Background The coronavirus disease 2019 (COVID-19) pandemic has significantly influenced antimicrobial resistance dynamics, leading to a rise in multidrug resistance (MDR) rates in several bacterial species. Carbapenem-resistant Pseudomonas aeruginosa (CRPA) has emerged as a significant global public health concern due to the scarcity of effective treatment options. This study aimed to assess the frequency and molecular determinants of carbapenem resistance in clinical CRPA isolates before and after the COVID pandemic. Methods A total of 67 clinical isolates of CRPA were identified from 300 P. aeruginosa isolates collected from patients with various infections. Phenotypic characterization of CRPA isolates was performed using the broth microdilution method. Conventional PCR analysis was employed to detect the presence of integrons and 14 carbapenemase-encoding genes among CRPA isolates. Results Out of 300 P. aeruginosa isolates, 67 were identified as CRPA. Among these, 36 out of 200 isolates (18%) were obtained before the COVID-19 pandemic and 31/100 (31%) were collected after the pandemic. In this study, post-COVID CRPA isolates showed significantly higher carbapenem MICs (≥ 128 µg/mL; 90.3%) compared to pre-COVID isolates (16.7%) (P = 0.0001). MDR was identified in 43 of 67 (64.2%) CRPA isolates, more frequently post-COVID (71% vs. 58.3%) (P = 0.2). The blaAmpC gene was most prevalent (73.1%), especially in post-COVID isolates (93.5% vs. 55.6%). Class B Metallo-β-lactamase (MBL) genes were the most prevalent, with 89.5% of the studied isolates carrying one or more of the tested MBL genes. Following this, Class A and D carbapenemase genes were found to be present, though in lower proportions. The blaVIM−1 gene was the most common (55.2%), while blaKPC was the least detected (7.5%). Class 1 and 2 integrons were found in 59.7% and 19.4% of CRPA isolates, respectively. The majority of carbapenem resistance genes and class 1 integrons were significantly higher in the post-COVID period. Overall, 62.7% of isolates co-carried more than three resistance genes. These multi-gene isolates exhibited elevated carbapenem MICs and were significantly associated with intI1 presence (P = 0.0001 and 0.002, respectively). Conclusion Our findings reveal a high prevalence of carbapenemase-encoding genes and class 1 integrons in post-COVID CRPA clinical isolates, highlighting the evolving nature of antimicrobial resistance and the critical role of integrons in gene transfer. The emergence of strains co-producing multiple enzymes is particularly alarming. Further molecular understanding of resistance mechanisms of CRPA strains is essential for effective clinical management and the development of robust infection control measures.

Increased Carbapenem resistance and gene carriage in Pseudomonas aeruginosa clinical isolates after the COVID-19 pandemic in Egypt

期刊论文
发表日期：

2026年6月3日

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Soha S. Abdelrahim,
Shaimaa Zaki,
Dalia N. Kotb

摘要

Background

The coronavirus disease 2019 (COVID-19) pandemic has significantly influenced antimicrobial resistance dynamics, leading to a rise in multidrug resistance (MDR) rates in several bacterial species. Carbapenem-resistant Pseudomonas aeruginosa (CRPA) has emerged as a significant global public health concern due to the scarcity of effective treatment options. This study aimed to assess the frequency and molecular determinants of carbapenem resistance in clinical CRPA isolates before and after the COVID pandemic.

Methods

A total of 67 clinical isolates of CRPA were identified from 300 P. aeruginosa isolates collected from patients with various infections. Phenotypic characterization of CRPA isolates was performed using the broth microdilution method. Conventional PCR analysis was employed to detect the presence of integrons and 14 carbapenemase-encoding genes among CRPA isolates.

Results

Out of 300 P. aeruginosa isolates, 67 were identified as CRPA. Among these, 36 out of 200 isolates (18%) were obtained before the COVID-19 pandemic and 31/100 (31%) were collected after the pandemic. In this study, post-COVID CRPA isolates showed significantly higher carbapenem MICs (≥ 128 µg/mL; 90.3%) compared to pre-COVID isolates (16.7%) (P = 0.0001). MDR was identified in 43 of 67 (64.2%) CRPA isolates, more frequently post-COVID (71% vs. 58.3%) (P = 0.2). The bla_AmpC gene was most prevalent (73.1%), especially in post-COVID isolates (93.5% vs. 55.6%). Class B Metallo-β-lactamase (MBL) genes were the most prevalent, with 89.5% of the studied isolates carrying one or more of the tested MBL genes. Following this, Class A and D carbapenemase genes were found to be present, though in lower proportions. The bla_VIM−1 gene was the most common (55.2%), while bla_KPC was the least detected (7.5%). Class 1 and 2 integrons were found in 59.7% and 19.4% of CRPA isolates, respectively. The majority of carbapenem resistance genes and class 1 integrons were significantly higher in the post-COVID period. Overall, 62.7% of isolates co-carried more than three resistance genes. These multi-gene isolates exhibited elevated carbapenem MICs and were significantly associated with intI1 presence (P = 0.0001 and 0.002, respectively).

Conclusion

Our findings reveal a high prevalence of carbapenemase-encoding genes and class 1 integrons in post-COVID CRPA clinical isolates, highlighting the evolving nature of antimicrobial resistance and the critical role of integrons in gene transfer. The emergence of strains co-producing multiple enzymes is particularly alarming. Further molecular understanding of resistance mechanisms of CRPA strains is essential for effective clinical management and the development of robust infection control measures.