Exploring Transcriptomic Changes in Antibiotic-ResistantSalmonellaHeidelberg Modulated by CommensalEscherichia coliin Vitro
Authors: Khan Yasir R. , Edison Lekshmi K. , Denagamage Thomas , Kariyawasam Subhashinie 
Published: December 2024

NontyphoidalSalmonella(NTS) are major foodborne pathogens primarily transmitted to humans through contaminated poultry products. The increase in antibiotic-resistant NTS, includingSalmonellaHeidelberg, 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 commensalEscherichia colican reduce antibiotic-resistant NTS colonization in the chicken intestines by modulating the fitness, virulence, and antibiotic resistance (AMR) potential ofSalmonella. To test this hypothesis, we co-cultured commensalE. coli47-1826 and antibiotic-resistantS. Heidelberg 18-9079 strains isolated from poultry and analyzed their transcriptomes using RNA sequencing. Our analysis revealed 4,890 differentially expressed genes inS. Heidelberg 18-9079 when co-cultured withE. coli47-1826. 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 inS. Heidelberg as compared to the control. Further, the study revealed the downregulation of genes associated with AMR and drug efflux inS.Heidelberg 18-9079 by up to twelvefold. These findings highlight that commensalE.coli47-1826 may reduce the fitness, persistence, virulence, and antimicrobial resistance (AMR) dissemination ofS.Heidelberg 18-9079, implying thatE. colistrain 47-1826 could be utilized as a strategy to mitigate antibiotic-resistant S. Heidelberg in poultry, ultimately enhancing food safety.

Importance

NontyphoidalSalmonella, 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-resistantS.Heidelberg and commensalE. coliin a mixed culture of the two will provide insight into the ability of commensalE. colito reduceS. Heidelberg colonization of chicken intestines and the genes involved in that change. Our study showed that commensalE. colistrain 47-1826 significantly reduced antibiotic-resistantS.Heidelberg 18-9079 counts and expression ofSalmonellagenes, which play a vital role in the growth and persistence of nontyphoidalSalmonellain poultry intestines. The study results suggest the potential use of commensalE. colistrain 47-1826 to control antibiotic-resistantS.Heidelberg colonization in poultry, leading to improved food safety through reduced NTS contamination of foods of poultry origin and reduced dissemination of antibiotic-resistantSalmonellaand their resistant determinants to humans via the food chain.