We would like to acknowledge Mathias S. Dick, Roland F. Dreier and Sebastian R&#252;hl for discussion. This work was supported by an SNSF Professorship PP00P3_139120/1 and a University of Basel project grant ID2153162 to P.B.

1. Digitonin Assay with mCherry-expressing Salmonella (FACS-based Analysis)
<ol>
	<li>Preparing bacteria 
	Note: Salmonella wild-type SL1344 (Streptomycin resistant) expressing mCherry from a plasmid (pFPV encoding mCherry under the rpsM promoter) is used in this assay. Bacterial phagocytosis and proliferation where not altered by the constitutive expression of mCherry (data not shown)&#160;16.
	<ol>
		<li>Inoculate the strain 1 day before the infection in 3 ml of LB medium supplemente...

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C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Disruption+of+the+Toxoplasma+gondii+parasitophorous+vacuole+by+IFNgamma-inducible+immunity-related+GTPases+(IRG+proteins)+triggers+necrotic+cell+death.">Disruption of the Toxoplasma gondii parasitophorous vacuole by IFNgamma-inducible immunity-related GTPases (IRG proteins) triggers necrotic cell death.</a> PLoS Pathog. 5, e1000288 (2009).</li><li>Meunier, E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Caspase-11+activation+requires+lysis+of+pathogen-containing+vacuoles+by+IFN-induced+GTPases.">Caspase-11 activation requires lysis of pathogen-containing vacuoles by IFN-induced GTPases.</a> Nature. 509, 366-370 (2014).</li><li>Yamamoto, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+cluster+of+interferon-gamma-inducible+p65+GTPases+plays+a+critical+role+in+host+defense+against+Toxoplasma+gondii.">A cluster of interferon-gamma-inducible p65 GTPases plays a critical role in host defense against Toxoplasma gondii.</a> Immunity. 37, 302-313 (2012).</li><li>Degrandi, D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Murine+guanylate+binding+protein+2+(mGBP2)+controls+Toxoplasma+gondii+replication.">Murine guanylate binding protein 2 (mGBP2) controls Toxoplasma gondii replication.</a> Proc Natl Acad Sci U S A. 110, 294-299 (2013).</li><li>Mariathasan, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Differential+activation+of+the+inflammasome+by+caspase-1+adaptors+ASC+and+Ipaf.">Differential activation of the inflammasome by caspase-1 adaptors ASC and Ipaf.</a> Nature. 430, 213-218 (2004).</li><li>Knodler, L. 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We have nothing to disclose.

Differential permeabilization is an easy and robust method to analyze and quantify the subcellular distribution of bacterial pathogens between vacuolar compartments and the cytosol. The same assay has been used successfully with bacteria such as Francisella novicida2,4 and Shigella flexneri12. However, since many intracellular pathogen alter or modify the host endomembrane structures, the robustness of the digitonin permeabilization will have to be determined on an individual basis...

Intracellular bacterial pathogens replicate either directly in the host cell cytosol, or in specialized vacuolar compartments1. During the initial stage of the infection most pathogens get internalized either by phagocytosis by specialized cells (such as macrophages) or by actively promoting their own uptake into non-phagocytic cells. In phagocytic cells, the phagosome normally fuses with lysosomes to form a degradative compartment, where the phagocytosed particles are digested. Specialized cytosolic bacteria, such as Francisella novicida or Shigella flexneri, escape phagosomal degradation by inducing the rupture of the phagosome and subsequently escape into the cytosol2,3. This requires virulence-associated mechanism such as the Francisella Pathogenicity Island (FPI) or the Shigella flexneri T3SS, which injects effector proteins that promote vacuolar rupture2-4. The host cell cytosol features a number of conserved pattern recognition receptors that normally recognize the presence of pathogens and induce innate immune signaling5. In addition, xenophagy, an anti-microbial form of autophagy can degrade bacteria that enter the cytosol. Cytosolic bacteria are normally well adapted to blunt or circumvent these responses using different strategies. For example, Francisella modifies its LPS to avoid host recognition and Shigella prevents autophagy recruitment using secreted effector proteins6,7.
Another strategy to escape lysosomal degradation is employed by the model vacuolar pathogen Salmonella enterica serovar Typhimurium, thereafter referred to as Salmonella typhimurium. Salmonella uses a T3SS to inject effectors that remodel the initial phagosome into its intracellular niche, the Salmonella-containing vacuole (SCV) 8,9. Continuous manipulation of host pathways is necessary to maintain this vacuole by recruiting lipids and other nutrients to the vacuole. Indeed, a sifA mutant of Salmonella fails to maintain vacuolar stability, and enters the cytosol of host cells within hours after infection, which results in activation of innate immune pathways and autophagy recruitment8. Vacuolar escape of Salmonella varies depending on the cell type that is studies, and several reports have shown that in epithelial cells even WT Salmonella can escape the SCV and hyperreplicate in the cytosol10. Recent reports show that innate immune detection of vacuolar pathogens also depends on the ability of the host to recognize and destabilize pathogen-containing vacuoles (PCVs) 11-14.
Given that both the host or bacteria genotype can affect the distribution of intracellular bacteria between the vacuolar and cytosolic compartment, it is necessary to quantify the number of vacuolar vs. cytosolic bacteria. Since, in most experimental setups host cells are infected with more than one bacterium, and subsequently can harbor several bacteria in different subcellular compartments, a technique is needed that allows quantification on the level of single bacteria. Differential permeabilization (also known as phagosomal protection assay) provides this resolution 2,4,10,12. The assay is based on selective permeabilization of the host cell plasma membrane with the detergent digitonin, which leaves vacuolar membranes intact and thus allows selective staining of cytosolic bacteria with antibodies. Here we provide two protocols for the quantification of cytosolic and vacuolar Salmonella typhimurium using differential permeabilization. The principle of this method is described in Figure 1: Bone-marrow derived macrophages (BMDMs) are infected with stationary phase mCherry-expressing Salmonella. Stationary phase Salmonella need to be used because they downregulate the expression of the SPI-1 T3SS, whose activity would otherwise be recognized by the NLRC4 inflammasome and induce rapid cell death (pyroptosis) of the BMDMs15. Following the infection cells are washed and treated with 50 &#956;g/ml&#160;of digitonin for 1 minute. Cells are washed again immediately and incubated with anti-Salmonella antibodies coupled to FITC to mark bacteria with access to the cytosol. After an additional washing step cells are lysed and the percentage of mCherry+ (vacuolar) and FITC+ / mCherry+ (cytosolic) bacteria is determined by FACS. We also report an adaptation of this method that can be used if no fluorescent protein-expressing strains are available (Figure 2). Additional steps are introduced after the FITC labeling in which cells are fixed and completely permeabilized. Thereafter all bacteria are stained with anti-Salmonella antibodies and corresponding secondary antibodies. Detection is then done by microscopy instead of FACS analysis.

<table border="0" cellpadding="0" cellspacing="0">
	<tbody>
		<tr>
			<td>Digitonin</td>
			<td>Sigma</td>
			<td>D5628</td>
			<td>50ug/mL</td>
		</tr>
		<tr>
			<td>PFA</td>
			<td>mpbio</td>
			<td>219998380</td>
			<td></td>
		</tr>
		<tr>
			<td>HEPES</td>
			<td>Life Technologies</td>
			<td>15630</td>
			<td></td>
		</tr>
		<tr>
			<td>Potassium Acetate</td>
			<td>Sigma</td>
			<td>791733</td>
			<td></td>
		</tr>
		<tr>
			<td>MgCl2</td>
			<td>Sigma</td>
			<td>M8266</td>
			<td></td>
		</tr>
		<tr>
			<td>BSA</td>
			<td>Sigma</td>
			<td>A2153</td>
			<td></td>
		</tr>
		<tr>
			<td>anti-Salmonella CSA-1-FITC</td>
			<td>KPL</td>
			<td>01-91-99-MG</td>
			<td>1/500</td>
		</tr>
		<tr>
			<td>anti-Salmonella CSA-1</td>
			<td>KPL</td>
			<td>02-91-99-MG</td>
			<td>1/500</td>
		</tr>
		<tr>
			<td>anti-Calnexin</td>
			<td>Enzo Lifesciences</td>
			<td>SPA-860D</td>
			<td>1/100</td>
		</tr>
		<tr>
			<td>anti-PDI</td>
			<td>Enzo Lifesciences</td>
			<td>SPA-890</td>
			<td>1/100</td>
		</tr>
		<tr>
			<td>Saponin</td>
			<td>Sigma</td>
			<td>47036</td>
			<td></td>
		</tr>
		<tr>
			<td>Vectashield mounting medium</td>
			<td>Vectorlabs</td>
			<td>H-1200</td>
			<td></td>
		</tr>
		<tr>
			<td>Anti Rabbit antibody-488</td>
			<td>Molecular Probes</td>
			<td>A-11070</td>
			<td>1/500</td>
		</tr>
		<tr>
			<td>Glycine</td>
			<td>Sigma</td>
			<td>G8898</td>
			<td></td>
		</tr>
		<tr>
			<td>Gentamicin</td>
			<td>Life Technologies</td>
			<td>15710-49</td>
			<td>100ug/mL and 10ug/mL</td>
		</tr>
		<tr>
			<td>Triton X-100</td>
			<td>Promega</td>
			<td>H5141</td>
			<td></td>
		</tr>
		<tr>
			<td>PBS</td>
			<td>Gibco</td>
			<td>20012-019</td>
			<td></td>
		</tr>
		<tr>
			<td>DMEM</td>
			<td>Sigma</td>
			<td>D6429</td>
			<td></td>
		</tr>
		<tr>
			<td>NEAA</td>
			<td>Amimed</td>
			<td>5-13K00-H</td>
			<td></td>
		</tr>
		<tr>
			<td>LSM700 Confocal microscope</td>
			<td>Zeiss</td>
			<td></td>
			<td>imaging done at 63x</td>
		</tr>
		<tr>
			<td>FACS Fortessa</td>
			<td>BD technologies</td>
			<td></td>
			<td>detection mCherry 610 nm</td>
		</tr>
		<tr>
			<td>FACS Fortessa</td>
			<td>BD technologies</td>
			<td></td>
			<td>detection FITC 530 nm</td>
		</tr>
	</tbody>
</table>

quantification of cytosolic vs. vacuolar salmonella in primary macrophages by differential permeabilization

Intracellular bacterial pathogens can replicate in the cytosol or in specialized pathogen-containing vacuoles (PCVs). To reach the cytosol, bacteria like Shigella flexneri and Francisella novicida need to induce the rupture of the phagosome. In contrast, Salmonella typhimurium replicates in a vacuolar compartment, known as Salmonella-containing vacuole (SCV). However certain mutants of Salmonella fail to maintain SCV integrity and are thus released into the cytosol. The percentage of cytosolic vs. vacuolar bacteria on the level of single bacteria can be measured by differential permeabilization, also known as phagosome-protection assay. The approach makes use of the property of detergent digitonin to selectively bind cholesterol. Since the plasma membrane contains more cholesterol than other cellular membranes, digitonin can be used to selectively permeabilize the plasma membrane while leaving intracellular membranes intact. In brief, following infection with the pathogen expressing a fluorescent marker protein (e.g. mCherry among others), the plasma membrane of host cells is permeabilized with a short incubation in digitonin containing buffer. Cells are then washed and incubated with a primary antibody (coupled to a fluorophore of choice) directed against the bacterium of choice (e.g. anti-Salmonella-FITC) and washed again. If unmarked bacteria are used, an additional step can be done, in which all membranes are permeabilized and all bacteria stained with a corresponding antibody. Following the staining, the percentage of vacuolar and cytosolic bacteria can be quantified by FACS or microscopy by counting single or double-positive events. Here we provide experimental details for use of this technique with the bacterium Salmonella typhimurium. The advantage of this assay is that, in contrast to other assay, it provides a quantification on the level of single bacteria, and if analyzed by microscopy provides the exact number of cytosolic and vacuolar bacteria in a given cell.

Figure 1 and Figure 2 show the schematics of the digitonin assay described in protocol 1 and protocol 2 illustrating the critical steps in the protocol and the results obtained. Figure 3 shows typical FACS results. Positive and negative controls are used to set the gates for mCherry+/FITC- bacteria (vacuolar Salmonella) and mCherry+/FITC+ bacteria (cytosolic Salmonella). Based on these gates the percentage of cytosolic and vacuolar bacteria can be determined in the experime...

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Quantification of Cytosolic vs. Vacuolar Salmonella in Primary Macrophages by Differential Permeabilization

We describe the quantification of cytosolic and vacuolar Salmonella typhimurium in bone-marrow derived macrophages using differential digitonin permeabilization.

Quantification of Cytosolic vs. Vacuolar Salmonella in Primary Macrophages by Differential Permeabilization

Intracellular bacterial pathogens can replicate in the cytosol or in specialized pathogen-containing vacuoles (PCVs). To reach the cytosol, bacteria like ...

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10.8K Views.  University of Basel. We describe the quantification of cytosolic and vacuolar Salmonella typhimurium in bone-marrow derived macrophages using differential digitonin permeabilization.