Antimicrobial Resistance Phenotypes and Genotypes of Cecal Digesta Escherichia coli of Pullets Fed Omega-3 Fatty Acids or Yeast Bioactives (Glycobolites).

Paul Kibaba Waliaula; Xianhua Yin; Dion Lepp; Nicole Ricker; Elijah G Kiarie; Moussa S Diarra

doi:10.1016/j.jfp.2026.100912

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Antimicrobial Resistance Phenotypes and Genotypes of Cecal Digesta Escherichia coli of Pullets Fed Omega-3 Fatty Acids or Yeast Bioactives (Glycobolites).

Paul Kibaba Waliaula·Xianhua Yin·Dion Lepp·Nicole Ricker·Elijah G Kiarie·Moussa S Diarra

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Abstract

Antimicrobial resistance (AMR) is a significant threat to poultry production and food safety. In laying hens, commensal Escherichia coli can serve as a reservoir of AMR and virulence genes. Although omega-3 fatty acids (N-3 FAs), yeast bioactives (YB), and spacing allowance (SA) influence gut health and immunity, their combined effects on AMR profiles of gut bacteria remain unclear. A total of 2,832 chicks were raised in enriched cages under high (HSA, 348 cm2/bird) or low (LSA, 284 cm2/bird) SA and fed a control diet (C), C+3% N-3 FA, or C+0.05% YB. At 4, 16, and 35 weeks of age (woa), cecal contents were cultured on ChromoCult agar to isolate E. coli. Susceptibilities of isolates to 14 antibiotics were determined. Of the 428 isolates, 35.7% were resistant to at least one antimicrobial, and overall, AMR prevalence decreased with age (P < 0.05). At each of 4 and 16 woa, N-3 FA-fed birds showed the lowest prevalance of ampicillin-resistant (P < 0.05). The prevalence of streptomycin resistance was higher in N-3 FA than in YB-fed birds at 16 woa (P = 0.02) but lower than in control-fed birds. Whole-genome sequencing and analysis of 237 selected isolates identified 19 antimicrobial resistance genes (ARGs) and 29 plasmids, with the distribution of 15 (78.9%) ARGs and 19 (65.5%) plasmid replicons affected by either diet, SA, or age (P < 0.05). Several virulence genes were identified in sequenced E. coli isolates, with the prevalence of those encoding fimbriae, pili, protectin, and toxins being higher in younger pullets (P < 0.05). Overall, isolates of phylogroups A and B1 were predominant; however, at 4 woa, phylogroup D isolates were most prevalent, depending on diet and SA (P < 0.05). Isolates of serotype O23:H16, ST2 were the most prevalent. Of the 237 sequenced isolates, 13 were related to human extraintestinal pathogenic Escherichia coli (ExPEC) strains. Overall, these findings suggest that N-3 FA YB and SA modulate AMR and virulence genotypes of E. coli in laying hens, highlighting their potential use of these agents in mitigating AMR.

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Paul Kibaba Waliaula, Xianhua Yin, Dion Lepp, Nicole Ricker, Elijah G Kiarie, Moussa S Diarra. 2026-09-04. Antimicrobial Resistance Phenotypes and Genotypes of Cecal Digesta Escherichia coli of Pullets Fed Omega-3 Fatty Acids or Yeast Bioactives (Glycobolites).. https://doi.org/10.1016/j.jfp.2026.100912

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