Antimicrobial resistance and antimicrobial resistance genes in marine bacteria from salmon aquaculture and non-aquaculture sites Syed Q. A. Shah, 1 Felipe C. Cabello, 2 Trine M. L’Abée-Lund, 1 Alexandra Tomova, 2 Henry P. Godfrey, 3 Alejandro H. Buschmann 4 and Henning Sørum 1 * 1 Norwegian University of Life Sciences, Ullevålsvein 72, Oslo, Norway. Departments of 2 Microbiology and Immunology and 3 Pathology, New York Medical College, Valhalla, NY 10595, USA. 4 Centro i-mar, Universidad de Los Lagos, Puerto Montt, Chile. Summary Antimicrobial resistance (AR) detected by disc diffu- sion and antimicrobial resistance genes detected by DNA hybridization and polymerase chain reaction with amplicon sequencing were studied in 124 marine bacterial isolates from a Chilean salmon aquaculture site and 76 from a site without aquaculture 8 km distant. Resistance to one or more antimicrobials was present in 81% of the isolates regardless of site. Resistance to tetracycline was most commonly encoded by tetA and tetG; to trimethoprim, by dfrA1, dfrA5 and dfrA12; to sulfamethizole, by sul1 and sul2; to amoxicillin, by bla TEM; and to streptomycin, by strA-strB. Integron integrase intl1 was detected in 14 sul1-positive isolates, associated with aad9 gene cas- settes in two from the aquaculture site. intl2 Integrase was only detected in three dfrA1-positive isolates from the aquaculture site and was not associated with gene cassettes in any. Of nine isolates tested for con- jugation, two from the aquaculture site transferred AR determinants to Escherichia coli. High levels of AR in marine sediments from aquaculture and non- aquaculture sites suggest that dispersion of the large amounts of antimicrobials used in Chilean salmon aquaculture has created selective pressure in areas of the marine environment far removed from the initial site of use of these agents. Introduction Chile is the second largest producer of farmed salmon and trout in the world after Norway (FAO, 2011). Infections by bacteria, parasites, fungi and viruses are a frequent cause of morbidity and mortality in intensive salmon aqua- culture in Chile, with concomitant decreases in production and income (Asche et al., 2010; Cabello et al., 2013). Efforts to increase productivity by high-stocking densities favour the emergence of infections and facilitate the free dissemination of epizootic pathogens (Asche et al., 2010; Ibieta et al., 2011). While infection control in salmon aqua- culture by vaccination and improved hygienic conditions provides the best long-term approach (Markestad and Grave, 1997; Berg et al., 2006; Bravo and Midtlyng, 2007; Midtlyng et al., 2011), antimicrobials are the current primary tools for prevention and treatment of bacterial infections (Grave et al., 1999; Sørum, 2006). In Chile, a lack of use of the few available vaccines, the continuous high prevalence of bacterial infections such as salmon rickettsial syndrome caused by Piscirickettsia salmonis, the presence of antimicrobial-resistant pathogens and the emergence of new pathogens has stimulated the use of large quantities of antimicrobials (Asche et al., 2010; Ibieta et al., 2011; Millanao et al., 2011; Cabello et al., 2013). Medicated feed and rarely, bath immersion, are com- monly used in salmon farming to prevent bacterial infec- tions (Sørum, 2006; Smith et al., 2009b). Some of the feed is not ingested, and its antimicrobial activity, along with that of metabolized and unmetabolized antimicrobials in fish urine and faeces, ends up in the surrounding envi- ronment (Cabello et al., 2013). Passage of antimicrobials into the environment can select for resistant bacteria and increase horizontal gene transfer (HGT) and genetic recombination of antimicrobial resistance genes (ARG). There appears to be an unimpeded flow of ARG between the resistome of environmental, animal and human bac- teria, so that increased antimicrobial resistance (AR) in the aquatic environment has the potential to introduce AR determinants into the resistomes of piscine and human Received 1 October, 2013; revised 29 January, 2014; accepted 31 January, 2014. *For correspondence. E-mail henning.sorum@ nmbu.no; Tel. +47 22964770; Fax +47 22964818. Environmental Microbiology (2014) 16(5), 1310–1320 doi:10.1111/1462-2920.12421 © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd