Draft Genome Sequence of Epilithonimonas sp. FP211-J200, Isolated from an Outbreak Episode on a Rainbow Trout (Oncorhynchus mykiss) Farm.

Here, we report the draft genome sequence of Epilithonimonas sp. FP211-J200, isolated from rainbow trout head kidney cells. The size of the genome is 4,110,772 bp, with a G+C content of 37.1%. The Epilithonimonas sp. FP211-J200 genome has genes related to tetracycline and β-lactam resistance. This is the first reported Epilithonimonas species genome isolated from a fish host.

GENOME ANNOUNCEMENT

The genus Epilithonimonas (1) belongs to the phylum Bacteriodetes, family Flavobacteriaceae, which also includes the Flavobacterium and Chryseobacterium genera. Currently, five species of Epilithonimonas have been described (2), including E. tenax (1), E. ginsengisoli (3), E. lactis (4), E. xixisoli (5), and E. psychrotolerans (6). Epilithonimonas sp. strains have been isolated from different environments, including soil (3, 6), freshwater (1, 5), and milk (4). Members of the genus Epilithonimonas are chemoorganotrophs and most likely play a role in natural carbon cycles in low-salinity ecosystems, such as soil and freshwater (7). However, associations of Epilithonimonas spp. with animals like fish are unknown. Here, we report the draft genome sequence of Epilithonimonas sp. FP211-J200, a yellow-pigmented strain isolated from rainbow trout (Oncorhynchus mykiss) head kidney cells during a flavobacteriosis outbreak in a freshwater aquaculture facility at X Region, Chile.

Epilithonimonas sp. FP211-J200 was routinely grown in tryptone-yeast extract-salt (TYES) (8) with aeration (180 rpm) at 28°C. The genomic DNA was extracted according to Wilson (9) and purified using silica (10). Sequencing was performed using the next-generation sequencer (NGS) Illumina MiSeq platform (Universidad Mayor, Center for Genomics and Bioinformatics, Huechuraba, Chile) and paired-end libraries. Low-quality sequences were examined by FastQC version 0.10.1 (11). The sequences were trimmed and assembled using the CLC Genomics Workbench 9.0.1 (Qiagen) de novo tool, resulting in 83 contigs over 1 kb, with an N50 value of 98,567 bp. The total length of the draft genome of the Epilithonimonas sp. FP211-J200 was 4,110,772 bp, with a G+C content of 37.01%.

The assembled sequences were annotated by the National Center for Biotechnology Information (NCBI) Prokaryotic Genome Annotation Pipeline (PGAP [https://www.ncbi.nlm.nih.gov/genome/annotation_prok/]). The tRNA genes were detected by tRNAscan-SE version 1.3 (12) and the rRNA with RNAmmer (13). A total of 3,882 coding sequences (CDSs), 88 pseudogenes, 1 complete rRNA operon (5S-16S-23S), 41 tRNAs, and 2 noncoding RNAs (ncRNAs) were predicted by the pipeline.

Genes encoding proteins for resistance to antibiotics were identified using the Comprehensive Antibiotic Resistance Database (CARD) (14). Epilithonimonas sp. FP211-J200 presented genes potentially responsible for antibiotic resistance. We found three types of multidrug efflux transporters, including acrB, mexD, and adeB (15). Also, we found the flavin-dependent monooxygenase tetX gene responsible for resistance to all clinical relevant tetracyclines (16). Additionally, we found the β-lactamase TLA-2, also present in Chryseobacterium gleum (17), and the metallo-β-lactamase GOB-1, also present in Chryseobacterium meningoseptica (18). Also, we identified the crfA gene, which is related to florfenicol resistance.

We identified several genes related to iron acquisition and virulence, including hemolysin, hemolysin III, ferritin, ferric siderophore ABC transporter substrate-binding protein, ferredoxin, hemin receptor, and the Fur transcriptional regulator, suggesting that Epilithonimonas sp. FP211-J200 might have pathogenesis potential.

Phylogenetic reconstruction using 16S rRNA showed that the Epilithonimonas sp. FP211-J200 strain is closely related to the genus Chryseobacterium. In silico DNA-DNA hybridization (http://cbrc.kaust.edu.sa/dna_hybridization/index.html) showed that strain FP211-J200 is different from other Epilithonimonas spp. and Chryseobacterium spp. The strain most closely related to FP211-J200 was E. ginsengisoli. This is the first reported Epilithonimonas sp. genome isolated from a fish host.

Accession number(s).

The whole-genome shotgun project (BioProject PRJNA310285) has been deposited at DDBJ/EMBL/GenBank under the accession number LSHB00000000. The version described in this paper is version LSHB01000000.