What’s up ducks? – Antimicrobial resistance of Escherichia coli isolated from duck farm environment in Poland extended with genomic characteristics of cephalosporin-resistant strains

Abstract

Antimicrobial resistance (AMR) in food-producing animals is a source of concern as it may pose a risk to public health. Studies of ducks in this area seem to be scarce. Thus, we aimed to evaluate the AMR occurrence in Escherichia coli from a duck farm environment in Poland. We applied official AMR monitoring methods to investigate AMR in E. coli isolated from boot swabs collected at 306 duck farms in Poland. The samples were screened for indicator, cephalosporin-, carbapenem- and colistin- resistant E. coli. Isolates were tested for antimicrobial susceptibility using the microbroth dilution method and interpreted with epidemiological cut-off values. Whole Genome Sequencing (WGS) of cephalosporin-resistant strains enabled an in-depth insight into specific resistance mechanisms, mobile genetic elements and phylogeny of strains. A total of 340 strains were isolated. The percentage of indicator E. coli equaled 89.9 %, while 19.3 % were obtained through selective screening for E. coli resistant to cephalosporins. Six were recovered on colistin-supplemented MacConkey agar. Among indicator E. coli 81.1 % were resistant and ciprofloxacin, ampicillin, tetracycline and nalidixic acid resistance were the most frequent, followed by folate-path inhibitors. Within the group of strains from cephalosporin resistance screening: 76.3 % exhibited ESBL-, 20.3 % AmpC-, and 3.4 % showed both ESBL- and AmpC- phenotypes. WGS of those strains revealed numerous AMR determinants, not only genes corresponding to mentioned phenotypes but also determinants encoding resistance to other medically important antimicrobials. Our study reveals that E. coli from duck farm environment constitute a reservoir of AMR determinants including those of public health concern.