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 IS Ecp1 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 IS Ecp1 , IS 26 , and IS 903-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.