Genomic characterization and multidrug resistance of Pseudomonas aeruginosa isolated from peregrine falcons in Saudi Arabia: A One Health perspective

Abstract

Background and aim: Pseudomonas aeruginosa is a multidrug-resistant (MDR) zoonotic pathogen increasingly implicated in infections in both humans and animals, including avian species. Raptors, particularly peregrine falcons, are vulnerable due to their exposure to diverse environments and intensive management practices. This study aimed to identify P. aeruginosa isolates from peregrine falcons in Saudi Arabia and to characterize their genomic features, phylogenetic relationships, and antimicrobial resistance (AMR) profiles using whole-genome sequencing (WGS).

Materials and methods: Eighty cloacal swabs were collected from adult peregrine falcons showing clinical signs of gastrointestinal distress and housed in falconry facilities in Eastern Saudi Arabia between 2022 and 2024. Samples underwent bacteriological culture, biochemical identification using the Vitek 2 system, and WGS of a representative isolate. Multilocus sequence typing (MLST) analysis, phylogenetic comparison, and resistance gene profiling were conducted using standard bioinformatic tools and the Comprehensive Antibiotic Resistance Database and PubMLST databases.

Results: Sixteen isolates (20%) were confirmed as P. aeruginosa through biochemical identification and BLAST analysis. One representative isolate underwent WGS and revealed a 6.0 Mbp genome with close phylogenetic relatedness (92% bootstrap) to a human-derived P. aeruginosa strain (CP050326), with a 4% genetic divergence. The MLST profile included allele numbers acsA (23), aroE (29), guaA (1), mutL (3), nuoD (1), ppsA (15), and trpE (9). Resistance genes identified included β-lactamase PAO-type (blaPAO), Class Dβ -lactamase OXA-type (variants 485 and 488) (blaOXA-485/488), aminoglycoside 3'-phosphotransferase type IIb (aph(3')-IIb), glutathione transferase FosA (fosA), and chloramphenicol acetyltransferase type B7 (catB7), indicating MDR to beta-lactams, aminoglycosides, fosfomycin, and chloramphenicol.

Conclusion: This is the first report of WGS-characterized, MDR P. aeruginosa in falcons from Saudi Arabia. The genomic similarity to human strains highlights the zoonotic potential and One Health implications. These findings emphasize the urgent need for integrated AMR surveillance in wildlife, especially in regions with widespread falconry practices. WGS offers valuable molecular insights for pathogen tracking, resistance monitoring, and epidemiological risk assessment. Broader genomic surveillance across bird species and regions is necessary to guide control strategies and reduce the risks of zoonotic transmission.

Keywords: One Health; Pseudomonas aeruginosa; antimicrobial resistance; falcons; phylogenetics; whole-genome sequencing.

Figure 1

Phylogenetic tree of Saudi Pseudomonas aeruginosa and reference Pseudomonas species. The P. aeruginosa falcon strain characterized in this study is indicated as “A.”