Genomic surveillance and resistome profiling of opportunistic pathogenic endophytes in ready-to-eat vegetables

A genomic understanding of the rapidly increasing dissemination of clinical pathogens in endophytes of raw vegetables—coupled with interactions between these endophytes and humans, their mobility potential, and the consequent risks of their resistomes—is essential to reveal the health relevance of lesser-known infections associated with environmental media in clinical settings. In this study, six types of raw vegetables were sampled, and high-throughput quantitative PCR (HT-qPCR) and amplicon sequencing were used to characterize the composition of the microbial community, antibiotic resistance genes (ARGs), and the correlation between pathogenic endophytes and clinical isolates. Results showed that the abundance and diversity of ARGs and endophytes were significantly affected by vegetable species, and a positive correlation was observed between ARGs and mobile genetic elements (MGEs)—a relationship that facilitates the transmission and propagation of ARGs. At the KEGG Level 2, metabolic pathways related to multidrug resistance and infectious diseases were the most abundant. Among global priority pathogens, Escherichia coli , Enterobacter cloacae , and Klebsiella pneumoniae and gram-positive Enterococcus were subjected to antibiotic susceptibility testing (AST) and whole-genome sequencing (WGS), the results revealed varying degrees of association between these endophytic pathogens and clinical isolates, as well as their carriage of diverse ARGs and virulence factors (VFs). Collectively, these results highlight the role of vegetable endophytes in the dissemination of ARGs and antibiotic-resistant bacteria (ARBs), and call for a robust evidence base to inform management policies for their control. • The abundance and diversity of ARGs and endophytes were significantly affected by vegetable species. • A positive correlation was observed between ARGs and mobile genetic elements (MGEs)—a relationship that facilitates the transmission and propagation of ARGs. • At the KEGG Level 2, metabolic pathways related to multidrug resistance and infectious diseases were the most abundant. • Varying degrees of association between the main endophytic pathogens and clinical isolates were observed, as well as their carriage of diverse ARGs and virulence factors (VFs).