Genetic Characterization of the Tetracycline-Resistance Gene <i>tet</i>(X) Carried by Two <i>Epilithonimonas</i> Strains Isolated from Farmed Diseased Rainbow Trout, <i>Oncorhynchus mykiss</i> in Chile

• Main Authors: Christopher Concha, Claudio D. Miranda, Javier Santander, Marilyn C. Roberts
• Format: Article
• Language: English
• Published: MDPI AG 2021-08-01
• Series: Antibiotics
• Subjects: <i>tet</i>(X); <i>Epilithonimonas</i>; salmon farming; fish pathogen; tetracycline resistance; aquaculture
• Online Access: https://www.mdpi.com/2079-6382/10/9/1051

The main objective of this study was to characterize the <i>tet</i>(X) genes, which encode a monooxygenase that catalyzes the degradation of tetracycline antibiotics, carried by the resistant strains FP105 and FP233-J200, using whole-genome sequencing analysis. The isolates were recovered from fin lesion and kidney samples of diseased rainbow trout <i>Oncorhynchus mykiss</i>, during two Flavobacteriosis outbreaks occurring in freshwater farms located in Southern Chile. The strains were identified as <i>Epilithonimonas</i> spp. by using biochemical tests and by genome comparison analysis using the PATRIC bioinformatics platform and exhibited a minimum inhibitory concentration (MIC) of oxytetracycline of 128 µg/mL. The <i>tet</i>(X) genes were located on small contigs of the FP105 and FP233-J200 genomes. The sequences obtained for the <i>tet</i>(X) genes and their genetic environment were compared with the genomes available in the GenBank database of strains of the <i>Chryseobacterium</i> clade belonging to the <i>Flavobacterium</i> family, isolated from fish and carrying the <i>tet</i>(X) gene. The Tet(X) proteins synthesized by the Chilean <i>Epilithonimonas</i> strains showed a high amino acid similarity (range from 84% to 100%), with the available sequences found in strains belonging to the genus <i>Chryseobacterium</i> and <i>Flavobacterium</i> isolated from fish. An identical neighborhood of <i>tet</i>(X) genes from both Chilean strains was observed. The genetic environment of <i>tet</i>(X) observed in the two strains of <i>Epilithonimonas</i> studied was characterized by the upstream location of a sequence encoding a hypothetical protein and a downstream located alpha/beta hydrolase-encoding gene, similar to the observed in some of the <i>tet</i>(X) genes carried by <i>Chryseobacterium</i> and <i>Flavobacterium</i> strains isolated from fish, but the produced proteins exhibited a low amino acid identity (25–27%) when compared to these synthesized by the Chilean strains. This study reports for the first time the carriage of the <i>tet</i>(X) gene by the <i>Epilithonimonas</i> genus and their detection in fish pathogenic bacteria isolated from farmed salmonids in Chile, thus limiting the use of therapies based on oxytetracycline, the antimicrobial most widely used in Chilean freshwater salmonid farming. This results suggest that pathogenic strains of the <i>Chryseobacterium</i> clade occurring in Chilean salmonid farms may serve as important reservoirs of <i>tet</i>(X) genes.