Exploring Transcriptomic Changes in Antibiotic-Resistant Salmonella Heidelberg Modulated by Commensal Escherichia coli in Vitro

Nontyphoidal Salmonella (NTS) are major foodborne pathogens primarily transmitted to humans through contaminated poultry products. The increase in antibiotic-resistant NTS, including Salmonella Heidelberg, 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 Escherichia coli can reduce antibiotic-resistant NTS colonization in the chicken intestines by modulating the fitness, virulence, and antibiotic resistance (AMR) potential of Salmonella. To test this hypothesis, we co-cultured commensal E. coli 47-1826 and antibiotic-resistant S. Heidelberg 18-9079 strains isolated from poultry and analyzed their transcriptomes using RNA sequencing. Our analysis revealed 4,890 differentially expressed genes in S. Heidelberg 18-9079 when co-cultured with E. coli 47-1826. 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 hemostasis, signal transduction and chemotaxis, stress response, transmembrane transport of xenobiotics, and cellular metabolism were down-regulated by as much as eighty-six folds in S. Heidelberg as compared to the control. Further, the study revealed the downregulation of genes associated with AMR and drug efflux in S. Heidelberg 18-9079 by up to twelvefold. These findings highlight that commensal E. coli 47-1826 may reduce the fitness, persistence, virulence, and antimicrobial resistance (AMR) dissemination of S. Heidelberg 18-9079, implying that E. coli strain 47-1826 could be utilized as a strategy to mitigate antibiotic-resistant S. Heidelberg in poultry, ultimately enhancing food safety. ImportanceNontyphoidal Salmonella, commonly transmitted to humans through contaminated poultry meat and eggs, is one of the most frequent causes 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 S. Heidelberg and commensal E. coli in a mixed culture of the two will provide insight into the ability of commensal E. coli to reduce S. Heidelberg colonization of chicken intestines and the genes involved in that change. Our study showed that commensal E. coli strain 47-1826 significantly reduced antibiotic-resistant S. Heidelberg 18-9079 counts and expression of Salmonella genes, which play a vital role in the growth and persistence of nontyphoidal Salmonella in poultry intestines. The study results suggest the potential use of commensal E. coli strain 47-1826 to control antibiotic-resistant S. Heidelberg colonization in poultry, leading to improved food safety through reduced NTS contamination of foods of poultry origin and reduced dissemination of antibiotic-resistant Salmonella and their resistant determinants to humans via the food chain.