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Colistin resistance in Parisian inpatient faecal Escherichia coli as the result of two distinct evolutionary pathways.
J Antimicrob Chemother. 2019 06 01; 74(6):1521-1530.JA

Abstract

BACKGROUND

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.

Authors+Show Affiliations

Laboratoire de Bactériologie et d'Hygiène Hospitalière, CHU Henri Mondor, Assistance Publique - Hôpitaux de Paris, Créteil, France.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.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.Laboratoire de Bactériologie et d'Hygiène Hospitalière, CHU Henri Mondor, Assistance Publique - Hôpitaux de Paris, Créteil, France.Laboratoire de Bactériologie et d'Hygiène Hospitalière, CHU Henri Mondor, Assistance Publique - Hôpitaux de Paris, Créteil, France.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.IAME, UMR1137 INSERM, Université Paris Diderot, Université Paris Nord, Emerging Antibiotic Resistance in Gram-Negative Bacteria, Paris, France.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.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.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.No affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

30863849

Citation

Bourrel, Anne Sophie, et al. "Colistin Resistance in Parisian Inpatient Faecal Escherichia Coli as the Result of Two Distinct Evolutionary Pathways." The Journal of Antimicrobial Chemotherapy, vol. 74, no. 6, 2019, pp. 1521-1530.
Bourrel AS, Poirel L, Royer G, et al. Colistin resistance in Parisian inpatient faecal Escherichia coli as the result of two distinct evolutionary pathways. J Antimicrob Chemother. 2019;74(6):1521-1530.
Bourrel, A. S., Poirel, L., Royer, G., Darty, M., Vuillemin, X., Kieffer, N., Clermont, O., Denamur, E., Nordmann, P., & Decousser, J. W. (2019). Colistin resistance in Parisian inpatient faecal Escherichia coli as the result of two distinct evolutionary pathways. The Journal of Antimicrobial Chemotherapy, 74(6), 1521-1530. https://doi.org/10.1093/jac/dkz090
Bourrel AS, et al. Colistin Resistance in Parisian Inpatient Faecal Escherichia Coli as the Result of Two Distinct Evolutionary Pathways. J Antimicrob Chemother. 2019 06 1;74(6):1521-1530. PubMed PMID: 30863849.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Colistin resistance in Parisian inpatient faecal Escherichia coli as the result of two distinct evolutionary pathways. AU - Bourrel,Anne Sophie, AU - Poirel,Laurent, AU - Royer,Guilhem, AU - Darty,Mélanie, AU - Vuillemin,Xavier, AU - Kieffer,Nicolas, AU - Clermont,Olivier, AU - Denamur,Erick, AU - Nordmann,Patrice, AU - Decousser,Jean-Winoc, AU - ,, PY - 2018/09/11/received PY - 2019/02/07/revised PY - 2019/02/07/accepted PY - 2019/3/14/pubmed PY - 2020/7/18/medline PY - 2019/3/14/entrez SP - 1521 EP - 1530 JF - The Journal of antimicrobial chemotherapy JO - J. Antimicrob. Chemother. VL - 74 IS - 6 N2 - BACKGROUND: 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. SN - 1460-2091 UR - https://www.unboundmedicine.com/medline/citation/30863849/Colistin_resistance_in_Parisian_inpatient_faecal_Escherichia_coli_as_the_result_of_two_distinct_evolutionary_pathways_ L2 - https://academic.oup.com/jac/article-lookup/doi/10.1093/jac/dkz090 DB - PRIME DP - Unbound Medicine ER -