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

• Published in: Microbial drug resistance (Larchmont, N.Y.) Vol. 24; no. 7; pp. 939 - 948
• Main Authors: Tadesse, Daniel A., Li, Cong, Mukherjee, Sampa, Hsu, Chih-Hao, Bodeis Jones, Sonya, Gaines, Stuart A., Kabera, Claudine, Loneragan, Guy H., Torrence, Mary, Harhay, Dayna M., McDermott, Patrick F., Zhao, Shaohua
• Format: Journal Article
• Language: English
• Published: United States Mary Ann Liebert, Inc 01.09.2018; Mary Ann Liebert, Inc., publishers
• Subjects: Amides; Animal products; Animals; Anti-Bacterial Agents - pharmacology; Antiinfectives and antibacterials; Antimicrobial agents; Antimicrobial resistance; Bacteria; Beef cattle; beta-Lactamases - genetics; Cattle; Chickens; Clinical isolates; Drug resistance; Drug Resistance, Bacterial - genetics; E coli; Epidemiology; Escherichia coli; Escherichia coli - drug effects; Escherichia coli - growth & development; Escherichia coli Infections - drug therapy; Escherichia coli Infections - microbiology; Escherichia coli Proteins - genetics; Feces; Food; Gene sequencing; Genes; Genomes; Humans; Infections; Meat; Meat - microbiology; Nucleotide sequence; Plasmids; Plasmids - genetics; Pork; Poultry; Salmonella; Transposition; United States; Whole Genome Sequencing - methods; β Lactamase; United States; Netherlands; United States > US; Maryland; Texas; CTX-M; ESBL; Escherichia coli
• ISSN: 1076-6294; 1931-8448
• DOI: 10.1089/mdr.2018.0206

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.