RNA-seq Brings New Insights to the Intra-Macrophage Transcriptome of Salmonella Typhimurium

PLoS Pathog. 2015 Nov 12;11(11):e1005262. doi: 10.1371/journal.ppat.1005262. eCollection 2015.


Salmonella enterica serovar Typhimurium is arguably the world's best-understood bacterial pathogen. However, crucial details about the genetic programs used by the bacterium to survive and replicate in macrophages have remained obscure because of the challenge of studying gene expression of intracellular pathogens during infection. Here, we report the use of deep sequencing (RNA-seq) to reveal the transcriptional architecture and gene activity of Salmonella during infection of murine macrophages, providing new insights into the strategies used by the pathogen to survive in a bactericidal immune cell. We characterized 3583 transcriptional start sites that are active within macrophages, and highlight 11 of these as candidates for the delivery of heterologous antigens from Salmonella vaccine strains. A majority (88%) of the 280 S. Typhimurium sRNAs were expressed inside macrophages, and SPI13 and SPI2 were the most highly expressed pathogenicity islands. We identified 31 S. Typhimurium genes that were strongly up-regulated inside macrophages but expressed at very low levels during in vitro growth. The SalComMac online resource allows the visualisation of every transcript expressed during bacterial replication within mammalian cells. This primary transcriptome of intra-macrophage S.-Typhimurium describes the transcriptional start sites and the transcripts responsible for virulence traits, and catalogues the sRNAs that may play a role in the regulation of gene expression during infection.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Gene Expression Regulation, Bacterial / genetics*
  • Genes, Bacterial / genetics
  • Genomic Islands / genetics
  • High-Throughput Nucleotide Sequencing
  • Macrophages / metabolism*
  • RNA, Bacterial / genetics*
  • Salmonella Vaccines / genetics
  • Salmonella typhimurium / genetics*
  • Transcriptome / genetics*
  • Virulence / genetics


  • Bacterial Proteins
  • RNA, Bacterial
  • Salmonella Vaccines

Associated data

  • GEO/GSM1462575
  • GEO/GSM1462579
  • GEO/GSM1914919

Grant support

This work was supported by the Stokes Professorship awarded to JCDH from the Science Foundation of Ireland (Grants 08/IN.1/B2104 and 07/IN.1/B918; www.sfi.ie). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.