Phenotypic and Genotypic Antibiotic Resistance in Escherichia coli from Artisanal Minas Frescal Cheese in the Federal District, Brazil ^†

Introduction: Artisanal Minas Frescal cheese, often produced under suboptimal hygienic/sanitary conditions, may harbor potentially pathogenic and antibiotic-resistant microorganisms. Therefore, this study aims to characterize the phenotypic and genotypic profiles of antibiotic resistance in 62 Escherichia coli isolates obtained from 10 artisanal Minas Frescal cheese samples from the Federal District (Brazil). Methodology: Antibiotic susceptibility was assessed using the disk diffusion method (Kirby–Bauer), and resistance genes (sul1/sul2, tetA/tetB, blaCTX-M/blaTEM/blaSHV, and cat1/clmA) were detected by polymerase chain reaction (PCR). Results: Phenotypic resistance was highest for sulfonamides (90.54%) and tetracyclines (33.78%). Overall, 98.38% of isolates were resistant to at least one antibiotic class, and 45.16% were multidrug-resistant (MDR). Genotypically, 74.19% carried sul genes (mainly sul1, 72.58%), 45.16% harbored tetA/tetB, and 41.93% possessed bla genes (notably blaCTX-M, 36.49%). A phenotype–genotype discordance was observed for β-lactams: 43.90% of bla-positive isolates were phenotypically susceptible. Genes linked to phenicol resistance (cat1/clmA) were detected in 33.87%, although only one strain showed chloramphenicol resistance. Conclusions: The high prevalence of E. coli carrying resistance genes, including “silent genes” in phenotypically susceptible strains, poses a public health risk due to the potential for dissemination through the food chain. These findings underscore the need for stricter oversight of artisanal cheese production and marketing, adherence to hygienic and sanitary best practices, and the integration of antimicrobial resistance monitoring.