Antibiotic resistance profile and molecular mechanism of enterococci in traditional fermented yogurts

Enterococci are present in traditional fermented foods, but their potential role as reservoirs of antibiotic resistance and virulence genes has raised concerns about food safety. To evaluate the prevalence of antibiotic-resistant enterococci in traditional fermented yogurt, microbial sequencing and culture methods were used to analyze the microbiota and Enterococcus composition in a total of 75 yogurts from Xinjiang Uygur Autonomous Region (Xinjiang, China). Enterococcus faecium and Enterococcus durans were the predominant enterococcal species and belonged to 20 and 5 biotypes, respectively, according to randomly amplified polymorphic DNA PCR analysis. Antibiotic resistance testing revealed that 98.92% of Enterococcus strains were resistant to at least one kind of antibiotic, of which E. faecium showed high resistance to gentamicin (96.92%), erythromycin (55.38%), and ciprofloxacin (49.23%), whereas E. durans was most resistant to tetracycline (58.82%) and chloramphenicol (55.82%), followed by gentamicin (47.06%). Multidrug-resistant strains were more abundant in E. faecium (37.3%). Furthermore, vancomycin resistance was observed in E. faecium strains, highlighting the risk of resistance spread. Molecular analysis revealed vancomycin and tetracycline resistance phenotypes were consistent with genotypes, but not for penicillin, gentamicin and erythromycin. Moreover, mobile genetic elements were detected, such as 5'ococs/3'ococs and IntI3, which facilitate gene transfer. Metagenomic sequencing further revealed the high abundance of antibiotic resistance genes, such as mlaF, macB, and ImrD. Additionally, the microbial co-occurrence network analysis revealed significant positive correlations between E. faecium and Acetobacter in the Zhaosu region. This study highlights that traditional fermented yogurt may serve as a reservoir for multidrug-resistant enterococci, posing a potential risk to public health.