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Background  Antibiotic resistance has necessitated fluoroquinolone use but little is known about the selective forces and resistance trajectory in malaria-endemic settings, where selection from the antimalarial chloroquine for fluoroquinolone-resistant bacteria has been proposed.    Methods  Antimicrobial resistance was studied in fecal  Escherichia coli  isolates in a Nigerian community. Quinolone-resistance determining regions of  gyrA  and  parC  were sequenced in nalidixic acid resistant strains and horizontally-transmitted quinolone-resistance genes were sought by PCR. Antimicrobial prescription practices were compared with antimicrobial resistance rates over a period spanning three decades.    Results  Before 2005, quinolone resistance was limited to low-level nalixidic acid resistance in fewer than 4% of  E. coli  isolates. In 2005, the proportion of isolates demonstrating low-level quinolone resistance due to elevated efflux increased and high-level quinolone resistance and resistance to the fluoroquinolones appeared. Fluoroquinolone resistance was attributable to single nucleotide polymorphisms in quinolone target genes  gyrA  and/or  parC . By 2009, 35 (34.5%) of isolates were quinolone non-susceptible with nine carrying  gyrA  and  parC  SNPs and six bearing identical  qnrS1  alleles. The antimalarial chloroquine was heavily used throughout the entire period but  E. coli  with quinolone-specific resistance mechanisms were only detected in the final half decade, immediately following the introduction of the fluoroquinolone antibacterial ciprofloxacin.    Conclusions  Fluoroquinolones, and not chloroquine, appear to be the selective force for fluoroquinolone-resistant fecal  E. coli  in this setting. Rapid evolution to resistance following fluoroquinolone introduction points the need to implement resistant containment strategies when new antibacterials are introduced into resource-poor settings with high infectious disease burdens.

Rapid evolution of fluoroquinolone-resistant Escherichia coli in Nigeria is temporally associated with fluoroquinolone use