تكامل الأنماط الظاهرية والجزيئية والحاسوبية لدراسة مقاومة المضادات الحيوية في العزلات السريرية لبكتيريا الزائفة الزنجارية

Integration of Phenotypic, Molecular and Computational Approaches for the Study of Antibiotic Resistance in Pseudomonas aeruginosa Clinical Isolates

Abstract

Pseudomonas aeruginosa is a complicated pathogen that causes infections with high mortality rates. Because of its ability acquired resistance to many first-line antibiotics, this study was designed to explore the distribution and association of carbapenemase , ESBL and PMQR genotype pattern (VIM, NDM, OXA, CTX, QNR-A, and QNR-B) with antibiotic resistance in local clinical Pseudomonas aeruginosa isolates.
A total of 240 samples (100 urines, 100 burn swabs, and 40 wound swabs) were included in this study. Among these Only 43 isolates of Pseudomonas aeruginosa were collected from different specimens between November 2024 to May 2025. The isolates included 29 from burns, 5 from wounds, and 9 from urinary tract infections (UTIs). Identification of the isolates was carried out using microscopically and cultural characterization using MacConkey agar, blood agar and cetrimide agar. identification was carried out by the VITEK_2_Compact system.
To assess the frequency of antibiotic resistance in P. aeruginosa (MDR and XDR), the antibiotic susceptibility test was done by the VITEK_2_Compact system. The test included two groups of antibiotics, totaling seven agents. The antibiotic susceptibility of Pseudomonas aeruginosa were analyzed according to the type of infection, whether UTIs, burns, or wounds. For Impenem, the highest percentage of isolates resistant to this antibiotic was those isolated from burns, at 93.1.
Regarding Meropenem, the highest percentage of resistant isolated from burns, with 86.2%.
As for Levofloxacin, Ciprofloxacin, Ofloxacin, and Norfloxacin, the highest percentage of isolates resistant to this antibiotic was those isolated from burns, at 62.1%, according to Nalidixic acid, all Pseudomonas aeruginosa Isolates Were Resistant to Nalidixic acid.
Gene Detection analysis was perform for six genes (OXA,VIM,CTX,NDM,QNR-A and QNR-B) across different infection type. (A) UTI Cases :The OXA, QNR_A, QNR_B, and VIM genes were 100% detected in UTI cases; the CTX gene was detected at 55% in those cases, while the NDM gene was detected only in 11.2% of UTI cases.
(B) BURN cases, all genes of P. aeruginosa showed high gene detection in burn cases, except the NDM gene, which was not detected in 90% of those samples (only 10% were positively detected), The highest percentage of genes that detected was QNR-B (97.7%).
(C) WOUND cases: The oxa, qnr_a, qnr_b, and vim genes were 100% detected in wound cases, the CTX and NDM genes were detected at 80% and 60%, respectively, in those cases.
Genetic sequence analysis revealed the spread of several mutations, among Pseudomonas aeruginosa Isolates. The CTX gene exhibited highest number of mutations followed by the OXA, VIM, and QNR-A genes in succession, while the NDM gene was the least prevalent in terms of the number of mutations.
Also, when studying mutations through a bioinformatics study, there were many missense and silent mutations, across the examined genes. The effect of these mutations on the resulting protein was studied through molecular docking.
In conclusion, the results of this study revealed a considerable prevalence of carbapenemase, ESBL and PMQR genes in Pseudomonas aeruginosa isolated from Al-Diwanyih hospitals. In addition, it was shown that the vast majority of carbapenemase Pseudomonas aeruginosa isolates were classified as XDR. Therefore, carbapenemase screening should be implemented for routine laboratory practice in Iraqi hospitals. In addition, infection control measures are needed to prevent further spreading of these organisms.