title: Characterization of a P1-like bacteriophage carrying an SHV-2 extended-spectrum β-lactamase from an Escherichia coli strain.
abstract: P1 bacteriophages lysogenize bacteria as independent plasmid-like elements. We describe here a P1-like bacteriophage, RCS47, carrying a blaSHV-2 gene, isolated from a clinical strain of Escherichia coli from phylogroup B1, and we report the prevalence of P1-like prophages in natural E. coli isolates. We found that 70% of the sequence of RCS47, a 115-kb circular molecule, was common to the reference P1 bacteriophage under GenBank accession no. AF234172.1, with the shared sequences being 99% identical. RCS47 had acquired two main foreign DNA fragments: a 9,636-bp fragment mobilized by two IS26 elements containing a blaSHV-2 gene, and an 8,544-bp fragment mobilized by two IS5 elements containing an operon encoding a dimethyl sulfoxide reductase. The reference P1 prophage plasmid replication gene belonged to the IncY incompatibility group, whereas that of RCS47 was from an unknown group. The lytic capacity of RCS47 and blaSHV-2 gene transduction, through the lysogenization of RCS47 in the recipient E. coli strains, were not demonstrated. The prevalence of P1-like prophages in various animal and human E. coli strain collections, as determined by the PCR detection of repL, the lytic replication gene, was 12.6%. No differences in the prevalences of these prophages were found between extended-spectrum β-lactamase (ESBL)-producing and non-ESBL-producing strains (P = 0.69), but this prevalence was lower in phylogroup B2 than in the other phylogroups (P = 0.008), suggesting epistatic interactions between P1 family phages and the genetic background of E. coli strains. P1-like phages are part of the mobile elements that carry antibiotic resistance. The high prevalence of P1-like prophages suggests their role may be underestimated.
authors.affiliation: INSERM, IAME, UMR 1137, Paris, France Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, Paris, France APHP, Hôpital Louis Mourier, Service de Microbiologie, Colombes, France.
authors.forename: Typhaine
authors.initials: T
authors.lastname: Billard-Pomares
authors.affiliation: Laboratoire de Finition, Institut de Génomique, Commissariat à l'Energie Atomique, Génoscope, Evry, France.
authors.forename: Stéphanie
authors.initials: S
authors.lastname: Fouteau
authors.affiliation: Laboratoire de Finition, Institut de Génomique, Commissariat à l'Energie Atomique, Génoscope, Evry, France.
authors.forename: Marie Elise
authors.initials: ME
authors.lastname: Jacquet
authors.affiliation: Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme, Institut de Génomique, Commissariat à l'Energie Atomique, Génoscope, CNRS-UMR 8030, Evry, France.
authors.forename: David
authors.initials: D
authors.lastname: Roche
authors.affiliation: Laboratoire de Finition, Institut de Génomique, Commissariat à l'Energie Atomique, Génoscope, Evry, France.
authors.forename: Valérie
authors.initials: V
authors.lastname: Barbe
authors.affiliation: INSERM, IAME, UMR 1137, Paris, France Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, Paris, France.
authors.forename: Miguel
authors.initials: M
authors.lastname: Castellanos
authors.affiliation: Laboratoire de Microbiologie et Génétique Moléculaires, CNRS UMR 5100, Toulouse, France Université Toulouse, Université Paul Sabatier, LMGM, Toulouse, France.
authors.forename: Jean Yves
authors.initials: JY
authors.lastname: Bouet
authors.affiliation: Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme, Institut de Génomique, Commissariat à l'Energie Atomique, Génoscope, CNRS-UMR 8030, Evry, France.
authors.forename: Stéphane
authors.initials: S
authors.lastname: Cruveiller
authors.affiliation: Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme, Institut de Génomique, Commissariat à l'Energie Atomique, Génoscope, CNRS-UMR 8030, Evry, France.
authors.forename: Claudine
authors.initials: C
authors.lastname: Médigue
authors.affiliation: Laboratorio de Referencia de E. coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), Lugo, Spain.
authors.forename: Jorge
authors.initials: J
authors.lastname: Blanco
authors.affiliation: INSERM, IAME, UMR 1137, Paris, France Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, Paris, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: Clermont
authors.affiliation: INSERM, IAME, UMR 1137, Paris, France Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, Paris, France.
authors.forename: Erick
authors.initials: E
authors.lastname: Denamur
authors.affiliation: INSERM, IAME, UMR 1137, Paris, France Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, Paris, France APHP, Hôpital Louis Mourier, Service de Microbiologie, Colombes, France catherine.branger@lmr.aphp.fr.
authors.forename: Catherine
authors.initials: C
authors.lastname: Branger
mesh_terms: D001483:Base Sequence; D027042:Chromosomes, Artificial, P1 Bacteriophage / Q000235:genetics*; D004926:Escherichia coli / Q000187:drug effects* / Q000235:genetics*; D004927:Escherichia coli Infections / Q000188:drug therapy / Q000382:microbiology; D006801:Humans; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA; D001618:beta-Lactamases / Q000235:genetics*
chemical_list: C062760:beta-lactamase SHV-2; D001618:beta-Lactamases