title: Antibiotic resistance plasmids spread among natural isolates of Escherichia coli in spite of CRISPR elements.
abstract: Clustered, regularly interspaced, short palindromic repeats (CRISPRs) are implicated in defence against foreign DNA in various archaeal and bacterial species. They have also been associated with a slower spread of antibiotic resistance. However, experimental and evolutionary studies raise doubts about the role of CRISPRs as a sort of immune system in Escherichia coli. We studied a collection of 263 natural E. coli isolates from human and animal hosts, representative of the phylogenetic and lifestyle diversity of the species and exhibiting various levels of plasmid-encoded antibiotic resistance. We characterized the strains in terms of CRISPRs, performed replicon typing of the plasmids and tested for class 1 integrons to explore the possible association between CRISPRs and the absence of plasmids and mobile antibiotic resistance determinants. We found no meaningful association between the presence/absence of the cas genes, reflecting the activity of the CRISPRs, and the presence of plasmids, integrons or antibiotic resistance. No CRISPR in the collection contained a spacer that matched an antibiotic resistance gene or element involved in antibiotic resistance gene mobilization, and 79.8 % (210/263) of the strains lacked spacers matching sequences in the 2282 plasmid genomes available. Hence, E. coli CRISPRs do not seem to be efficient barriers to the spread of plasmids and antibiotic resistance, consistent with what has been reported for phages, and contrary to reports concerning other species.
authors.affiliation: 1Institut Pasteur, Microbial Evolutionary Genomics, Département Génomes et Génétique, F-75015 Paris, France 2CNRS, UMR3525, 25 R. Dr Roux, F-75015 Paris, France.
authors.forename: Marie
authors.initials: M
authors.lastname: Touchon
authors.affiliation: 3AP-HP, Hôpital Louis Mourier, Service de Microbiologie-Hygiène, Colombes F-92701, France 4INSERM, UMR-S 722, Paris, F-75018, France 5Univ Paris Diderot, Sorbonne Paris Cité, UMR-S 722, Faculté de Médecine, Site Xavier Bichat, Paris, F-75018, France.
authors.forename: Sophie
authors.initials: S
authors.lastname: Charpentier
authors.affiliation: 3AP-HP, Hôpital Louis Mourier, Service de Microbiologie-Hygiène, Colombes F-92701, France.
authors.forename: Dominique
authors.initials: D
authors.lastname: Pognard
authors.affiliation: 4INSERM, UMR-S 722, Paris, F-75018, France 6Univ Paris Nord, Sorbonne Paris Cité, UMR-S 722, Faculté de Médecine, Site Xavier Bichat, Paris, F-75018, France.
authors.forename: Bertrand
authors.initials: B
authors.lastname: Picard
authors.affiliation: 7Univ Pierre et Marie Curie, Faculté de Médecine, Site Saint-Antoine, Laboratoire de Bactériologie, ER8, Paris, F-75012, France 8AP-HP, Hôpital Tenon, Service de Bactériologie-Hygiène, Paris, F-75020, France.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Arlet
authors.affiliation: 1Institut Pasteur, Microbial Evolutionary Genomics, Département Génomes et Génétique, F-75015 Paris, France 2CNRS, UMR3525, 25 R. Dr Roux, F-75015 Paris, France.
authors.forename: Eduardo P C
authors.initials: EP
authors.lastname: Rocha
authors.affiliation: 4INSERM, UMR-S 722, Paris, F-75018, France 5Univ Paris Diderot, Sorbonne Paris Cité, UMR-S 722, Faculté de Médecine, Site Xavier Bichat, Paris, F-75018, France.
authors.forename: Erick
authors.initials: E
authors.lastname: Denamur
authors.affiliation: 3AP-HP, Hôpital Louis Mourier, Service de Microbiologie-Hygiène, Colombes F-92701, France 4INSERM, UMR-S 722, Paris, F-75018, France 5Univ Paris Diderot, Sorbonne Paris Cité, UMR-S 722, Faculté de Médecine, Site Xavier Bichat, Paris, F-75018, France.
authors.forename: Catherine
authors.initials: C
authors.lastname: Branger