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The objective of this experiment was to elucidate the persistence mechanism of\n                      <jats:italic toggle=\"yes\">S<\/jats:italic>\n                      . Infantis by analyzing transcriptomic changes in the presence of litter. To achieve this, four treatments were arranged: (1) BHI, (2) BHI+Litter, (3) PBS, and (4) PBS+Litter. Each treatment was inoculated with\n                      <jats:italic toggle=\"yes\">S<\/jats:italic>\n                      . Infantis, and RNA was extracted. Quality, quantity, and integrity of RNA were assessed and then subjected to Illumina sequencing. HISAT2 was used to align reads to the reference genome, HTSeq to obtain read counts, and DESeq to study differential gene expression. The compared treatments were BHI vs BHI+Litter, PBS vs PBS+Litter, and PBS vs BHI. Starvation stress was pronounced in bacteria with upregulated expression of\n                      <jats:italic toggle=\"yes\">rpoS<\/jats:italic>\n                      and\n                      <jats:italic toggle=\"yes\">dksA<\/jats:italic>\n                      genes in nutrient-poor media, like PBS, in comparison to BHI and litter treatments. Additionally, the genes\n                      <jats:italic toggle=\"yes\">fad, eutS,<\/jats:italic>\n                      and\n                      <jats:italic toggle=\"yes\">pduF,<\/jats:italic>\n                      associated with alternative carbon utilization, were upregulated in PBS compared to PBS+Litter and BHI. Compared to non-litter media, alternative respiration system genes\n                      <jats:italic toggle=\"yes\">dmsA, dmsB, dmsC<\/jats:italic>\n                      ,\n                      <jats:italic toggle=\"yes\">ttrB, ttrC<\/jats:italic>\n                      ,\n                      <jats:italic toggle=\"yes\">fdnH,<\/jats:italic>\n                      and\n                      <jats:italic toggle=\"yes\">fdnG<\/jats:italic>\n                      upregulation in litter highlights\n                      <jats:italic toggle=\"yes\">S<\/jats:italic>\n                      . Infantis\u2019 ability for metabolic adaptation to oxygen-limited environments. Furthermore, virulent genes such as\n                      <jats:italic toggle=\"yes\">invA<\/jats:italic>\n                      and\n                      <jats:italic toggle=\"yes\">sopD<\/jats:italic>\n                      were found to be upregulated in BHI in comparison to BHI+Litter. In contrast, genes associated with amino acid-dependent acid resistance mechanisms including\n                      <jats:italic toggle=\"yes\">adiA, cadA,<\/jats:italic>\n                      and\n                      <jats:italic toggle=\"yes\">cadB<\/jats:italic>\n                      were downregulated in BHI in comparison to BHI+Litter. In conclusion,\n                      <jats:italic toggle=\"yes\">S<\/jats:italic>\n                      . Infantis upregulated stress response and metabolic genes to survive in challenging environments.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>IMPORTANCE<\/jats:title>\n                    <jats:p>\n                      Poultry litter plays a pivotal role in the persistence, proliferation, and transmission of\n                      <jats:italic toggle=\"yes\">Salmonella<\/jats:italic>\n                      . Recent studies have reported the increased prevalence of\n                      <jats:italic toggle=\"yes\">Salmonella<\/jats:italic>\n                      Infantis in the broiler houses and chicken meat in the United States and Europe. Moreover,\n                      <jats:italic toggle=\"yes\">Salmonella<\/jats:italic>\n                      strains could persist in the recycled litter despite undergoing several treatment methods. In commercial production systems, it is a common practice to reuse poultry litter for raising multiple broiler flocks in the United States. Therefore, it is crucial to understand the mechanism of the survival of bacteria in reused litter to curb the prevalence of\n                      <jats:italic toggle=\"yes\">Salmonella<\/jats:italic>\n                      . The objective of this study was to determine the transcriptional variations in\n                      <jats:italic toggle=\"yes\">S<\/jats:italic>\n                      . Infantis in the presence and absence of litter. The findings from this study will provide insights into the potential persistence mechanism of\n                      <jats:italic toggle=\"yes\">S<\/jats:italic>\n                      . Infantis within the litter environments.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.03307-25","type":"journal-article","created":{"date-parts":[[2026,3,10]],"date-time":"2026-03-10T13:00:25Z","timestamp":1773147625000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":2,"title":["Assessing transcriptomic responses of\n                    <i>Salmonella<\/i>\n                    Infantis in the presence of poultry litter"],"prefix":"10.1128","volume":"14","author":[{"given":"Ruby","family":"Paudel","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02v80fc35","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Poultry Science, Auburn University","place":["Auburn, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dianna","family":"Bourassa","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02v80fc35","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Poultry Science, Auburn University","place":["Auburn, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5421-4256","authenticated-orcid":true,"given":"Sabin","family":"Poudel","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02v80fc35","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Poultry Science, Auburn University","place":["Auburn, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_4_2_2","unstructured":"Centers for Disease Control and Prevention. 2025. 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