A genome-wide association study of antibiotic resistance in dairy products-associated Enterococcus faecium isolates

Abstract

Food-associated Enterococcus faecium are commonly used as food starters and probiotics. However, their use is controversial due to the increasing multidrug resistance. This study aimed to investigate the phenotype-genotype association of antibiotic resistance in 50 dairy products-associated Enterococcus faecium isolates. The antibiotic-resistant phenotype of these isolates was determined based on the minimum inhibitory concentration of 15 antibiotics. The isolates were variably resistant to most tested antibiotics (12/15) but were sensitive to vancomycin, ampicillin, and linezolid. They were subjected to comparative genomic analysis along with 11 and 15 fecal isolates from patients and healthy individuals, respectively. The dairy isolates have a significantly smaller genome size and coding sequence number than the fecal isolates from patients (P < 0.05). A Comprehensive Antibiotic Resistance Database search spotted 47 antibiotic resistance genes, but only four were identified in the dairy-associated isolates. A genome-wide association study was performed to uncover hidden antibiotic resistance genes, identifying 122 potential resistance-linked genes associated with three antibiotics, i.e., chloramphenicol, ciprofloxacin, and rifampicin. Ninety-one genes encoded defined biological functions, while the other genes encoded hypothetical proteins. Although their phenotype-specific role remains to be investigated, our results have provided interesting targets for further elucidating the antibiotic resistance mechanism in Enterococcus faecium.