Antimicrobial resistance in functional fruits-associated lactic acid bacteria within agri-food systems

Antimicrobial resistance (AMR) in fermented food-origin Lactic Acid Bacteria (LAB) has raised significant concern for food safety. However, AMR in the LAB of unfermented functional fruits consumed raw or minimally processed remains understudied. Here, two hundred sixty samples of unfermented functional fruits (pineapple, wood apple, banana, Indian jujube, guava, papaya, orange, pomegranate, dried grapes) were collected between May 2023 and December 2025 from different agri-food systems (agricultural fields, n = 43; rural markets, n = 38; urban markets, n = 43). Among the presumptive LAB recovered as epiphytes or endophytes from the collected samples, a total of 124 LAB isolates were further identified and confirmed at genus ( Lactobacillus sp., n = 37 and Leuconostoc sp., n = 87) level using a 16S rRNA-gene-targeted genus-specific-PCR followed by DNA sequencing. All Lactobacillus sp. and Leuconostoc sp. were further tested to determine their susceptibility to 23 antimicrobials commonly used in human/veterinary medicine or in animal/plant agriculture by the disk diffusion method following the Clinical and Laboratory Standards Institute and European Food Safety Authority guidelines. In vitro antimicrobial susceptibility testing revealed that all Lactobacillus / Leuconostoc sp. exhibited a wide range of resistance (9-96%) to drugs of human/veterinary importance, irrespective of their epiphytic/endophytic or agri-food system status. Of great concern, all Lactobacillus / Leuconostoc sp. were multidrug-resistant to at least one drug ranked by WHO as a highest-priority critically important/critically important/highly important antimicrobial. Overall, our study represents an important contribution to providing a large data set to identify AMR in unfermented functional fruits-origin Lactobacillus or Leuconostoc sp. with their plant-association lifestyle or agri-food system background.