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Life sciences · Journal article
Frontiers in Microbiology · September 15, 2026
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Introduction Brazil is the world’s largest exporter of chicken meat, and poultry products are recognized as important reservoirs of foodborne pathogens. Salmonella enterica serovar Minnesota has emerged as the predominant serovar in the poultry industry and is frequently associated with multidrug-resistant strains carrying multiple antimicrobial resistance genes. In addition, Escherichia coli and ESKAPE pathogens have been increasingly isolated from poultry products worldwide, representing a growing public health concern due to their antimicrobial resistance and dissemination potential. This study aimed to characterize the antimicrobial resistance profiles of Salmonella spp., E. coli, and ESKAPE pathogens isolated from chicken carcasses using phenotypic and genomic approaches. Methods The study was conducted in a poultry slaughterhouse inspected by the Brazilian Ministry of Agriculture that supplies both the domestic and international markets. Thirty carcasses with visible gastrointestinal contamination and 30 without visible contamination were sampled. To investigate the epidemiology of ESBL-producing strains, representative isolates with distinct resistance profiles were subjected to whole-genome sequencing ( n = 9). Results A total of 48 Salmonella spp. and 99 E. coli isolates were recovered. Among the ESKAPE pathogens, Klebsiella pneumoniae ( n = 68), Enterobacter spp. ( n = 53), Pseudomonas aeruginosa ( n = 59), Acinetobacter baumannii ( n = 14), and Staphylococcus aureus ( n = 10) were also isolated. Salmonella Minnesota was the predominant serovar. Members of the Enterobacterales exhibited high frequencies of multidrug resistance and extended-spectrum β-lactamase (ESBL) production, detected in 52.1% of Salmonella spp., 56.6% of E. coli, and 13.2% of K. pneumoniae isolates. Genomic analysis identified clinically relevant resistance determinants, including bla CMY-2 in Salmonella spp. and ESBL-associated genes such as bla CTX-M-15 and bla CTX-M-55 in E. coli and K. pneumoniae. MLST identified internationally disseminated high-risk clones, including E. coli ST38 and K. pneumoniae ST307, while SNP analysis demonstrated close genetic relatedness to isolates recovered from human infections. Discussion These findings highlight the potential role of chicken products as reservoirs of clinically relevant multidrug-resistant bacteria and reinforce the importance of continuous antimicrobial resistance surveillance throughout the poultry production chain.