The genus Pseudomonas comprises more than 300 valid species, most of which are non-pathogenic, while some are opportunistic pathogens. P. aeruginosa has the greatest clinical relevance, causing respiratory infections and severe pneumonia with bacteremia. Due to the emergence of multidrug-resistant clones causing hospital outbreaks, this species is considered a critical priority for the development of new treatments by the WHO. One strategy to attenuate infections caused by multidrug-resistant clones is the inhibition of virulence factors (VFs) that impact bacterial infectivity and host damage (Liao et al., 2022). Several VFs have already been described in P. aeruginosa and may be used as targets for these treatments. The use of VFs, predominantly found in pathogens, may reduce resistance dissemination, as it does not affect the viability of most beneficial microbiota bacteria, unlike conventional antibiotics that target both pathogens and microbiota (Totsika, 2017).

To evaluate the distribution of VFs in genomes of clinical and non-clinical Pseudomonas isolates through in silico analyses, prioritizing potential targets common to most clinical isolates.

Genomic data from more than 800 isolates were retrieved from RefSeq, and isolation source was determined based on BioSample information. Orthofinder 2 software was used to predict phylogenetic relationships and gene orthology among genomes. A total of 368 experimentally confirmed VFs in the reference strain P. aeruginosa PAO1 were retrieved from the PseudomonasGenomeDB database. The prevalence of these VFs in recovered genomes was assessed using scripts developed in Python.

Among the VFs, 347 were found in more than 90% of the 314 clinical isolates. Of these, 103 were also distributed in less than 50% of non-clinical isolates. This group of VFs of interest includes systems whose potential as targets for new antimicrobials is already under investigation, such as the type III secretion system (Jiang et al., 2024), as well as others such as the type VI secretion system (Sana et al., 2015), alpha-2-macroglobulins (Wong and Dessen, 2014), and others that may still be explored.

This study identified 103 VFs prevalent in clinical Pseudomonas isolates that may serve as targets for the treatment of multidrug-resistant clones.