We recently reported a simple new in situ diffusion assay, developed as a kit, to visualize DNA fragmentation in single bacterial cells. Use of this assay in a collection of 95 genetically unrelated Escherichia coli clinical strains resulted in correct identification of all of the isolates as resistant or susceptible to ciprofloxacin, consistent with the MIC results. This relevant information is obtained in 80 min.Fluoroquinolones are among the most frequently prescribed antimicrobial agents worldwide, with ciprofloxacin (CIP) being one of the most widely used. The activity of these agents is mediated by the production of DNA fragmentation through trapping of DNA gyrase and/or topoisomerase IV on bacterial DNA (6). Fluoroquinolone MICs are mainly increased by mutations in the genes encoding the protein targets DNA gyrase (gyrA and gyrB) and topoisomerase IV (parC and parE) but also by increasing the levels of specific efflux pumps, such as AcrAB-TolC, or by the presence of plasmid-mediated mechanisms, such as QnrA, QnrB, QnR, or the recently described aminoglycoside resistance gene aac(6Ј)- .Escherichia coli causes almost 50% of community-acquired urinary infections. Treatment with fluoroquinolones is recommended in such cases, especially in areas with predominant resistance to trimethoprim-sulfamethoxazole. However, over 22% of clinical isolates of E. coli may be resistant to CIP, and this tendency appears to be increasing (5,14). Resistance to CIP in clinical isolates of E. coli obtained from blood cultures has reached 19% in Spain. In a recent study, 43% of E. coli isolates from the normal intestinal microflora of humans were found to be resistant to quinolones (2).Given the alarming progressive increase in antibiotic resistance worldwide, it is of great importance to identify the resistant bacteria as soon as possible to avoid treatment failure and the spread of resistant microorganisms through misuse of antibiotics. Our research group recently developed a diffusionbased assay, developed as a kit, which enables straightforward and rapid (45 min) discrimination of bacteria with fragmented DNA. The kit can be used to evaluate DNA damage induced by antimicrobial agents. Since the activity of quinolones such as CIP depends on the production of fragmentation of bacterial DNA, we investigated the potential usefulness of the kit as a simple, fast procedure for detecting resistance to CIP in clinical situations by processing a collection of clinical strains of E. coli isolated from patients attending the Juan Canalejo Hospital.Bacterial strains, antibiotic susceptibility testing, and growth conditions. The procedure for determining chromosomal DNA fragmentation in situ was first assayed for control E. coli strains harboring known mechanisms of quinolone resistance as well as for 95 E. coli clinical strains isolated from outpatients (only 1 strain per patient was selected for further studies) attending the hospital in 2006 and 2007 and displaying different degrees of susceptibility to CIP. The E. coli isolates were r...