title: Commensal Escherichia coli strains in Guiana reveal a high genetic diversity with host-dependant population structure.
abstract: We undertook a large-scale epidemiological survey of commensal Escherichia coli in Trois-Sauts, an isolated village located in the south of French Guiana where human population exchanges are restricted and source of antibiotics controlled. Stools from 162 Wayampi Amerindians and rectal swabs from 33 human associated and 198 wild animals were collected in the close proximity of the village. The prevalence of E. coli was decreasing from humans (100%) to human associated (64%) and wild (45%) animals. A clear genetic structure between these three E. coli populations was observed with human strains belonging very rarely to B2 phylogroup (3.7%), exhibiting few virulence genes and bacteriocins but being antibiotic resistant whereas wild animal strains were characterized by 46.1% of B2 phylogroup belonging, with very unique and infrequent sequence types, numerous extraintestinal genes and bacteriocins but no antibiotic resistance; the human-associated animal strains being intermediate. Furthermore, an unexpected genetic diversity was observed among the strains, as the housekeeping gene nucleotide diversity per site of the Trois-Sauts's strains was higher than the one of reference strains representative of the known species diversity. The existence of such E. coli structured phylogenetic diversity within various hosts of a single localization has never been reported.
authors.affiliation: UMR 722 INSERM, Paris, France.
authors.forename: Mathilde
authors.initials: M
authors.lastname: Lescat
authors.forename: Olivier
authors.initials: O
authors.lastname: Clermont
authors.forename: Paul Louis
authors.initials: PL
authors.lastname: Woerther
authors.forename: Jérémy
authors.initials: J
authors.lastname: Glodt
authors.forename: Sara
authors.initials: S
authors.lastname: Dion
authors.forename: David
authors.initials: D
authors.lastname: Skurnik
authors.forename: Felix
authors.initials: F
authors.lastname: Djossou
authors.forename: Claire
authors.initials: C
authors.lastname: Dupont
authors.forename: Gilles
authors.initials: G
authors.lastname: Perroz
authors.forename: Bertrand
authors.initials: B
authors.lastname: Picard
authors.forename: François
authors.initials: F
authors.lastname: Catzeflis
authors.forename: Antoine
authors.initials: A
authors.lastname: Andremont
authors.forename: Erick
authors.initials: E
authors.lastname: Denamur
mesh_terms: D000818:Animals; D000835:Animals, Wild; D000900:Anti-Bacterial Agents / Q000494:pharmacology; D001430:Bacteriocins / Q000494:pharmacology; D004269:DNA, Bacterial / Q000235:genetics; D024881:Drug Resistance, Bacterial / Q000187:drug effects; D004926:Escherichia coli / Q000145:classification / Q000235:genetics / Q000302:isolation & purification* / Q000472:pathogenicity; D005243:Feces / Q000382:microbiology; D005616:French Guiana; D014644:Genetic Variation; D058507:Host Specificity; D006801:Humans; D010802:Phylogeny; D014774:Virulence
chemical_list: D000900:Anti-Bacterial Agents; D001430:Bacteriocins; D004269:DNA, Bacterial