Comparative Analysis of Pseudomonas aeruginosa Isolated from Different Clinical Sources Using Whole Genome Sequencing and Bioinformatics

Yaaqop Khadem, Ansejam; Radwan Ali, Munim; Jaffar Saleem, Ali

doi:10.30491/jabr.2025.555514.1934

Comparative Analysis of Pseudomonas aeruginosa Isolated from Different Clinical Sources Using Whole Genome Sequencing and Bioinformatics

Document Type : Original Article

Authors

Ansejam Yaaqop Khadem ¹

Munim Radwan Ali ²

Ali Jaffar Saleem ¹

¹ College of Education for Pure Science, Diyala University, Diyala, Iraq

² College of Science, Mustansiriyah University, Baghdad, Iraq

10.30491/jabr.2025.555514.1934

Abstract

Introduction: This study aimed to evaluate the antibiotic resistance patterns, virulence characteristics, and genetic and epidemiological relationships of clinical isolates of Pseudomonas aeruginosa obtained from various sources in hospitals and clinics in the city of Baqubah, Iraq.
Materials and Methods: P. aeruginosa isolates (n = 80) were tested for antimicrobial susceptibility. Eight isolates, selected for diversity, underwent Whole Genome Sequencing (WGS). Analyses included the identification of Antibiotic Resistance Genes (ARGs), antimicrobial Resistance (AMR) Mechanism, Multi-Locus Sequence Typing (MLST), and Virulence Factors (VFs). A biofilm production assay was performed, and results were correlated with resistance patterns.
Results: High resistance rates were observed for the isolates, with the majority being multi-drug resistant: MDR 42.5%, XDR 27.5%, and PDR 10%. The highest resistance rates were recorded against Piperacillin (97.5%) and Polymyxin B (97.5%). Statistically significant resistance was also documented against Cefepime (70%, p = 0.0003) and Meropenem (36.3%, p = 0.013). 100% of the isolates were biofilm producers (68.75% strong, 31.25% moderate). Statistical analysis revealed a significant correlation between resistance patterns (MDR/XDR/PDR) and the capacity for strong biofilm formation (X squared = 18, p = 0.0004). Using MLST and WGS, the spread of high-risk clones was confirmed: ST-235 (in PA4 and PA18) and ST-244 (in PA7 and PA40). A substantial accumulation of ARGs was identified. Isolate PA 56 (ST-654) carried the most dangerous combination: bla_NDM-1, bla_KPC-2 (carbapenemases), and rmtF (high-level aminoglycoside resistance). The core set of essential VFs (such as the Type III Secretion System (TTSS), Exotoxin A, and Quorum Sensing) was conserved across all eight isolates.
Conclusions: Findings confirm widespread Multidrug-Resistant P. aeruginosa in Iraqi hospitals, driven by high-risk international clones and acquired carbapenemase genes. The combination of Mobile Genetic Elements (MGEs) in resistance transfer and strong biofilm formation presents a major therapeutic and epidemiological challenge, necessitating strict genomic surveillance and infection control. However, these findings are based on a local, small-scale comparison.

Keywords

Pseudomonas aeruginosa

Whole Genome Sequencing

Comparative Genomics

Antimicrobial Resistance

Virulence Factors