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Article

Antimicrobial Resistance in Chicken Meat: Comparing Salmonella, Escherichia coli, and Enterococcus from Conventional and Antibiotic-Free Productions

by
Camila Koutsodontis Cerqueira-Cézar
1,
Aryele Nunes da Cruz Encide Sampaio
1,
Evelyn Fernanda Flores Caron
1,
Thaisy Tino Dellaqua
2,
Lucas Franco Miranda Ribeiro
1,
Leonardo Ereno Tadielo
1,
José Carlos de Figueiredo Pantoja
1,
Gustavo Guimarães Fernandes Viana
1,
Gabriel Augusto Marques Rossi
3,
Carlo Spanu
4,
Fábio Sossai Possebon
1,5,† and
Juliano Gonçalves Pereira
1,*,†
1
Department of Animal Production and Preventive Veterinary Medicine, School of Veterinary Medicine and Animal Science (FMVZ), São Paulo State University (UNESP), Prof. Dr. Walter Mauricio Correa Street, Botucatu 18618-681, SP, Brazil
2
Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu 18618-970, SP, Brazil
3
Department of Veterinary Medicine, University Vila Velha (UVV), Av. Comissário José Dantas de Melo, n.21, Vila Velha 29102-920, ES, Brazil
4
Department of Veterinary Medicine, University of Sassari (UNISS), 07100 Sassari, Italy
5
Institute for Biotechnology, São Paulo State University (UNESP), Tecomarias av, Botucatu 18607-440, SP, Brazil
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Microorganisms 2025, 13(10), 2227; https://doi.org/10.3390/microorganisms13102227
Submission received: 4 September 2025 / Revised: 19 September 2025 / Accepted: 22 September 2025 / Published: 23 September 2025
(This article belongs to the Special Issue Epidemiology, Prevention and Control of Foodborne Microbial Pathogens, Second Edition)
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Abstract

Chicken meat production is a critical component of the global protein supply, significantly influenced by rearing advancements, including the use of antimicrobial agents. However, the pervasive use of antibiotics has raised concerns regarding the occurrence of antimicrobial resistance (AMR). This study examined the prevalence and AMR profiles of Salmonella spp., Escherichia coli, and Enterococcus spp. in chicken meat from conventional and antibiotic-free (ABF) production chains. A total of 284 samples were analyzed for Salmonella spp. and E. coli, while 164 samples were tested for Enterococcus spp. From that, 143 were from conventional production chains and 141 were from ABF chains. The results indicated a 10.9% prevalence of Salmonella spp., 22.1% for E. coli, and 93.9% for Enterococcus spp. Regarding production chains, the conventional chain had 18.2% of the isolates for Salmonella spp., 20.3% for E. coli, and 91.6% for Enterococcus spp., while the ABF chain had 3.5% of the isolates for Salmonella spp., 24.1% for E. coli, and 96.3% for Enterococcus spp. In terms of AMR, 86.1% of the Salmonella spp. isolates that underwent the disk diffusion test were resistant to at least one antibiotic tested, 95.1% of E. coli, and 88.4% of Enterococcus spp. Notably, carbapenem resistance was detected in Salmonella spp., with 2.3% of isolates being resistant to imipenem, while resistance to vancomycin and linezolid was detected in Enterococcus spp., all of which are critically important antimicrobials. Comparisons between these production chains revealed significant differences in antibiotic resistance patterns in Salmonella spp. for two antibiotics, amoxicillin/clavulanic acid and nitrofurantoin, while no differences were observed in E. coli. For Enterococcus spp., resistance varied for three antibiotics: streptomycin, penicillin, and tetracycline. For all other antibiotics tested, the resistance profiles were consistent across both conventional and ABF production chains. Multidrug resistance (MDR) was observed in 90.7% of Salmonella spp. isolates, 42.9% of E. coli isolates, and 12.0% of Enterococcus spp. isolates. Statistically significant differences were noted in MDR prevalence between production chains, with conventional production systems exhibiting higher levels of MDR isolates compared to ABF systems. These findings underscore the need for targeted AMR control strategies that consider the complexity of resistance dynamics across production systems.
Keywords: foodborne pathogens; food safety; multidrug resistance; poultry; one health foodborne pathogens; food safety; multidrug resistance; poultry; one health

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MDPI and ACS Style

Cerqueira-Cézar, C.K.; Sampaio, A.N.d.C.E.; Caron, E.F.F.; Dellaqua, T.T.; Ribeiro, L.F.M.; Tadielo, L.E.; Pantoja, J.C.d.F.; Viana, G.G.F.; Rossi, G.A.M.; Spanu, C.; et al. Antimicrobial Resistance in Chicken Meat: Comparing Salmonella, Escherichia coli, and Enterococcus from Conventional and Antibiotic-Free Productions. Microorganisms 2025, 13, 2227. https://doi.org/10.3390/microorganisms13102227

AMA Style

Cerqueira-Cézar CK, Sampaio ANdCE, Caron EFF, Dellaqua TT, Ribeiro LFM, Tadielo LE, Pantoja JCdF, Viana GGF, Rossi GAM, Spanu C, et al. Antimicrobial Resistance in Chicken Meat: Comparing Salmonella, Escherichia coli, and Enterococcus from Conventional and Antibiotic-Free Productions. Microorganisms. 2025; 13(10):2227. https://doi.org/10.3390/microorganisms13102227

Chicago/Turabian Style

Cerqueira-Cézar, Camila Koutsodontis, Aryele Nunes da Cruz Encide Sampaio, Evelyn Fernanda Flores Caron, Thaisy Tino Dellaqua, Lucas Franco Miranda Ribeiro, Leonardo Ereno Tadielo, José Carlos de Figueiredo Pantoja, Gustavo Guimarães Fernandes Viana, Gabriel Augusto Marques Rossi, Carlo Spanu, and et al. 2025. "Antimicrobial Resistance in Chicken Meat: Comparing Salmonella, Escherichia coli, and Enterococcus from Conventional and Antibiotic-Free Productions" Microorganisms 13, no. 10: 2227. https://doi.org/10.3390/microorganisms13102227

APA Style

Cerqueira-Cézar, C. K., Sampaio, A. N. d. C. E., Caron, E. F. F., Dellaqua, T. T., Ribeiro, L. F. M., Tadielo, L. E., Pantoja, J. C. d. F., Viana, G. G. F., Rossi, G. A. M., Spanu, C., Possebon, F. S., & Pereira, J. G. (2025). Antimicrobial Resistance in Chicken Meat: Comparing Salmonella, Escherichia coli, and Enterococcus from Conventional and Antibiotic-Free Productions. Microorganisms, 13(10), 2227. https://doi.org/10.3390/microorganisms13102227

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