Ciprofloxacin was introduced for treatment of patients with cholera in Bangladesh because of resistance to other agents, but its utility has been compromised by the decreasing ciprofloxacin susceptibility of Vibrio cholerae over time. We correlated levels of susceptibility and temporal patterns with the occurrence of mutation in gyrA, which encodes a subunit of DNA gyrase, followed by mutation in parC, which encodes a subunit of DNA topoisomerase IV. We found that ciprofloxacin activity was more recently further compromised in strains containing qnrVC3, which encodes a pentapeptide repeat protein of the Qnr subfamily, members of which protect topoisomerases from quinolone action. We show that qnrVC3 confers transferable low-level quinolone resistance and is present within a member of the SXT integrating conjugative element family found commonly on the chromosomes of multidrug-resistant strains of V. cholerae and on the chromosomes of Escherichia coli transconjugants constructed in the laboratory. Thus, progressive increases in quinolone resistance in V. cholerae are linked to cumulative mutations in quinolone targets and most recently to a qnr gene on a mobile multidrug resistance element, resulting in further challenges for the antimicrobial therapy of cholera.Cholera remains a major public health problem in many areas of the developing world. In addition to maintenance oral rehydration therapy, adjunctive antimicrobial therapy reduces the extent and duration of diarrhea, resulting in reduced fluid requirements and hospitalizations, reductions that are particularly important in resource-limited areas. Antimicrobial therapies have included tetracycline, azithromycin, and fluoroquinolones, such as ciprofloxacin, but the activity of fluoroquinolones has decreased in some areas, and this decreased activity has been associated with substantial reductions in the efficacy of ciprofloxacin relative to that of azithromycin (15,20). To evaluate the evolution of ciprofloxacin resistance in Vibrio cholerae, we studied isolates from Bangladesh available over a 6-year period in which poor clinical responses of cholera patients to ciprofloxacin were recognized. We determined the presence of resistance mutations in genes encoding the subunits of the quinolone target enzymes DNA gyrase (gyrA and gyrB) and DNA topoisomerase IV (parC and parE) and the presence of qnr and other acquired genes that confer additional resistance to quinolones (25). Some qnr gene products have been shown to protect gyrase and topoisomerase IV from quinolone action in enteric bacteria (26,27). qnr genes are usually located on mobile genetic elements, such as plasmids, that can transfer between strains but have been found on the chromosomes of some Vibrio spp. (5, 18). In V. cholerae, a qnr homolog, qnrVC1, has been described for isolates from Brazil (9) but has not been shown to confer transferable quinolone resistance or to be linked to incremental quinolone resistance and poor response to ciprofloxacin therapy of cholera. We show here that progressiv...