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

Introduction: Salmonella enterica is a major cause of foodborne illness in the United States. A multi-drug resistant (MDR) emergent Salmonella 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 bla CTX-M-65 on a pESI-like plasmid and a mutation in the gyr 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 S. infantis 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 gyr A gene conferring reduced susceptibility to ciprofloxacin and harbored a combination of 6-10 resistance genes: bla CTX-M-65, aac (3)-IVa, aad A1, aph (4)-Ia, aph (3')-Ia, flo R, sul 1, dfr A14, tet A, and fos A. These 11 isolates carried class I and class II integrons and three virulence genes: sinH, involved in adhesion and invasion, ybt Q and ybt 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.
Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
(Copyright © 2023 Srednik, Morningstar-Shaw, Hicks, Tong, Mackie and Schlater.)