Identification of ESBL-producing enterobacterales from vegetable plants in a rural area of Madagascar: insights into AMR transmission at the human-animal-environment-plant interface

Abstract

Extended-spectrum b-lactamases (ESBL)-producing enterobacterales are considered a key indicator for antimicrobial resistance (AMR) epidemiological surveillance in animal, human and environment compartments. In this study we aim to investigate the presence and genetic diversity of ESBL-producing enterobacterales on vegetable plants. We isolated beta-lactam resistant enterobacterales from several vegetable plants and sequenced their whole genome. Utilizing cutting-edge genomic and phylogenetic methods, we sought to i) characterize their resistome and plasmidome, ii) investigate the genetic structure of the plant-isolated strains and iii) determine their relationships with strains from other reservoirs. Among the 22 strains collected from vegetable plants, 6 showed resistance to beta-lactam antibiotics, with 5 of them identified as ESBL producers. Resistome analysis indicated the presence of multidrug-resistant (MDR) strains containing multiple antibiotic resistance genes (ARGs). Importantly, no host-specific lineages were identified among the plant-isolated ESBL-producing E. coli (ESBL-Ec). Instead, these strains exhibited genetic and epidemiological connections with strains isolated from animals, humans, and the environment, suggesting transfer of ESBL-Ec between plants and other sources in rural Madagascar. These findings suggest that vegetable plants are contaminated as a result of human activities, posing a potential risk of human and animal exposure to antibiotic-resistant bacteria and genes.