Critical priority third-generation cephalosporin-resistant Escherichia coli in antibiotic- free retail meat

Abstract Contamination of food by critical priority third-generation cephalosporin-resistant Escherichia coli poses a significant risk to consumers, potentially leading to foodborne illnesses, silent colonization, and/or antibiotic resistance dissemination. In this study, we report the microbiological and genomic features of ESβL/pAmpC-producing E. coli in conventional (CN) and antibiotic-free (AF) retail meat samples sold in different markets in São Paulo city. Nine representative chicken isolates were investigated by whole-genome sequencing. E. coli ST38 (CTX-M-2), ST350 (CMY-2), ST2179 (CTX-M-8), and ST2040 (CTX-M-55) clones were identified in meat samples from CN, and E. coli clones ST57 (CMY-2), ST117 (CTX-M-55), ST443 (CTX-M-2), ST15579 (CTX-M-8), and ST3258 (CTX-M-55) from AF farming systems. Resistomes to other clinically relevant antibiotics, hazardous heavy metals, disinfectants, and herbicides, were also predicted; whereas a broad virulome was detected in E. coli ST2040 and ST350. High-risk lineages ST38 and ST117 were identified in frozen meat from CN and AF, respectively, whereas phylogenetic analysis revealed relationship with poultry clones previously identified in the United States of America and Brazil. Our findings add new perspectives to current epidemiological knowledge regarding the occurrence of ESβL/pAmpC-producing E. coli in the meat industry, reinforcing the need for genomic surveillance of WHO critical priority pathogens in different rearing systems.