Species composition and antimicrobial resistance genes of <i>Enterococcus</i> spp., isolated from integrated and traditional fish farms in Thailand

<jats:title>Summary</jats:title><jats:p>Integrated fish farming uses the manure from animal husbandry as fertilisers in the fish ponds. A total of 410 enterococcal isolates, from integrated and traditional fish farms in Thailand, were collected to assess whether the input of manure from chickens receiving feed containing growth promoters and antimicrobial treatments influenced the species composition and the bacterial antimicrobial resistance in the fish pond environment. <jats:italic>Enterococcus faecium</jats:italic> and <jats:italic>E. faecalis</jats:italic> were the predominate species isolated from the integrated farms, whereas <jats:italic>E. casseliflavus</jats:italic> and <jats:italic>E. mundtii</jats:italic> isolates were most prevalent in traditional farms. <jats:italic>Enterococcus faecalis</jats:italic> and <jats:italic>E. faecium</jats:italic> demonstrated the highest prevalence of resistance, whereas <jats:italic>E. mundtii</jats:italic> isolates were susceptible to all antimicrobials tested. All the enterococci species isolated from the integrated farms, generally demonstrated higher resistance phenotypes to the tested antimicrobials compared with the same species from traditional farms. The <jats:italic>erm</jats:italic>(B) and <jats:italic>tet</jats:italic>(M) genes, associated with resistance to erythromycin and tetracycline, respectively, were found in 87% of the erythromycin‐resistant and 95% of the oxytetracycline‐resistant enterococci isolates respectively. These results suggest that the species composition and antimicrobial resistance of enterococci in tropical aquatic environments are influenced by faecal and antimicrobial pollution.</jats:p>