Broiler litter moisture and trace metals contribute to the persistence of <i>Salmonella</i> strains that harbor large plasmids carrying siderophores

Abstract

ABSTRACT Broiler litter sampling has proven to be an effective method for determining the Salmonella status of a broiler chicken flock and understanding the ecology of Salmonella prior to harvest. In this study, we investigated the ecology of Salmonella within the litter ( n = 224) from two commercial broiler houses in the United States. We employed culture enrichment methods and quantitative polymerase chain reaction to determine the prevalence and load of Salmonella and utilized antimicrobial susceptibility testing and whole-genome sequencing (WGS) to characterize select isolates. Additionally, we applied machine learning algorithms and in vitro experiments to identify environmental selective pressures that may contribute to the persistence of Salmonella in litter. Our findings indicate that the prevalence and abundance of Salmonella in broiler litter are influenced by the downtime between flocks as well as by the flock raised on the litter. A Decision Tree Classifier model developed demonstrated that the moisture in the caked part of litter was the most influential environmental parameter for predicting the prevalence of viable Salmonella . WGS analysis revealed that Typhimurium, Infantis, and Kentucky strains that harbored large self-conjugative plasmids encoding fitness factors for iron siderophore production were the dominant Salmonella population found in litter, and exposure to iron-limiting and copper-enriched culture media affected Salmonella growth. Our results suggest that trace metals may select for siderophores harbored on plasmids, and interventions that reduce litter moisture can potentially curtail the persistence of Salmonella in pre-harvest environments. IMPORTANCE Broiler chicken meat is the most consumed protein worldwide, and global poultry imports are projected to reach 17.5 million tons by 2031. To raise billions of chickens, litter is reused multiple times by the top global producers and exporters of chicken (Brazil and the United States). Chickens are in continuous contact with litter and depend on it for warmth and coprophagy. Consequently, litter serves as a major route for pathogens such as Salmonella to infect chickens, making it crucial to understand the environmental and genetic selective pressures that might explain why certain Salmonella strains persist on broiler farms more than others. In this study, we demonstrated that Salmonella strains that harbored siderophores on large conjugative plasmids persisted in litter and suggested that reducing litter moisture would significantly control Salmonella prevalence. However, a complete eradication of persisting Salmonella strains will require novel, innovative, and multifaceted approaches.

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