Non-antibiotic alternative strategies in poultry: Evaluating organic farming systems and integrated vaccination-nutrition strategies

Abstract

Poultry health, human health and economic losses caused by pathogenic zoonotic bacteria including Salmonella remain a major concern, despite ongoing prevention and control efforts. The use of antibiotics for prophylaxis, treatment and growth promotion has led to selection and dissemination of antibiotic-resistant bacteria which significantly impacts human health, animal health as well as the environmental health. To mitigate antimicrobial resistance (AMR), poultry producers have increasingly adopted non-antibiotic strategies including organic farming practices to satisfy the consumer demands, vaccination programs, and nutritional interventions. However, it is not clear to which extent organic farming systems reduce antibiotic resistance compared to conventional counterparts. Furthermore, interactions between Salmonella vaccines and nutritional dietary components such as SQMFe® iron (an organic iron with a complexation process that enables time- and tissue-specific release of this critical nutrient) has not been characterized in poultry. This thesis addresses these knowledge gaps through two studies. Chapter 1 presents a global comparison of antimicrobial resistance trends between organic and conventional farming systems across food animal products and environment and how various regulatory policies impact AMR prevalence across multiple geographical regions. Chapter 2 examines the interactive effects of Salmonella vaccination and supplemental iron (SQMFe®) on the poultry cecal microbiota composition. The results show that organic farming systems have lower AMR prevalence compared to conventional counterparts. Additionally, SQM® Iron enriched fermentative taxa such as Pygmaiobacter and Odoribacter, while reducing Streptococcus. Vaccination alone promoted short-chain fatty acid (SCFA)-producing members of the Bacillota phylum. However, when vaccination was combined with SQM® Iron, several beneficial taxa were suppressed and Staphylococcus was markedly increased, suggesting that co-management strategies can produce unexpected and potentially counterproductive outcomes. These findings indicate that integrated approaches including organic farming, vaccination and micronutrient supplementation can reduce AMR and selectively remodel the poultry gut microbiome. This work has implication for nutrient utilization, developing targeted policy to control AMR and zoonotic pathogens while supporting animal health.