Genetic Structure and Antimicrobial Resistance of Escherichia coli and Cryptic Clades in Birds with Diverse Human Associations

Abstract

ABSTRACTThe manner and extent to which birds associate with humans may influence the genetic attributes and antimicrobial resistance of their commensalEscherichiacommunities through strain transmission and altered selection pressures. In this study, we determined whether the distribution of the differentEscherichia coliphylogenetic groups and cryptic clades, the occurrence of 49 virulence associated genes, and/or the prevalence of resistance to 12 antimicrobials differed between four groups of birds from Australia with contrasting types of human association. We found that birds sampled in suburban and wilderness areas had similarEscherichiacommunities. TheEscherichiacommunities of backyard domestic poultry were phylogenetically distinct from theEscherichiacommunities sourced from all other birds, with a large proportion (46%) of poultry strains belonging to phylogenetic group A and a significant minority (17%) belonging to the cryptic clades. Wild birds sampled from veterinary and wildlife rehabilitation centers (in-care birds) carriedEscherichiaisolates that possessed particular virulence-associated genes more often thanEscherichiaisolates from birds sampled in suburban and wilderness areas. TheEscherichiaisolates from both the backyard poultry and in-care birds were more likely to be multidrug resistant than theEscherichiaisolates from wild birds. We also detected a multidrug-resistantE. colistrain circulating in a wildlife rehabilitation center, reinforcing the importance of adequate hygiene practices when handling and caring for wildlife. We suggest that the relatively high frequency of antimicrobial resistance in the in-care birds and backyard poultry is due primarily to the use of antimicrobials in these animals, and we recommend that the treatment protocols used for these birds be reviewed.