Genotypic characterization of carbapenem-resistant enterobacterales and their antibiotic susceptibility pattern in a tertiary care hospital

Background: Carbapenems have been considered as a robust antibiotic to treat extended-spectrum β-lactamases (ESBLs) in the past ten years. Carbapenems, among the β- lactams, are the most effective against gram-positive and gram-negative bacteria presenting a broad spectrum of antibacterial activity. Detection of carbapenemase-producing isolates by clinical microbiology laboratories is essential to provide targeted therapy, antimicrobial stewardship, and to update local antibiotic guidelines for clinicians. Objectives: To identify and characterize carbapenem-resistant Enterobacterales (CRE) by phenotypic and genotypic methods, and the antibiotic sensitivity patterns of CRE isolated from the different clinical samples. Methods: The samples were collected for a period of one year. Enterobacterales strains were identified through standard biochemical reactions and subjected to phenotypic screening for detection of carbapenemase, and confirmed with multiplex PCR. Antibiotic sensitivity patterns were also studied. Results: A total of 447 strains of Enterobacterales species were isolated from various clinical samples over a period of one year. Out of these, 38 (8.5%) of them showed decreased susceptibility to carbapenems including 12 Escherichia coli, 11 Klebsiella pneumonia, 1 Klebsiella oxytoca, 6 Proteus mirabilis, 2 Proteus vulgaris, and 6 Citrobacter freundii. 20 isolates of them showed the presence of carbapenemase genes in Multiplex PCR, isolates included NDM, IMP, OXA-48. Two strains showed simultaneous co-existence of two genes including NDM with OXA-48 in Klebsiella pneumonia, and NDM with IMP in Proteus mirabilis. No KPC genes were detected in our study. 97% of isolates showed sensitivity to fosfomycin (for urine samples only), 73.68% of them to tigecycline, 36.84% of them to polymyxin B, 50% to colistin, 26.31% to amikacin, 18.42% to aztreonam, 21.05% to piperacillin-tazobactam, and 10.52% to cefoperazone + sulbactam combinations. There were seven isolates of urine sample, and the sensitivity of nitrofurantoin to these isolates was 42.85%. Conclusion: The frequency of CRE was found to be low. E. coli and K. pneumoniae were the most common isolates. NDM was the commonest gene detected. Highest sensitivity was found with fosfomycin and tigecycline.