High stability of fluoroquinolone-resistant Escherichia coli in the gut during and after ciprofloxacin treatment

Background Fluoroquinolones (FQ) have demonstrated mutagenic properties in E. coli, by SOS-dependent or -independent pathways. However, the impact of the mutagenic properties of FQ treatment on commensal E. coli from the gut microbiota is unknown. We used a collection of commensal quinolone-resistant E. coli (QREC) from healthy subjects before and after a 14-day treatment of ciprofloxacin to follow the evolution of these strains in their natural environment. Our aim was to determine whether these strains had evolved at the genomic and/or phenotypic levels. Material and Methods Commensal QREC from before day-0 (D0), during (D8) and after 14 days (D14 and D42) of ciprofloxacin treatment were compared in three volunteers. Growth experiments were performed in various minimum media and acetate levels were measured as a proxy of central metabolism. Genomes were sequenced using the Illumina HiSeq®. Single nucleotide polymorphisms (SNPs) between each D0 and D42 strain genome pair were analyzed using the DiscoSNP and the breseq method. Cytoplasmic proteins were extracted, HPLC was performed, proteins were identified using X!tandem software and abundances were measured by mass spectrometry using the Spectral Counting (SC) and eXtraction Ion Chromatograms (XIC) integration methods. Results No difference was observed in growth characteristics or acetate concentrations between QREC from before and after ciprofloxacin treatment. Phylogroups, O-and H-types, fimH alleles and sequence types were similar on D0 and D42 for each couple of strains. No SNP was evidenced between D0 and D42 isolates for 2/3 subjects. In one subject, only 2 SNPs were evidenced. At the protein level, very few significant protein abundance differences were identified, only with the SC method, between D0 and D42. Conclusion No fitness, metabolic or genetic evolution of commensal QREC was observed overtime, despite high concentrations of ciprofloxacin in the gut. The three strains behaved as if they were unaffected by ciprofloxacin despite a major stress induced by 14 days of treatment, suggesting the gut can be a sanctuary where bacteria are protected from the effect of antibiotics and survive without any detrimental effect of stress.