Genetic determinants of virulence and extensive drug resistance in Pseudomonas aeruginosa PPA14 isolated from eggplant rhizosphere

Abstract

Pseudomonas aeruginosa is one of the Priority Level I critical pathogens that are least sensitive to antibiotics and can cause fatal hospital-acquired infections. This bacterium is predominantly present in the agricultural ecosystem. However, there are very limited studies on health threats associated with P. aeruginosa strains flourishing in edible plants. Previously, we isolated and characterized 18 P. aeruginosa strains from vegetable plants directly harvested from the farms. In the current work, it has been hypothesized that plant-associated P. aeruginosa harbors genetic determinants for virulence and resistance. To test this hypothesis, in vitro resistome profiles of the plant-associated P. aeruginosa strains were assessed based on the Kirby-Bauer disk diffusion method. Hierarchical clustering analysis was done to identify the plant-associated strains that are phenotypically similar to clinical isolates. An eggplant-associated strain, PPA14, that exhibited high virulence and extensive in vitro resistance against eight antibiotic classes was selected for complete genome analyses. The PPA14 genome was sequenced using the Solexa-Illumina and Oxford-Nanopore platforms, assembled, and annotated. The presence of virulence-related and antibiotic resistance (ABR) genes were predicted using the ABRicate tool and validated based on standard reference databases such as VFDB, NCBI AMRFinderPlus, MEGARes, CARD, and ResFinder. IslandViewer4 tool was used to predict the genes acquired through horizontal gene transfer. Additionally, comparative analyses of all the plant-associated and environmental P. aeruginosa genomes characterized so far were done using the Roary tool. The PPA14 genome size was 6.72 Mbp, encoding 6315 open reading frames. The genome harbored 49 ABR genes, including those coding for multiple families of efflux pumps that collectively confer resistance against 11 antibiotic classes. In addition, we detected 225 virulence-related genes, 83 genomic islands, and 235 unique genes in the PPA14 genome. Over 4% of the PPA14 genome is devoted to conferring virulence and extensive drug resistance. Our report highlights the health threat associated with an eggplant-associated P. aeruginosa.