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International trade with ornamental fish is gradually recognized as an important source of a wide range of different antibiotic resistant bacteria. In this study we therefore characterized the prevalence of selected antibiotic resistance genes in the microbiota found in the carriage water of ornamental fish originating from 3 different continents. Real-time PCR quantification showed that the  sul1  gene was present in 11 out of 100 bacteria.  tet(A)  was present in 6 out of 100 bacteria and  strA ,  tet(G) ,  sul2  and  aadA  were present in 1–2 copies per 100 bacteria. Class I integrons were quite common in carriage water microbiota, however, pyrosequencing showed that only 12 different antibiotic gene cassettes were present in class I integrons. The microbiota characterized by pyrosequencing of the V3/V4 variable region of 16S rRNA genes consisted of  Proteobacteria  (48%),  Bacteroidetes  (29.5%),  Firmicutes  (17.8%),  Actinobacteria  (2.1%) and  Fusobacteria  (1.6%). Correlation analysis between antibiotic resistance gene prevalence and microbiota composition verified by bacterial culture showed that major reservoirs of  sul1 sul2, tet(A) ,  tet(B) tet(G) ,  cat ,  cml ,  bla ,  strA ,  aacA ,  aph  and  aadA  could be found among  Alpha-, Beta-  and  Gammaproteobacteria  with representatives of  Enterobacteriaceae, Pseudomonadaceae, Rhizobiaceae  and  Comamonadaceae  being those most positively associated with the tested antibiotic resistance genes.

Characterization of Microbiota Composition and Presence of Selected Antibiotic Resistance Genes in Carriage Water of Ornamental Fish