Phenotypic and genotypic characterization of extended spectrum beta-lactamase producing E. coli harboring carbapenem and colistin resistant genes from poultry farms in Egypt

Abstract

Background: Extended spectrum beta-lactamase (ESBL) producing E. coli is implicated in high rate of human infections globally. Uprising of carbapenem and colistin resistance further hinders the treatment potentials of these infections. This study was conducted to assess the phenotypic and genotypic characterization of carbapenem and colistin resistance between ESBL producing E. coli isolates obtained from chicken respiratory tract in El-Sharkia government, Egypt. Methods: Lung samples, 250, from 50 chicken farms were processed for isolation, identification and serotyping of E. coli. Antimicrobial resistance was detected by disk diffusion. ESBL phenotypic occurrence was also examined by double disc synergy. PCR/sequencing were used to investigate ESBL (β-lactamase (bla)- TEM, bla SHV, and bla CTX-M ), colistin (mcr-1), and carbapenem (bla NDM, bla VIM and bla KPC) resistant genes. Results: The results displayed that 140/250 (56%) were detected to be E. coli. All E. coli isolates had an elevated multi-antimicrobial resistance (MAR) index value (>0.2) and 65.7 % were proven to produce ESBL. Among 92 ESBL phenotypes 55 (59.7%), 32 (34.7%), 18 (19.6%), and 37 (40.2%) isolates harbor bla TEM-3, bla SHV-4, bla CTX-M-1, bla CTX-M-14 respectively. The bla NDM-1 gene was detected in all 40/50 carbapenem resistant phenotypes that represents 28.5% of all E. coli and 43.4% of ESBL isolates. The bla VIM and bla KPC were not found in any E. coli isolate. In addition, mobilized colistin resistance (mcr)-1 gene exhibited high prevalence; 64 (69.5%) among ESBL isolates. Conclusion: The reported high frequency of ESBL-producers especially carbapenem and colistin-resistant E. coli would account for a public health threat in the society.