Whole-genome sequencing and phylogenetic analysis capture the emergence of a multi-drug resistant serovar Infantis clone from diagnostic animal samples in the United States.

Introduction: is a major cause of foodborne illness in the United States. A multi-drug resistant (MDR) emergent Infantis (ESI) with a megaplasmid (pESI) was first identified in Israel and Italy and subsequently reported worldwide. The ESI clone carrying an extended spectrum β-lactamase CTX-M-65 on a pESI-like plasmid and a mutation in the A gene has recently been found in the United States in poultry meat.

Methods: We analyzed the phenotypic and genotypic antimicrobial resistance, genomics and phylogeny of 200 isolates from animal diagnostic samples.

Results: Of these, 33.5% were resistant to at least one antimicrobial and 19.5% were multi-drug resistant (MDR). Eleven isolates from different animal sources were phenotypically and genetically similar to the ESI clone. These isolates had a D87Y mutation in the A gene conferring reduced susceptibility to ciprofloxacin and harbored a combination of 6-10 resistance genes: CTX-M-65, (3)-IVa, A1, (4)-Ia, (3')-Ia, R, 1, A14, A, and A. These 11 isolates carried class I and class II integrons and three virulence genes: sinH, involved in adhesion and invasion, Q and P, associated with iron transport. These isolates were also closely related to each other (separated by 7 to 27 SNPs) and phylogenetically related to the ESI clone recently found in the U.S.

Discussion: This dataset captured the emergence of the MDR ESI clone in multiple animal species and the first report of a pESI-like plasmid in isolates from horses in the U.S.