Multidrug-Resistant Escherichia coli Harboring ESBL and MCR-1 Genes in Raw Milk Cheese and Chicken Carcasses in Egypt: Characterization and Control Using Algal Extracts.

Objectives: This study investigates the occurrence and characteristics of extended-spectrum β-lactamase (ESBL)-producing and polymyxin-resistant Escherichia coli isolated from raw milk cheese and chicken carcasses in Egypt. In addition, the study evaluates the antibacterial activity of various algal extracts from Padina pavonica and Polycladia myrica, collected from the Red Sea, Egypt, against selected virulent and multidrug-resistant E. coli isolates. Methods: A total of 200 samples, comprising raw milk cheese samples (n = 100) and chicken carcass samples (n = 100), were examined for the presence of E. coli. Antimicrobial susceptibility testing was performed for all isolates using the disk diffusion and broth microdilution techniques. Phenotypic confirmation of various resistance traits was conducted to confirm resistance patterns. PCR screening was performed for various resistance genes and virulence-associated genes. Phylogenetic grouping analysis of the E. coli isolates examined was also performed. Two algal extracts of P. pavonica and P. myrica were screened using gas chromatography-mass spectrometry and evaluated against our panel of virulent MDR foodborne E. coli isolates using the resazurin-based microtiter dilution method. Results: Among the 200 food samples, E. coli was recovered from 14% of samples and confirmed by using phoA gene detection. Of the recovered isolates, 64.3% were multidrug-resistant (MDR), with the majority originating from chicken carcasses (88.9%). Most isolates (92.9%) carried ≥3 virulence genes, with iss (100%), iutA (92.9%), and eaeA (89.3%) being the predominant determinants. Potential EPEC profiles were the most frequently detected (60.7%), followed by EHEC profiles (28.6%), whereas potential STEC/non-EHEC hybrid and ExPEC profiles were detected in 7.1% and 3.6% of isolates, respectively. The blaCTX-M gene predominated among ESBL determinants (96.4%), while blaSHV, blaCMY-2, and mcr-1 were also detected. Notably, mcr-1 was identified in 82.1% of isolates, with frequent co-occurrence of mcr-1 and ESBL genes. Phylogenetic analysis revealed that most isolates belonged to group B1 (85.7%), whereas groups D and B2 accounted for 10.7% and 3.5%, respectively. In vitro antibacterial assays demonstrated that the P. pavonica methanol and ethyl acetate extracts and the P. myrica ethyl acetate extract exhibited inhibitory activity against MDR E. coli, with minimum inhibitory concentrations (MICs) ranging from 2.5 to 10 mg/mL. Overall, the P. myrica extract showed stronger antibacterial activity (MICs, 2.5-5 mg/mL) than the P. pavonica extracts (MICs, 5-10 mg/mL), highlighting their potential as natural antibacterial agents against MDR E. coli. Conclusions: These findings raise important public health concerns, as contaminated food products can act as reservoirs for the dissemination of multidrug-resistant (MDR) E coli, thereby increasing the risk of human infections ranging from mild gastrointestinal illnesses to severe, potentially life-threatening diseases. In addition, the present findings demonstrate the promising antibacterial activity of methanolic and ethyl acetate extracts of P. myrica and P. pavonica against MDR E. coli isolates, supporting their potential as sources of natural antibacterial compounds and warranting further investigation of their efficacy, mechanisms of action, and active constituents.