Single-cell RNA-seq ties macrophage polarization to growth rate of intracellular Salmonella


Intracellular bacterial pathogens can exhibit large heterogeneity in growth rate inside host cells, with major consequences for the infection outcome. If and how the host responds to this heterogeneity remains poorly understood. Here, we combined a fluorescent reporter of bacterial cell division with single-cell RNA-sequencing analysis to study the macrophage response to different intracellular states of the model pathogen Salmonella enterica serovar Typhimurium. The transcriptomes of individual infected macrophages revealed a spectrum of functional host response states to growing and non-growing bacteria. Intriguingly, macrophages harbouring non-growing Salmonella display hallmarks of the proinflammatory M1 polarization state and differ little from bystander cells, suggesting that non-growing bacteria evade recognition by intracellular immune receptors. By contrast, macrophages containing growing bacteria have turned into an anti-inflammatory, M2-like state, as if fast-growing intracellular Salmonella overcome host defence by reprogramming macrophage polarization. Additionally, our clustering approach reveals intermediate host functional states between these extremes. Altogether, our data suggest that gene expression variability in infected host cells shapes different cellular environments, some of which may favour a growth arrest of Salmonella facilitating immune evasion and the establishment of a long-term niche, while others allow Salmonella to escape intracellular antimicrobial activity and proliferate.

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Figure 1: Experimental strategy to sort single MΦs with different bacterial content.
Figure 2: Single-cell RNA-seq profiling reveals specific transcriptional signatures associated with MΦs containing non-growing or growing Salmonella.
Figure 3: Different bacterial loads correlate with divergent macrophage polarization transcription programs.
Figure 4: Bacterial growth triggers a different MΦ polarization pattern.

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  • 14 July 2017

    In the PDF version of this article previously published, the year of publication provided in the footer of each page and in the 'How to cite' section was erroneously given as 2017, it should have been 2016. This error has now been corrected. The HTML version of the article was not affected.


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The authors thank T. Achmedov, V. McParland, H. Merkert and B. Plaschke for technical support. A.-E.S. was supported by the PostDoc Plus program of the University of Würzburg. A.J.W. was the recipient of an Elite Advancement PhD stipend from Universität Bayern e.V. S.H. was supported by an MRC Career Development Award (MR/M009629/1). D.A.C.S. was the recipient of an EMBO postdoctoral fellowship (ALTF 441-2015).

Author information




A.-E.S., A.J.W. and J.V. designed and A.-E.S. performed the experiments. L.L. and S.A. performed bioinformatics analysis. S.H. and D.A.C.S. performed flow cytometry experiments. A.J.W., S.H. and L.N.S. provided reagents. A.-E.S., A.J.W., S.H. and J.V. wrote the manuscript.

Corresponding author

Correspondence to Jörg Vogel.

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The authors declare no competing financial interests.

Supplementary information

Supplementary information

Supplementary Figures 1–12, Supplementary References (PDF 1900 kb)

Supplementary Table 1

Sequencing results summary (XLSX 15 kb)

Supplementary Table 2

Cell clustering and differentially expressed genes between subpopulations (XLSX 1371 kb)

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Saliba, A., Li, L., Westermann, A. et al. Single-cell RNA-seq ties macrophage polarization to growth rate of intracellular Salmonella. Nat Microbiol 2, 16206 (2017).

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