Emergence of Antimicrobial Resistant Escherichia coli of Animal Origin Spreading in Humans

In the context of the great concern about the impact of human activities on the environment, we studied 403 commensalEscherichia coli/Escherichia clade strains isolated from several animal and human populations that have variable contacts to one another. Multilocus sequence typing(MLST) showed a decrease of diversity 1) in strains isolated from animals that had an increasing contact with humans and 2) in all strains that had increased antimicrobialresistance. A specific B1 phylogroup clonal complex (CC87, Institut Pasteur schema nomenclature) of animal origin was identified and characterized as being responsible for the increased antimicrobialresistance prevalence observed in strains from the environments with a high human-mediated antimicrobialpressure. CC87 strains have a high capacity of acquiring and disseminating resistance genes with specific metabolic and genetic determinantsas demonstrated by high-throughput sequencing and phenotyping. They are good mouse gut colonizers but are not virulent. Our data confirm the predominant role of human activities in the emergence of antimicrobialresistance in the environmental bacterial strains and unveil a particular E. coli clonal complex of animal origin capable of spreading antimicrobialresistance to other members of microbial communities.