Commensal <i>Escherichia coli</i> inhibits the growth and modulates the fitness, virulence, and antimicrobial resistance of <i>Salmonella</i> Heidelberg <i>in vitro</i>

Nontyphoidal <i>Salmonella</i> (NTS) are major foodborne pathogens primarily transmitted to humans through contaminated poultry products. Increased antimicrobial resistance (AMR) in NTS, including <i>Salmonella</i> Heidelberg (SH), has recently become a public health issue. Current control measures are inadequate, emphasizing the need for novel approaches to mitigate NTS colonization in poultry and contamination of poultry products. We hypothesized that commensal <i>Escherichia coli</i> can reduce antibiotic-resistant NTS colonization in the chicken intestines by modulating the fitness, virulence, and AMR potential of <i>Salmonella</i>. To test this hypothesis, we co-cultured a commensal <i>E. coli</i> strain (EC47-1826) isolated from a commercial broiler chicken and an antibiotic-resistant SH strain (SH18-9079) isolated from the liver of a turkey and analyzed their transcriptomes using RNA-sequencing. Our analysis revealed 4,890 differentially expressed genes in SH when co-cultured with commensal <i>E. coli</i>. After filtering the expression data, we found 193 genes were significantly upregulated, while 202 genes were downregulated. Notably, several genes involved in bacterial growth, pathogenicity and virulence, biofilm formation, metal-ion homeostasis, signal transduction and chemotaxis, stress response, transmembrane transport of xenobiotics, and cellular metabolism were downregulated by as much as 86-folds in SH as compared to the control. Furthermore, this study revealed the downregulation of genes associated with AMR and drug efflux in SH by up to 12 folds. These findings highlight that commensal <i>E</i>. c<i>oli</i> may reduce the fitness, persistence, virulence, and AMR dissemination of SH, implying that <i>E. coli</i> strains could be utilized to mitigate antibiotic-resistant SH in poultry, ultimately enhancing food safety.IMPORTANCENTS, commonly transmitted to humans through contaminated poultry meat and eggs, is a frequent cause of foodborne illness. Augmenting the situation, foodborne outbreaks of antibiotic-resistant NTS have become an additional food safety and public health concern. Evaluation of growth changes and transcriptomic profiling of antibiotic-resistant SH and commensal <i>E. coli</i> in a mixed culture of the two will provide insights into the ability of commensal <i>E. coli</i> to reduce SH colonization of chicken intestines and the genes involved in that change. Our study showed that commensal <i>E. coli</i> significantly reduced antibiotic-resistant SH counts and expression of <i>Salmonella</i> genes, which play a vital role in their growth and persistence. This suggests the potential use of commensal <i>E. coli</i> to control antibiotic-resistant SH colonization in poultry, leading to improved food safety through reduced NTS contamination of foods of poultry origin and reduced dissemination of antibiotic-resistant <i>Salmonella</i> to humans via the food chain.