Genomic Characterization of Virulence and Resistance Genes in Bacterial Isolates from Lettuce Irrigation Water

¹ Division of Food Science and Technology, Faculty of Engineering and Technology, IPB University, Darmaga Campus, Bogor 16680, Indonesia
² South-East Asia Food and Agricultural Science and Technology (SEAFAST) Center, IPB University, Darmaga Campus, Bogor 16680, Indonesia

^* Corresponding author: This email address is being protected from spambots. You need JavaScript enabled to view it.

Abstract

Antibiotic resistance and virulence genes in the environment pose significant risk to food safety, particularly in fresh produce that is commonly consumed raw, such as lettuce. Lettuce agriculture is highly dependent on irrigation water, which can serve as a crucial reservoir for bacteria that transmit antibiotic resistance and virulence factors. Tetracycline is among the most commonly detected antibiotics in agriculture. This has an impact on the presence of bacteria that carry resistance and virulence genes in water systems. This study aimed to characterize the genomic profile, including virulence, antibiotic resistance genes, and plasmids of bacteria isolated from lettuce irrigation water. This study consists of two parts: part 1 tests the resistance of 19 bacterial isolates to tetracycline using the Kirby-Bauer method and part 2 confirms the bacterial isolates using real-time PCR. The second step is characterize the genome using Whole-genome sequencing (WGS) using the GenoLab M platform (GeneMind), followed by bioinformatics analysis. Among the 19 isolates tested, 4 (21.05%) were resistant, 1 (5.26%) exhibited intermediate resistance, and 14 (73.68%) were susceptible to tetracycline. All isolates tested negative for the invA gene, indicating the absence of Salmonella enteric pathogenic strains. WGS-based phylogeny identified H.1.2 as Pseudomonas peradeniyensis, harboring 45 virulence-associated and 4 stress-related genes. Resistance profiling revealed the mexE (abriTAMR) and yajC (CARD) genes. However, no plasmids were detected in H.1.2 isolate based on PlasmidFinder. This indicates that the isolate H.1.2 in this study is not hazardous to humans.