Third-Generation Cephalosporin- and Tetracycline-Resistant Escherichia coli and Antimicrobial Resistance Genes from Metagenomes of Mink Feces and Feed

Abstract

American mink (Neovison vison) is a significant source of global fur production. Except for a few studies from Denmark and Canada reporting antimicrobial resistance in bacteria isolated from clinical cases, studies from the general mink population are scarce and absent in the United States. Mink feces (n = 42) and feed (n = 8) samples obtained from a mink farm were cultured for the enumeration and detection of tetracycline-resistant (TET^r)- and third-generation cephalosporin-resistant (TGC^r)-Escherichia coli. Isolates were characterized phenotypically for their resistance to other antibiotics and genotypically for resistance genes. TET^rE. coli were detected from 98% of feces samples (mean concentration = 6 log₁₀) and from 100% of feed samples (mean concentration = 3.2 logs). Among TET^rE. coli isolates, 44% (n = 41) of fecal- and 50% (n = 8) of feed isolates were multidrug resistant (MDR; resistance to ≥3 antimicrobial classes), and 96% (n = 49) of TET^r isolates were positive for tet(A) and/or tet(B). TGC^rE. coli were detected from 95% of feces and 75% of feed samples with 78% (n = 40) of fecal isolates, and all six of the feed isolates were MDR. Nearly two-thirds (65%) of the TGC^rE. coli isolates (n = 46) were positive for bla_CMY-2; the remaining 35% were positive for bla_CTX-M, with the bla_CTX-M-14 being the predominant (75%, n = 16) variant detected. Metagenomic DNA was extracted directly from feces and feed samples, and it was tested for 84 antimicrobial resistance genes by using quantitative polymerase chain reaction (PCR) array; selected genes were also quantified by droplet digital PCR. The genes detected from the fecal samples belonged mainly to five antimicrobial classes: macrolide-lincosamide-streptogramin B (MLS_B; 100% prevalence), TETs (88.1%), β-lactams (71.4%), aminoglycosides (66.7%), and fluoroquinolones (47.6%). β-Lactam, MLS_B, and TET resistance genes were also detected from feed samples. Our study serves as a baseline for further studies and to streamline antimicrobial use in mink production in accordance with current regulations as in food animals.

Keywords: E. coli; ESBLs; antimicrobial resistance; antimicrobial resistance genes; feed; metagenomics; mink.