Colistin resistance in Parisian inpatient faecal Escherichia coli as the result of two distinct evolutionary pathways

Bourrel, Anne-Sophie; Poirel, Laurent; Royer, Guilhem; Darty, Mélanie; Vuillemin, Xavier; Kieffer, Nicolas; Clermont, Olivier; Denamur, Erick; Nordmann, Patrice; Decousser, Jean-Winoc; The IAME Resistance Group,

doi:10.1093/jac/dkz090

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Colistin resistance in Parisian inpatient faecal Escherichia coli as the result of two distinct evolutionary pathways

Bourrel, Anne-Sophie Laboratoire de Bactériologie et d’Hygiène Hospitalière, CHU Henri Mondor, Assistance Publique - Hôpitaux de Paris, Créteil, France
Poirel, Laurent Laboratoire Européen Associé INSERM, Emerging Antibiotic Resistance in Gram-Negative Bacteria, Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland - National Reference Centre for Emerging Antibiotic Resistance (NARA), Fribourg, Switzerland
Royer, Guilhem Laboratoire de Bactériologie et d’Hygiène Hospitalière, CHU Henri Mondor, Assistance Publique - Hôpitaux de Paris, Créteil, France - IAME, UMR1137 INSERM, Université Paris Diderot, Université Paris Nord, Emerging Antibiotic Resistance in Gram-Negative Bacteria, Paris, France - LABGeM, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
Darty, Mélanie Laboratoire de Bactériologie et d’Hygiène Hospitalière, CHU Henri Mondor, Assistance Publique - Hôpitaux de Paris, Créteil, France
Vuillemin, Xavier Laboratoire de Bactériologie et d’Hygiène Hospitalière, CHU Henri Mondor, Assistance Publique - Hôpitaux de Paris, Créteil, France
Kieffer, Nicolas Laboratoire Européen Associé INSERM, Emerging Antibiotic Resistance in Gram-Negative Bacteria, Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland - National Reference Centre for Emerging Antibiotic Resistance (NARA), Fribourg, Switzerland
Clermont, Olivier IAME, UMR1137 INSERM, Université Paris Diderot, Université Paris Nord, Emerging Antibiotic Resistance in Gram-Negative Bacteria, Paris, France
Denamur, Erick IAME, UMR1137 INSERM, Université Paris Diderot, Université Paris Nord, Emerging Antibiotic Resistance in Gram-Negative Bacteria, Paris, France - Laboratoire de Génétique Moléculaire, Hôpital Bichat, Assistance Publique - Hôpitaux de Paris, Paris, France
Nordmann, Patrice Laboratoire Européen Associé INSERM, Emerging Antibiotic Resistance in Gram-Negative Bacteria, Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland - National Reference Centre for Emerging Antibiotic Resistance (NARA), Fribourg, Switzerland
Decousser, Jean-Winoc Laboratoire de Bactériologie et d’Hygiène Hospitalière, CHU Henri Mondor, Assistance Publique - Hôpitaux de Paris, Créteil, France - IAME, UMR1137 INSERM, Université Paris Diderot, Université Paris Nord, Emerging Antibiotic Resistance in Gram-Negative Bacteria, Paris, France
The IAME Resistance Group,

01.06.2019

Published in:

Journal of Antimicrobial Chemotherapy. - 2019, vol. 74, no. 6, p. 1521–1530

English Beyond plasmid-encoded resistance (mcr genes) prevalence in strain collections, large epidemiological studies to estimate the human burden of colistin-resistant Escherichia coli gut carriage are lacking.Objectives: To evaluate the prevalence of colistin-resistant E. coli carriage in inpatients and decipher the molecular support of resistance and the genetic background of the strains.Methods: During a 3 month period in 2017, we prospectively screened patients in six Parisian hospitals for rectal carriage of colistin-resistant E. coli using a selective medium, a biochemical confirmatory test and MIC determination. WGS of the resistant strains and their corresponding plasmids was performed.Results: Among the 1217 screened patients, 153 colistin-resistant E. coli strains were isolated from 152 patients (12.5%). The mcr- 1 gene was identified in only seven isolates (4.6%) on different plasmid scaffolds. The genetic background of these MCR-1 producers argued for an animal origin. Conversely, the remaining 146 colistin-resistant E. coli exhibited a phylogenetic distribution corresponding to human gut commensal/clinical population structure (B2 and D phylogroup predominance); 72.6% of those isolates harboured convergent mutations in the PmrA and PmrB proteins, constituting a two-component system shown to be associated with colistin resistance.Conclusions: We showed that the occurrence at a high rate of colistin resistance in human faecal E. coli is the result of two distinct evolutionary pathways, i.e. the occurrence of chromosomal mutations in an endogenous E. coli population and the rare acquisition of exogenous mcr-1- bearing strains probably of animal origin. The involved selective pressures need to be identified in order to develop preventative strategies.

Faculty

Faculté des sciences et de médecine

Department

Médecine 3ème année

Language