Comparative genomics insights into Pseudomonas rhodesiae: environmental distribution, resistance determinants, virulence factors, and evolutionary implications

Pseudomonas rhodesiae is a member of the Pseudomonas genus that is ecologically adaptable but has received little research. Despite its presence in clinical, environmental, agricultural, and aquaculture contexts, there is just a small amount of genomic information available for this species. We sequenced the genome of P. rhodesiae strain SK22, which was identified after a mortality outbreak in Dicentrarchus labrax (European seabass) farming in Turkey, and conducted a thorough comparison with 32 other publicly accessible P. rhodesiae genomes sourced from different environments. Whole-genome-based core genome phylogeny and Average Nucleotide Identity (ANI) identified two misclassified strains, 26B3 and CIP104664, that grouped with P. quebecensis (> 99% ANI). After eliminating these genomes, comparative studies revealed significant strain-specific variability in AMR determinants, virulence-associated genes, integrons, prophage content, and secretion systems. Class 1 integron was found only in one mineral-water isolate, whereas environmental isolates—particularly those from aquaculture, agricultural systems, and urban areas—had the largest AMR gene loads, suggesting their potential involvement in the dissemination of resistance and opportunistic pathogenicity. All genomes expressed key virulence characteristics such as T1SS-T6SS secretion systems, type IV pili, flagella, and siderophore-related genes, but supplementary virulence factors differed significantly. Prophage profiling found intact phage regions throughout all genomes, with agricultural and aquaculture isolates having abnormally large prophage loads, indicating phage-mediated adaptation and gene acquisition. This study provides the first high-resolution genomic framework for P. rhodesiae, identifies incorrectly classified genomes within public databases, and highlights the species’ extensive genomic plasticity. The combination of diverse AMR determinants, mobile genetic elements, and virulence factors suggests that P. rhodesiae has the potential to function not only as an environmental saprophyte but also as an opportunistic pathogen capable of disseminating resistance genes across ecosystems. These findings highlight the importance of increased surveillance and functional validation in understanding the ecological and clinical roles of this emerging species.