High prevalence of antibiotic resistance in traditionally fermented foods as a critical risk factor for host gut antibiotic resistome

Abstract

Disrupted gut microbiota as a critical risk factor for many noncommunicable diseases is largely driven by gut microbiota-impacting drugs, especially orally administered and biliary excreted antibiotics. Fermented food consumption has been encouraged to replenish disrupted gut microbiota; however, its overall impact on host gut health remains to be elucidated. This study examined traditionally fermented foods and the gut microbiota of consumers of fermented foods for antibiotic resistance. Dietary intervention with fermented foods was found to lead to a surge in the antibiotic resistome in the gut microbiota of most human subjects. The antibiotic resistome was further illustrated in traditionally fermented food samples, and antibiotic-resistant bacteria were isolated from approximately 90% of the retail kimchi and all artisan cheeses assessed in this pilot screening. The identified isolates included pathogens of importance in nosocomial infections such as Klebsiella pneumoniae and Enterococcus, as well as commensals and lactic acid bacteria, and some isolates exhibited extremely high minimum inhibitory concentration (MIC) against antibiotics of clinical significance. Exposing fermented food microbiota to representative antibiotics further led to a boost in the corresponding antibiotic and multidrug resistance gene pools and disturbed microbiota. The results revealed an underestimated public health risk associated with fermented food interventions, particularly in susceptible populations with gastrointestinal tract symptoms and compromised immune functions seeking gut microbiota rescue. These findings call for more comprehensive assessments of the benefits and potential safety challenges associated with traditionally fermented foods and strategic movements to mitigate unnecessary damage to the host gut microbiota and improve food safety.