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Sixty extended-spectrum β-lactamase (ESBL)-producing  Escherichia coli  isolated from rivers and lakes in Switzerland were screened for individual strains additionally exhibiting a reduced quinolone susceptibility phenotype. Totally, 42 such isolates were found and further characterized for their molecular (fluoro)quinolone resistance mechanisms. PCR and sequence analysis were performed to identify chromosomal mutations in the quinolone resistance-determining regions (QRDR) of  gyrA ,  gyrB ,  parC  and  parE  and to describe the occurrence of the following plasmid-mediated quinolone resistance genes:  qepA ,  aac-6′-Ib-cr ,  qnrA ,  qnrB ,  qnrC ,  qnrD  and  qnrS . The contribution of efflux pumps to the resistance phenotype of selected strains was further determined by the broth microdilution method in the presence and absence of the efflux pump inhibitor phe-arg-β-naphthylamide (PAβN). Almost all strains, except two isolates, showed at least one mutation in the QRDR of  gyrA.  Ten strains showed only one mutation in  gyrA , whereas thirty isolates exhibited up to four mutations in the QRDR of  gyrA, parC  and/or  parE . No mutations were detected in  gyrB.  Most frequently the amino-acid substitution Ser83→Leu was detected in GyrA followed by Asp87→Asn in GyrA, Ser80→Ile in ParC, Glu84→Val in ParC and Ser458→Ala in ParE. Plasmid-mediated quinolone resistance mechanisms were found in twenty isolates bearing QnrS1 (4/20), AAC-6′-Ib-cr (15/20) and QepA (1/20) determinants, respectively. No  qnrA, qnrB, qnrC and qnrD  were found. In the presence of PAβN, the MICs of nalidixic acid were decreased 4- to 32-fold. (Fluoro) quinolone resistance is due to various mechanisms frequently associated with ESBL-production in  E. coli  from surface waters in Switzerland.

Quinolone Resistance Mechanisms among Extended-Spectrum Beta-Lactamase (ESBL) Producing Escherichia coli Isolated from Rivers and Lakes in Switzerland