The role of class 1 and 2 integrons in mediating antimicrobial resistance among canine and feline clinical E. coli isolates from the US

Integrons are mobile genetic elements that incorporate an open reading frame or gene cassettes. They have an important role in the acquisition and dissemination of antimicrobial resistance genes. Yet the occurrence of integrons carrying antimicrobial resistance genes in bacterial pathogens of pet animals is seldom addressed. The purpose of this study was to describe the incidence of class 1 and 2 integrons in clinical isolates of Escherichia coli (n = 82) from cats and dogs provided by diagnostic laboratories in five States of the USA. An association between resistance genes in the integrons and the isolates’ phenotypes was found. Integrons were detected using PCR and then further characterized by restriction fragment-length polymorphism analysis and amplicon sequencing. Class 1 integrons were detected in 27% of the isolates, while only 2% (n = 2) of the isolates were positive for the presence of class 2 integrons. Seventy-two percent (n = 59) of the isolates did not carry integrons. Eleven gene cassettes were found either alone or in combination with other gene cassettes, which encoded resistance to aminoglycosides (aadA1, aadA2, aadA5, aacA4, and aadB), trimethoprim (dfrA1, dhfrA17, and dfrA12), chloramphenicol (catB3 and cmlA6), and streptothricin (sat1), respectively. All integron-positive isolates were characterized by resistance to least two drug classes and 35% produced extended-spectrum β-lactamases. The association of integrons carried on plasmids and antimicrobial resistance was confirmed by curing experiments for three isolates. Resistance was resolved once large plasmids (size range 97–169 kb) carrying the class 1 integron were lost. Therefore, integrons appear to have an essential role in facilitating the dissemination of the resistance genes and contributing to the creation of multi-drug resistant phenotypes.