Phenotypic and genomic analysis of pathogenic Enterobacteriaceae strains isolated from leafy vegetables: antibiotic resistance implications for public health

Pathogenic Enterobacteriaceae (PE) pose significant public health threats, particularly with the emergence of antibiotic-resistant isolates that frequently cause foodborne infection outbreaks through the consumption of contaminated leafy vegetables. However, there is currently a lack of comprehensive genomic analysis for PE in leafy vegetables, hindering insights into the distribution patterns and resistance capacity of these PE in diverse agricultural settings around the world. This study addresses this gap by performing a genomic analysis of PE related to leafy vegetables, encompassing 458 publicly available genomes and 49 newly sequenced genomes from our study. The newly sequenced genomes correspond to PE isolates from organic fertilizer, fertilizer-applied soils, and various parts of Brassica rapa grown in fertilizer-applied soils (31 from B. rapa plants, 18 from organic fertilizer and soils), for which we also performed antibiotic susceptibility testing as a supplement. Results showed extensive multidrug resistance among PE isolates (>95 %), and a significant progressive increase of high-risk antibiotic resistance genes (ARGs) from roots to leaves. We established a genome dataset comprising 489 PE isolates (458 public isolates plus 31 B. rapa isolates from our study) from leafy vegetables worldwide and identified Escherichia coli as harboring substantially higher numbers of both high-risk ARGs (mean 9.71 per genome) and virulence factor genes (mean 72.45 per genome) compared to other PE taxa. This study provides a valuable genomic resource for investigating PE contamination in leafy vegetables and underscores the urgent need for enhanced surveillance targeting antibiotic-resistant PE, particularly E. coli, in leafy vegetables to mitigate emerging public health threats.