Whole-Genome Sequence Analysis of CTX-M Containing Escherichia coli Isolates from Retail Meats and Cattle in the United States

In recent years, there have been increased reports on the detection of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli and Salmonella strains from food-producing animals and animal products in the United States. We characterized 18 ESBL E. coli isolates from cattle (n = 5), chicken breast (n = 5), ground turkey (n = 6), ground beef (n = 1), and pork chops (n = 1) that were collected by the National Antimicrobial Resistance Monitoring System (NARMS) between 2011 and 2015. In vitro antimicrobial susceptibility testing was done against a panel of 14 antimicrobials followed by a secondary panel of 9 β-lactam agents. Whole-genome sequencing was used to characterize the resistome, plasmids, and the genetic structures of the ESBL genes. All ESBL-producing E. coli isolates were resistant to at least three antimicrobial classes and carried various bla(CTX-M) genes. Most of the cattle and ground turkey isolates carried bla(CTX-M-27). In chicken breast isolates, bla(CTX-M-1) was present as part of an ISEcp1 transposition unit carried on a plasmid that shares sequence similarity with the backbone structure of the IncI plasmid. Isolates carrying the bla(CTX-M-14) and bla(CTX-M-15) genes, widely distributed in human clinical isolates, were also isolated. To our knowledge, this is the first report of the widely distributed bla(CTX-M-14) and bla(CTX-M-15) in E. coli isolates from retail meat samples in the United States. Different insertional sequences were identified upstream of these bla(CTX-Ms), including ISEcp1, IS26, and IS903-D. CTX-M in E. coli from food animals and retail chicken breast were often present on plasmids with other resistance genes. Other resistance genes identified included aadA, strA, strB, aac(3)-IId, aac(3)-VIa, aph(3′)-Ic, bla(TEM), bla(HERA-3), floR, sul1, sul2, catA1, tetA, tetB, dfrA, and qacE. These data describe the emergence of CTX-M-carrying E. coli isolates in food animals and animal products monitored by NARMS program.