Quinolone-resistant Escherichia coli from the faecal microbiota of healthy volunteers after ciprofloxacin exposure are highly adapted to a commensal lifestyle

Objectives: Quinolone-resistant Escherichia coli (QREC) primarily emerge in commensal bacteria under selective pressure. The aim of this work was to investigate the characteristics of QREC from the faecal microbiota after quinolone exposure, as they remain largely unknown. Methods: Forty-eight healthy volunteers received ciprofloxacin from day 1 to day 14. QREC were detected in stools from 14 subjects at day 42. QREC were compared in terms of genetic background, metabolic properties, stress resistance and intestinal colonization abilities with quinolone-susceptible E. coli (QSEC) from the same 14 individuals and from 29 volunteers who remained QREC-free. Results: QREC always belonged to a single clone for a given volunteer and to restricted phylogenetic groups. QREC carried significantly more iron capture systems than QSEC. Maximum growth rates in minimal medium with gluconate, general stress regulator RpoS activity assessed by iodine staining and resistance to oxidative and acid stresses were significantly higher for QREC than for QSEC. In a mouse colonization model, QREC efficiently colonized the intestine microbiota despite the presence of QSEC competitors. At day 42, QREC and QSEC faecal counts from the 14 volunteers were comparable except in three subjects where only QREC could be detected. Conclusions: These results suggest that QREC do not have a fitness cost, probably as a result of genetic co-selection, but are highly adapted to a commensal lifestyle. They may not be eliminated easily from the faecal microbiota from healthy subjects once selected.