Genome analysis and antimicrobial resistance characteristics of Chryseobacterium aquaticum isolated from farmed salmonids

Abstract

Abstract Fish diseases caused by bacterial genera belonging to the family Flavobacteriaceae, especially Tenacibaculum, Flavobacterium, and Chryseobacterium, are responsible for losses in wild and farmed fish around the world. In the last decade, the genus Chryseobacterium has rapidly grown in parallel with numerous novel Chryseobacterium species described from systemic infections of fish. Members of the family Flavobacteriaceae, isolated from fish, the environment, and clinical samples, have been reported to show low susceptibility to a broad range of antimicrobials. In this study, seventy C. aquaticum strains were isolated from diseased salmonids in Turkey. The phylogenetic analysis of all C. aquaticum strains, together with the reference strains in GenBank, which were obtained from different sources, including fish, plants, soil, water, and other animals, was performed by 16S rRNA gene sequence analysis. The antimicrobial susceptibility of each C. aquaticum strain was determined by a minimum inhibitory concentration (MIC) test. The isolate with the highest level of antimicrobial resistance, strain C-174, underwent a more detailed whole-genome sequence analysis for virulence and antimicrobial resistance genes (AMR) genes, genome size, and guanine-cytosine (GC) content. Phylogenetically, the 70 strains isolated from Turkey were assigned to three genogroups. Strains previously recovered from the rainbow trout, brown trout, and Siberian sturgeon were genetically very close to our strains. Most of the strains isolated in this study grew even in the presence of high concentrations of the tested antimicrobials, excluding enrofloxacin. Strain C-174 carried 74 putative functional genes encoding AMR and virulence. The number of putative AMR genes detected in the genome of strain C-174 was 46. The regulatory mechanisms of these genes involve antibiotic efflux (13), antibiotic target alteration (17), antibiotic inactivation (7), antibiotic target replacement (3), and antibiotic target protection (6). AMR genes confer resistance to multiple antibiotic groups, including among others, macrolides, fluoroquinolones, beta-lactams, tetracyclines, phenicols, sulphonamides, and diaminopyrimidines. We concluded that antimicrobial resistance could be of intrinsic nature. Furthermore, we detected three putative virulence genes in the genome of strain C-174 that have not been reported for C. aquaticum before. The results of this study demonstrated a strong correlation between these genes in the genome of C-174 and mortality in the rainbow trout.