Low prevalence of mobile colistin-resistance in U.S. meat, catfish, poultry and genomic characterization of a mcr-1 positive Escherichia coli strain

Abstract This paper describes the results and outcomes of a survey conducted to investigate the presence of mcr-1 in 5169 domestic animal-origin samples collected by the USDA-Food Safety and Inspection Service between October 2018 and May 2019. Samples from chicken rinse (N = 1787), ground beef (N = 1369), beef trim (N = 1057), poultry (N = 363), raw pork (N = 416) and catfish (N = 177) were enriched in non-selective media and transferred to 96 well plates with a selection medium containing CaCl2, colistin and vancomycin. A novel ELISA was used to screen for the mcr-1 gene product (MCR-1). Only a single colistin resistant Escherichia coli carrying a mcr-1 gene was isolated from raw pork with a MIC of 8 mg/L, which resulted in an overall mcr-1 presence in raw pork of 0.24% and less than 0.02% in the total samples tested. This study represents the first large-scale investigation of mcr-1 in the U.S. meat, poultry, and catfish. Further examination of the positive isolate, Escherichia coli 2492 (EC2492), by whole genome sequencing revealed that this strain contained a 4.8 Mb chromosome and six plasmids. The mcr-1 gene was located on an IncI2 type plasmid and other five resistance genes, tetA, tetR, sul2, aph (3”)-Ib and aph (6)-Id identified were located on an IncB/O/K/Z plasmid. In silico analysis assigned EC2492 to ST101 and serotype O54:H21. In conclusion, while the survey results indicated that mcr-1 is rare in the U.S. animal derived foods, that one positive isolate was found suggests that continued vigilance to minimize further spread of mobile colistin resistance is warranted.