417	DSM 21791	F. reichenbachii	51	5,579,055	33.61	71	4,848	4,784	4,744	64	MUHF00000000
CVM 43442	ATCC 19366	F. pectinovorum	51	5,607,986	33.56	64	4,697	4,644	4,600	53	MUHB00000000
CVM 43416	DSM 18293	F. aquidurense	88	5,724,426	34.69	58	4,949	4,893	4,834	56	MUGR00000000
CVM 41393	ATCC 29551	F. hydatis	73	5,903,360	32.68	68	5,026	4,955	4,921	71	MUGY00000000
CVM 43413	DSM 24704	F. araucananum	177	5,934,833	34.39	57	4,968	4,910	4,826	58	MUGS00000000
WGS0043	CCUG 60099	F. piscis	105	5,880,206	34.05	32	5,020	4,961	4,910	59	MUHC00000000
CVM 41394	ATCC 17061	F. johnsoniae	60	6,041,815	34.04	62	5,220	5,164	5,107	56	MUGZ00000000

Accession number(s).

These draft genome sequences have been deposited in GenBank under the accession numbers indicated in Table 1.