ENVIRONMENTAL MICROBIOLOGY Plasmid-Mediated Quinolone Resistance (PMQR) Genes and Class 1 Integrons in Quinolone-Resistant Marine Bacteria and Clinical Isolates of Escherichia coli from an Aquacultural Area Alexandra Tomova 1,2 & Larisa Ivanova 1 & Alejandro H. Buschmann 3 & Henry P. Godfrey 4 & Felipe C. Cabello 1 Received: 25 January 2017 /Accepted: 12 June 2017 # Springer Science+Business Media, LLC 2017 Abstract Antimicrobial usage in aquaculture selects for antimicrobial-resistant microorganisms in the marine environ- ment. The relevance of this selection to terrestrial animal and human health is unclear. Quinolone-resistance genes qnrA, qnrB, and qnrS were chromosomally located in four randomly chosen quinolone-resistant marine bacteria isolated from an aquacultural area with heavy quinolone usage. In quinolone- resistant uropathogenic clinical isolates of Escherichia coli from a coastal area bordering the same aquacultural region, qnrA was chromosomally located in two E. coli isolates, while qnrB and qnrS were located in small molecular weight plas- mids in two other E. coli isolates. Three quinolone-resistant marine bacteria and three quinolone-resistant E. coli contained class 1 integrons but without physical association with PMQR genes. In both marine bacteria and uropathogenic E. coli, class 1 integrons had similar co-linear structures, identical gene cassettes, and similarities in their flanking regions. In a Marinobacter sp. marine isolate and in one E. coli clinical isolate, sequences immediately upstream of the qnrS gene were homologous to comparable sequences of numerous plasmid-located qnrS genes while downstream sequences were different. The observed commonality of quinolone resis- tance genes and integrons suggests that aquacultural use of antimicrobials might facilitate horizontal gene transfer be- tween bacteria in diverse ecological locations. Keywords Quinolone resistance . Aquaculture . Class 1 integrons . PMQR genes . Marine bacteria . Uropathogenic clinical isolates Introduction There is increasing evidence for bidirectional flow of antimi- crobial resistance genes (ARGs) between free-living environ- mental bacteria and human/animal pathogens through hori- zontal gene transfer (HGT) [1–4]. This flow is facilitated by the commonality of mobile genetic elements (plasmids, integrons, transposons, integrative conjugative elements) that carry and disseminate ARG between bacteria occupying di- verse ecological niches [3–6]. HGT can be stimulated by an- timicrobials in the environment resulting from their use in terrestrial animal husbandry and in aquaculture [7, 8]. These antimicrobials can select for multi-resistant environmental bacteria that become donors of ARG and mobile genetic ele- ments [2, 3, 8–11]. They can also stimulate mutagenesis, integron recombination, and HGT through mobilization of genetic elements carrying ARG in terrestrial and aquatic en- vironments contaminated with animal and human commen- sals and pathogens [2, 3, 9, 10]. Moreover, they can promote passage of ARG by HGT to commensals and pathogens in the human intestine by selecting resistant bacteria contaminating food staples [1, 12–16]. Plasmid-mediated quinolone resistance (PMQR) genes represent an important challenge to the effectiveness of * Felipe C. Cabello cabello@nymc.edu 1 Department of Microbiology and Immunology, New York Medical College, Valhalla, NY, USA 2 Institute of Physiology, Faculty of Medicine, Comenius University in Bratislava, Bratislava, Slovakia 3 Centro i~mar and CeBiB, Universidad de Los Lagos, Puerto Montt, Chile 4 Department of Pathology, New York Medical College, Valhalla, NY, USA Microb Ecol DOI 10.1007/s00248-017-1016-9