Phenotypic versus molecular assays for detecting carbapenemase-producing Enterobacterales from urinary tract infections

Background: Carbapenem-resistant Enterobacterales (CRE) have been identified as a public health problem. Treatment options for CRE are limited as they are mostly resistant to βeta-lactams, aminoglycosides, and fluoroquinolones as well as carbapenems. The present study aims to evaluate the performance of three phenotypic methods compared to a molecular-based technique for carbapenemase detection in Enterobacterales and determining their applicability in clinical and epidemiological settings. Methods: A total of 1,158 Enterobacterales were isolated from the urine samples in the microbiology laboratory of Alexandria main university hospital during the period from April 2020 to April 2021. Fifty randomly selected (39 Klebsiella and 11 E. coli) Enterobacterales were screened for carbapenem resistance by disc diffusion method. They were subjected to 3 phenotypic tests which are: Carba NP method, Modified carbapenem inactivation method (m CIM) and EDTA- modified carbapenem inactivation method (e CIM). Detection of 5 carbapenemase genes (blaKPC, blaIMP, blaVIM, blaOXA-48 and blaNDM-1) was performed using real time PCR. Results: CRE represented 33% of Enterobacterales isolates. Twenty-six cases (52%) were males and 94% of the cases were above 40 years old. Carba NP test was positive in 43/50 (86%) of the selected isolates, m CIM was positive in 35/50 (70%) and e CIM was positive in 30/50 (60%). The most common carbapenemase gene detected was blaNDM-1 (94%), followed by blaOXA-48 gene (72%) and blaVIM gene (24%). The blaKPC gene and blaIMP gene were not detected. Coexistence of the blaOXA-48 and the blaNDM-1 genes was detected in 48% isolates, while the blaNDM-1, the blaOXA-48 and the blaVIM genes were found in 22% isolates. The sensitivity of Carba NP, m CIM and e CIM was 87.5%, 72.9%, and 85.7% respectively. Conclusion: The study highlights the necessity of early detection of CRE. Carba NP test assists in the rapid identification of carbapenemase production. However, the genotypic test remains the gold standard for detection of CRE.