Emergence of carbapenem resistant gram-negative pathogens with high rate of colistin resistance in Egypt: A cross sectional study to assess resistance trends during the COVID-19 pandemic

• Published in: Journal of Genetic Engineering and Biotechnology Vol. 22; no. 1; p. 100351
• Main Authors: Afify, Fatma A., Shata, Ahmed H., Aboelnaga, Nirmeen, Osama, Dina, Elsayed, Salma W., Saif, Nehal A., Mouftah, Shaimaa F., Shawky, Sherine M., Mohamed, Ahmed A., Loay, Omar, Elhadidy, Mohamed
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier Inc 01.03.2024; Elsevier
• Subjects: Acinetobacter baumannii; antibiotic resistance; beta-lactamase; biotechnology; Carbapenem resistance; carbapenems; class; Class 1 integron; colistin; Colistin resistance; COVID-19 infection; cross-sectional studies; Egypt; genes; Gram negative bacteria; health services; Klebsiella pneumoniae; monitoring; Multidrug resistance; multiple drug resistance; phenotype; Pseudomonas aeruginosa; quinolones; species; Egypt; Class 1 integron; Carbapenem resistance; Colistin resistance; Multidrug resistance; Gram negative bacteria
• ISSN: 1687-157X; 2090-5920
• DOI: 10.1016/j.jgeb.2024.100351

The current study investigated the temporal phenotypic and genotypic antimicrobial resistance (AMR) trends among multi-drug resistant and carbapenem-resistant Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa recovered from Egyptian clinical settings between 2020 and 2021. Bacterial identification and antimicrobial sensitivity of 111 clinical isolates against a panel of antibiotics were performed. Molecular screening for antibiotic resistance determinants along with integrons and associated gene cassettes was implemented. An alarming rate (98.2%) of these isolates were found to be phenotypically resistant to carbapenem. Although 23.9 % K. pneumoniae isolates were phenotypically resistant to colistin, no mobile colistin resistance (mcr) genes were detected. Among carbapenem-resistant isolates, blaNDM and blaOXA-48-like were the most prevalent genetic determinants and were significantly overrepresented among K. pneumoniae. Furthermore, 84.78% of K. pneumoniae isolates co-produced these two carbapenemase genes. The plasmid-mediated quinolone resistance genes (qnrS and qnrB) were detected among the bacterial species and were significantly more prevalent among K. pneumoniae. Moreover, Class 1 integron was detected in 82% of the bacterial isolates. This study alarmingly reveals elevated resistance to last-resort antibiotics such as carbapenems as well as colistin which impose a considerable burden in the health care settings in Egypt. Our future work will implement high throughput sequencing-based antimicrobial resistance surveillance analysis for characterization of novel AMR determinants. This information could be applied as a step forward to establish a robust antibiotic stewardship program in Egyptian clinical settings, thereby addressing the rising challenges of AMR.