Molecular detection of plasmid mediated bla(TEM), bla(CTX−M,)and bla(SHV) genes in Extended Spectrum β-Lactamase (ESBL) Escherichia coli from clinical samples

BACKGROUND: Extended spectrum β-lactamases (ESBLs) are a group of beta-lactamase enzymes that confer resistance to the oxyimino-cephalosporins and monobactams. The emergence of ESBL - producing genes possesses a serious threat for treating infections since it is associated with multi-drug resistance. This study was focused to identify the ESBLs producing genes from Escherichia coli isolates from clinical samples from a referral-level tertiary care hospital in Lalitpur. METHODS: This was a cross-sectional study conducted from September 2018 to April 2020 at the Microbiology Laboratory of Nepal Mediciti Hospital. Clinical samples were processed, and culture isolates were identified and characterized following standard microbiological techniques. An antibiotic susceptibility test was performed by a modified Kirby-Bauer disc diffusion method as recommended by Clinical and Laboratory Standard Institute guidelines.Extended -spectrum beta-lactamases were phenotypically confirmed by the combined disc method. The ESBL-producing genes bla(TEM), bla(CTX−M) and bla(SHV) were confirmed by PCR. RESULTS: Of the 1449 total E. coli isolates, 22.29% (323/1449) isolates were multi-drug resistant (MDR). Among the total MDR E. coli isolates, 66.56% (215/323) were ESBL producers. The maximum number of ESBL E. coli was isolated from urine 90.23% (194) followed by sputum 5.58% (12), swab 2.32% (5), pus 0.93% (2), and blood 0.93% (2). The antibiotic susceptibility pattern of ESBL E. coli producers showed the highest sensitivity toward tigecycline (100%) followed by polymyxin b, colistin and meropenem. Out of 215 phenotypically confirmed ESBL E. coli, only 86.51% (186) isolates were found to be positive by PCR for either bla(TEM) or bla(CTX−M) genes. Among the ESBL genotypes, the most common were bla(TEM) 63.4% (118) followed by bla(CTX−M) 36.6% (68). CONCLUSION: The emergence of MDR and ESBL – producing E. coli isolates with high antibiotic – resistant rates to commonly used antibiotics and increased predominance of major gene types bla(TEM) is a serious concern to the clinicians and microbiologists. Periodic monitoring of antibiotic susceptibility and associated genes would help guide the rationale use of antibiotics for treating the predominant pathogen E. coli in the hospitals and healthcare facilities of the communities. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12941-023-00584-0.