Mice were treated humanely in accordance with all appropriate government guidelines for the Care and Use of Laboratory Animals of the National Institutes of Health and their use was approved for this entire study by the University of Miami Institutional Animal Care and Use Committee (protocol 16-053).
1. Preparing Cells for Infection
<ol>
	<li>Propagate mouse macrophage-like cell line RAW 264.7 in DMEM tissue culture media supplemented with 10% fetal calf serum (henceforth referred to as DMEM/FCS) using a 125 mL flask and a tissue culture incubator maintained at 37 &#176;C/5% CO2.</li>
	<li>The day before the infection, use a cell scraper to remove cells from the expansion flask and collect in a 15 mL screw cap conical tube. Centrifuge cells at 800 x g for 10 min, decant supernatant and suspend the cell pellet in 1 mL of DMEM/FCS (without antibiotics) and determine the titer using a hemocytometer or an automated cell counter.</li>
	<li>Adjust titer to 2 x 106 cells/mL and add 0.10 mL (2 x 105 cells) to wells of a 48-well tissue culture dish. Ensure that the cell suspension covers the entire surface of the well.
	<ol>
		<li>Plate cells in additional wells for a later source of conditioned media. Also place 0.10 mL of DMEM/FCS in three additional wells to serve as a &#39;no cell control&#39;.</li>
	</ol>
	</li>
	<li>Incubate overnight in a tissue culture incubator at 37 &#176;C/5% CO2. The next day, do not remove from incubator until the bacterium inoculum is prepared and ready to use.</li>
</ol>
2. Preparing Listeria monocytogenes (Lm) for infection
<ol>
	<li>Inoculate 2 mL of brain-heart infusion (BHI) with a single colony from a freshly-streaked agar plate (&#60;2 days) of Lm and incubate overnight at 37 &#176;C with shaking at 130 rotations/min.</li>
	<li>The next day, add 0.10 mL of overnight culture to 2 mL pre-warmed BHI and continue incubating at 37 &#176;C with shaking until the optical density (OD600) is between 0.4 and 0.6.</li>
	<li>Determine approximate bacterial titer using an empirically-derived conversion formula. In our lab, an exponentially growing Lm culture in BHI is approximately 1.3 x 109 colony forming units (CFU)/OD600. Minimize the amount of time bacterial cultures are exposed to room temperature.</li>
	<li>Just prior to infection adjust the titer to 5 x 107 CFU/mL using pre-warmed DMEM/FCS as diluent.</li>
</ol>
3. Infection
<ol>
	<li>Working quickly and precisely, add 20 &#181;L (1 x 106 CFU; multiplicity of infection, MOI = 5) of the freshly-prepared Lm inoculum (step 2.4 above) to wells by slightly tilting the dish and carefully placing the pipet tip in the overlying media; 
	NOTE:&#160;avoid touching the walls of the well with the pipet tip.</li>
	<li>Gently pipet the contents of each well to ensure complete mixing; do not shake or significantly tilt the plate as this will spread Lm over the walls of the well. Return cell culture dish to 37 &#176;C/5% CO2 incubator.</li>
	<li>Prepare a 10 &#181;g/mL gentamicin solution using conditioned media from uninfected wells as diluent.</li>
	<li>At 30 minutes post infection (mpi), carefully add 30 &#181;L of the gentamicin solution (final concentration 2.5 &#181;g/mL) and gently pipet the contents of the well as before and return cell culture dish to 37 &#176;C/5% CO2 incubator.</li>
	<li>At 60 mpi, harvest appropriate wells for either CFU assay (60 mpi time point) or FCM analysis (as described below in sections 4 and 5, respectively).</li>
	<li>For remaining wells, at various times thereafter either harvest cells as before or, for the Lm emergence assay, entirely remove media from well and replace with 150 &#181;L of gentamicin-free conditioned media.</li>
</ol>
4. Sampling Processing and Analysis of Intracellular and Emergent Lm by CFU Assay
<ol>
	<li>To harvest, slightly tilt the dish and carefully remove the entire media from the well. Add 0.50 mL of distilled sterile water (dsH2O) to the well. After 30 s, transfer the resulting water lysate (100) to a 1.5 mL microcentrifuge tube and vortex vigorously for 10 s.</li>
	<li>Prepare 10-1 and 10-2 dilutions by adding either 4.5 &#181;L or 50 &#181;L of the water lysate to 450 &#181;L of dsH2O and briefly vortex to ensure thorough mixing.</li>
	<li>Spread 50 &#181;L of the 100, 10-1 and/or 10-2 samples onto lysogeny broth (LB) agar plates.</li>
	<li>To assay for emergent Lm (step 3.6 above), remove 10 &#181;L of the overlaying media and divide it into two 5 &#181;L aliquots: to one aliquot add 5 &#181;L of DMEM/FCS and to the second aliquot add 5 &#181;L of DMEM/FCS containing 5 &#181;g/mL gentamicin. The latter control distinguishes between extracellular Lm (gentamicin sensitive) and intracellular Lm (gentamicin resistant) in the subsequent CFU assay.</li>
	<li>After 5 min at room temperature, add 90 &#181;L of dsH2O, vortex vigorously for 10 s, and spread 50 &#181;L on LB agar plates.</li>
	<li>Enumerate Lm colonies on LB agar plates following 2 days of incubation at 37 &#176;C.</li>
</ol>
5. Sampling Processing and Analysis of Intracellular and Emergent Lm by Flow Cytometry (FCM)
<ol>
	<li>Prepare RAW 264.7 cells as described in steps 1.1-4. Adjust cells to 1 x 106 cells/mL and add 1 mL (1 x 106 cells) to wells of a 6-well tissue culture dish.</li>
	<li>Prepare bacterium inoculum as described in step 2.1-2.3 and infect cells with volume of inoculum corresponding to a MOI of 50 (5 x 107 CFU).</li>
	<li>At 1.5 hours post infection (hpi), collect media from first set of wells and place in a 1.5 mL microcentrifuge tube with 500 &#181;L of 4% paraformaldehyde (PFA) and place on ice until all wells have been processed.</li>
	<li>To collect intracellular Lm, add 1 mL of dsH2O to the well and after 60 s, transfer the resulting water lysate to a 1.5 mL microcentrifuge tube with 500 &#181;L of 4% PFA. Vortex vigorously for 10 s and place on ice until all wells have been processed. (Sample processing is described in step 5.8 below.)</li>
	<li>For remaining wells, remove media and replace with 1 mL of DMEM/FCS with 5 &#181;g/mL gentamicin to kill extracellular Lm and promptly return cells to incubator.</li>
	<li>After 30 min (2 hpi) remove media and replace with DMEM/FCS without gentamicin.</li>
	<li>After 2 and 4 h (4 and 6 hpi) take second and third time points by collecting media and lysates as steps 5.3 and 5.4.</li>
	<li>Centrifuge tubes at 10,000 x g for 7 min. Remove supernatant without disturbing pellet.</li>
	<li>Suspend each pellet in staining cocktail of 50 &#181;L of 4% PFA and 15 &#181;L of phalloidin. Incubate tubes in the dark at 4 &#176;C for 20 min.</li>
	<li>After incubation add 1 mL of FACS buffer to each tube and pipette up and down to mix.</li>
	<li>Spin tubes at 10,000 x g for 7 min. Remove supernatant without disturbing pellet.</li>
	<li>Suspend each pellet in 400 &#181;L of FACS buffer for immediate use, or 200 &#181;L of FACS buffer and 200 &#181;L of 4% PFA if storing for later analysis.</li>
	<li>Run samples on a flow cytometry and analyze the collected data.</li>
</ol>
6. Sampling Processing and Analysis of Lm Colonization and Host Responses in the Liver
<ol>
	<li>Prepare Lm for infection as described in step 2.1-2.3.</li>
	<li>Calculate the necessary amount of subculture for desired titer of 3 x 106 CFU/mL.</li>
	<li>Just prior to infection dilute the amount of calculated bacteria with pre-warmed Hank&#39;s Balanced Salt Solution (HBSS) in a final volume of 1 mL. This is the input inoculum that is injected into the mouse.</li>
	<li>Using a 28 G&#189; 100U insulin syringe, draw 100 &#181;L (3 x 105 CFU) of input inoculum and remove any visible air bubbles.</li>
	<li>Place the mouse (strain C57BL/6; males between 6 and 12 weeks old) into the holding restraint and use warm water (no more than 45 &#176;C) to dilate the tail vein, then inject the input inoculum into the vein.</li>
	<li>Plate 10-2 and 10-3 dilutions of the input inoculum onto LB agar 10bcm plates and incubate overnight at 37 &#176;C to determine the actual input dosage.</li>
	<li>At 18 hpi, humanely euthanize mouse (CO2 asphyxiation followed by cervical dislocation) and using sterile scissors cut open mouse peritoneum to collect frontal lobe of the liver using separate pairs of tweezers and scissors for the outside and inside of the mouse. Place the liver in a 6 cm Petri dish on ice.</li>
	<li>Cut the liver into small cubes and place into a glass vial with a magnetic stir bar. Add 2 mL of 2 mg/mL collagenase D reconstituted in DMEM without FCS. Incubate vials at 37 &#176;C on a magnetic stirrer for 30&#8722;45 min. Once the tissue is homogenized, add 3 mL of DMEM/FCS to inactivate the collagenase.</li>
	<li>Filter the cells through a 70 &#181;m cell strainer into a conical tube, adding more DMEM/FCS if necessary.</li>
	<li>Centrifuge cells at 800 x g to pellet at 4 &#176;C for 10 min, remove supernatant and suspend cell pellet in 500 &#181;L of ACK buffer to lyse red blood cells.</li>
	<li>Incubate cells at room temperature for 5 min in ACK buffer. Suspend cells in 1 mL of DMEM/FCS.</li>
	<li>Centrifuge cells at 800 x g to pellet at 4 &#176;C for 10 min, remove supernatant and suspend in 1 mL of DMEM/FCS. Then, count the cells using a hemocytometer or an automated cell counter.</li>
	<li>Transfer 1 x 106 cells to 1.5 mL microcentrifuge tube and spin to pellet. Then suspend in 1 mL of dsH2O and vortex to lyse the cells. Plate 50 &#181;L on LB plates at undiluted and 10-2 dilutions and incubate at 37 &#176;C to enumerate Lm for CFU analysis.</li>
	<li>Transfer 1 x 106 cells into FACS tubes for each tissue sample according to the cell counts and wash with 1 mL of FACS buffer.</li>
	<li>Centrifuge cells at 800 x g to pellet at 4 &#176;C for 10 min and remove supernatant.</li>
	<li>Prepare an antibody cocktail containing the antibodies of interest based on the recommended concentration for each antibody and FACS buffer. See Table of Materials for recommended amounts used in the analysis.</li>
	<li>Suspend pellet in 100 &#181;L of antibody cocktail and incubate tubes in the dark at 4 &#176;C for 30 min.</li>
	<li>After incubation, add 2 mL of FACS buffer to each tube and suspend cells.</li>
	<li>Centrifuge cells at 800 x g to pellet at 4 &#176;C and discard the supernatant. Then suspend the pellet in 400 &#181;L of FACS buffer for immediate use, or 200 &#181;L of FACS buffer and 200 &#181;L of 4% PFA if storing for later.</li>
	<li>Analyze cells by flow cytometry (see step 5.13).</li>
</ol>

<ol>
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E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Functional+impact+of+mutational+activation+on+the+Listeria+monocytogenes+central+virulence+regulator+PrfA.">Functional impact of mutational activation on the Listeria monocytogenes central virulence regulator PrfA.</a> Microbiology. 154, 3579-3589 (2008).</li><li>McCormack, R., 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=Perforin-2+Protects+Host+Cells+and+Mice+by+Restricting+the+Vacuole+to+Cytosol+Transitioning+of+a+Bacterial+Pathogen.">Perforin-2 Protects Host Cells and Mice by Restricting the Vacuole to Cytosol Transitioning of a Bacterial Pathogen.</a> Infection and Immunity. 84, 1083-1091 (2016).</li><li>Gregory, S. H., 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=Complementary+adhesion+molecules+promote+neutrophil-Kupffer+cell+interaction+and+the+elimination+of+bacteria+taken+up+by+the+liver.">Complementary adhesion molecules promote neutrophil-Kupffer cell interaction and the elimination of bacteria taken up by the liver.</a> Journal of Immunology. 168, 308-315 (2002).</li><li>Shi, C., 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=Monocyte+trafficking+to+hepatic+sites+of+bacterial+infection+is+chemokine+independent+and+directed+by+focal+intercellular+adhesion+molecule-1+expression.">Monocyte trafficking to hepatic sites of bacterial infection is chemokine independent and directed by focal intercellular adhesion molecule-1 expression.</a> Journal of Immunology. 184, 6266-6274 (2010).</li><li>Pitts, M. 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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=Specific+depletion+reveals+a+novel+role+for+neutrophil-mediated+protection+in+the+liver+during+Listeria+monocytogenes+infection.">Specific depletion reveals a novel role for neutrophil-mediated protection in the liver during Listeria monocytogenes infection.</a> European Journal of Immunology. 41 (9), 2666-2676 (2011).</li><li>Bl&#233;riot, C., 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=Liver-resident+macrophage+necroptosis+orchestrates+type+1+microbicidal+inflammation+and+type-2-mediated+tissue+repair+during+bacterial+infection.">Liver-resident macrophage necroptosis orchestrates type 1 microbicidal inflammation and type-2-mediated tissue repair during bacterial infection.</a> Immunity. 42 (1), 145-158 (2015).</li><li>Jones, G. S., D'Orazio, S. E. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Monocytes+are+the+predominant+cell+type+associated+with+Listeria+monocytogenes+in+the+gut,+but+they+do+not+serve+as+an+intracellular+growth+niche.">Monocytes are the predominant cell type associated with Listeria monocytogenes in the gut, but they do not serve as an intracellular growth niche.</a> Journal of Immunology. 198, 2796-2804 (2017).</li><li>Agaisse, H., 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=Genome-wide+RNAi+screen+for+host+factors+required+for+intracellular+bacterial+infection.">Genome-wide RNAi screen for host factors required for intracellular bacterial infection.</a> Science. 309, 1248-1251 (2005).</li><li>Cheng, L. W., 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=Use+of+RNA+interference+in+Drosophila+S2+cells+to+identify+host+pathways+controlling+compartmentalization+of+an+intracellular+pathogen.">Use of RNA interference in Drosophila S2 cells to identify host pathways controlling compartmentalization of an intracellular pathogen.</a> Proceedings of the National Academy of Science U S A. 102, 13646-13651 (2005).</li><li>Singh, R., Jamieson, A., Cresswell, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=GILT+is+a+critical+host+factor+for+Listeria+monocytogenes+infection.">GILT is a critical host factor for Listeria monocytogenes infection.</a> Nature. 455, 1244-1247 (2008).</li><li>Burrack, L. S., Harper, J. W., Higgins, D. 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The authors have nothing to disclose.

Due to its rapid and processive cellular infection program, Lm is an ideal pathogen to probe cellular activities that impact infection. A number of host factors have been identified that either positively or negatively affect Lm cellular infection11,12,13,14. Two such host factors characterized in our laboratory, Perforin-2 and the Heme Regulated Inhibitor (P2 and hI), regulat...

Infection-based experimental models are inherently challenging due to their dependence on the starting state conditions of the host and pathogen, the various pathogen infection strategies, and the difficulty of attributing pathogen- and host-driven processes based on outcomes. The bacterium Listeria monocytogenes (Lm) has become an ideal pathogen to probe host defense responses because of its genetic and microbiological tractability, its rapid and processive cellular infection strategy, and the relatively clear relationship between its cellular- and organismic-level infection phenotypes. The cellular infection of Lm proceeds through four distinct phases1: (i) cellular invasion that concludes with Lm being enclosed within a vacuole; (ii) Lm-directed dissolution of the vacuole membrane and release of Lm into the cytosol; (iii) intracytosolic replication; and (iv) physical penetration of the plasma membrane that results in either the infection of directly adjacent cells (such as in an epithelial sheet) or, in solitary cells, release of Lm into the extracellular milieu. Each of these phases are promoted by specific Lm-encoded factors (referred to as &#39;virulence factors&#39;) that, when deleted, cause infection defects in both cellular and animal models. This general infection strategy has been independently evolved by a number of the so-called &#39;cytosolic&#39; pathogens2.
Colony-forming unit (CFU) assays are widely employed to evaluate both in vitro (i.e., cellular) as well as in vivo (i.e., organismic) infection outcomes. In addition to their high sensitivity, particularly for in vivo infections, CFU assays provide an unambiguous readout for pathogen invasion and intracellular survival/proliferation. CFU assays have been extensively used to analyze both Lm and host cell determinants that impact infection. As informative as these prior studies have been to analyze cellular invasion and intracytosolic replication, CFU assays have not, to the best of our knowledge, been used to track the fourth phase of the Lm infection process: cellular escape. Here, we describe relatively simple means of how cellular escape (hereafter referred to as &#39;emergence&#39;) can be monitored by CFU assay (as well as by flow cytometry) and show examples of how both pathogen- and host-encoded factors regulate this phase of the Lm infection cycle. The analysis of the terminal phase of the cellular Lm infection cycle may make it possible to identify additional pathogen and host cell infection-specific factors and activities.

<table border="0" cellpadding="0" cellspacing="0" style="width:776px;" width="776">
	<colgroup>
		<col />
		<col />
		<col />
		<col />
	</colgroup>
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">ACK Lysing Buffer</td>
			<td style="width:128px;">Gibco&#160;</td>
			<td style="width:119px;">A1049201</td>
			<td style="width:313px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">ArC Amine Reactive Compensation Beads&#160;</td>
			<td style="width:128px;">Life Technologies</td>
			<td style="width:119px;">A10346</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">BHI (Brain Heart Infusion) broth</td>
			<td>EMD Milipore</td>
			<td>110493</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Cell Strainer, 70 &#181;m</td>
			<td style="width:128px;">VWR</td>
			<td style="width:119px;">10199-656</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Collagenase D</td>
			<td style="width:128px;">Roche</td>
			<td>11088858001</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">DMEM media&#160;</td>
			<td style="width:128px;">Gibco&#160;</td>
			<td>11965-092</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">FACS tubes&#160;</td>
			<td style="width:128px;">BD Falcon</td>
			<td style="width:119px;">352054</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">FBS - Heat Inactivated&#160;</td>
			<td>Sigma-Aldrich</td>
			<td>F4135-500ML</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Hanks&#8217; Balanced Salt solution</td>
			<td style="width:128px;">Sigma-Aldrich</td>
			<td>H6648-6X500ML</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">LB agar</td>
			<td style="width:128px;">Grow Cells MS</td>
			<td style="width:119px;">MBPE-4040</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">LIVE/DEAD Fixable Yellow Dead Cell Stain kit&#160;</td>
			<td style="width:128px;">Life Technologies</td>
			<td style="width:119px;">L349S9</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Rhodamine Phalloidin&#160;</td>
			<td style="width:128px;">Thermo Fischer</td>
			<td>R415</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">SP6800 Spectral Analyzer</td>
			<td style="width:128px;">Sony</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Syringe 28G 1/2&#34; 1cc</td>
			<td style="width:128px;">BD</td>
			<td style="width:119px;">329461</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">TPP Tissue Culture 48 Well Plates&#160;</td>
			<td style="width:128px;">MIDSCI</td>
			<td>TP92048</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">TPP Tissue Culture 6 Well Plates&#160;</td>
			<td style="width:128px;">MIDSCI</td>
			<td>TP92406</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">UltraComp eBeads</td>
			<td style="width:128px;">eBioscience</td>
			<td style="width:119px;">01-2222-42</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Antigen</td>
			<td style="width:128px;"></td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">CD11b&#160;</td>
			<td style="width:128px;">Biolegend</td>
			<td style="width:119px;"></td>
			<td>Flurochrome = PE Cy5, Dilution = 1/100, Clone = M1/70</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">CD11c</td>
			<td style="width:128px;">Biolegend</td>
			<td style="width:119px;"></td>
			<td>Flurochrome = AF 647, Dilution = 1/100, Clone = N418</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">CD45</td>
			<td style="width:128px;">Biolegend</td>
			<td style="width:119px;"></td>
			<td>Flurochrome = APC Cy7, Dilution = 1/100, Clone = 30-F11</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">F4/80</td>
			<td style="width:128px;">Biolegend</td>
			<td style="width:119px;"></td>
			<td>Flurochrome = PE, Dilution = 1/100, Clone = BM8</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Live/Dead</td>
			<td style="width:128px;">Invitrogen</td>
			<td style="width:119px;"></td>
			<td>Flurochrome = AmCyN, Dilution = 1/100</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Ly6C</td>
			<td style="width:128px;">Biolegend</td>
			<td style="width:119px;"></td>
			<td>Flurochrome = PacBlue, Dilution = 1/200, Clone = HK1.4</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">MHC II</td>
			<td style="width:128px;">Biolegend</td>
			<td style="width:119px;"></td>
			<td>Flurochrome = AF 700, Dilution = 1/200, Clone = M5/114.15.2</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">NK 1.1</td>
			<td style="width:128px;">Biolegend</td>
			<td style="width:119px;"></td>
			<td>Flurochrome = BV 605, Dilution = 1/100, Clone = PK136</td>
		</tr>
	</tbody>
</table>

using a bacterial pathogen to probe for cellular and organismic-level host responses

There are a variety of strategies bacterial pathogens employ to survive and proliferate once inside the eukaryotic cell. The so-called 'cytosolic' pathogens (Listeria monocytogenes, Shigella flexneri, Burkholderia pseudomallei, Francisella tularensis, and Rickettsia spp.) gain access to the infected cell cytosol by physically and enzymatically degrading the primary vacuolar membrane. Once in the cytosol, these pathogens both proliferate as well as generate sufficient mechanical forces to penetrate the plasma membrane of the host cell in order to infect new cells. Here, we show how this terminal step of the cellular infection cycle of L. monocytogenes (Lm) can be quantified by both colony-forming unit assays and flow cytometry and give examples of how both pathogen- and host-encoded factors impact this process. We also show a close correspondence of Lm infection dynamics of cultured cells infected in vitro and those of hepatic cells derived from mice infected in vivo. These function-based assays are relatively simple and can be readily scaled up for discovery-based high-throughput screens for modulators of eukaryotic cell function.

Assessing the role of pathogen and host-encoded factors impacting cellular infection 
Using the infection conditions described above, 0.15% of the input wild-type Lm is recovered after 1.5 h of co-incubation with cultured macrophages (Figure 1A). In the subsequent 1.5 h of co-incubation (3 h post infection, hpi), there was a 4-fold increase in recovery of viable Lm and from 3 to 6 hpi there was an addit...

Watch this Scientific Journal Video about Using a Bacterial Pathogen to Probe for Cellular and Organismic-level Host Responses at JoVE.com

Using a Bacterial Pathogen to Probe for Cellular and Organismic-level Host Responses

We describe both in vitro and in vivo infection assays that can be used to analyze the activities of host-encoding factors.

There are a variety of strategies bacterial pathogens employ to survive and proliferate once inside the eukaryotic cell. The so-called 'cytosolic' ...

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Research

JoVE Journal

Immunology and Infection

5.7K Views.  University of Miami Miller School of Medicine. We describe both in vitro and in vivo infection assays that can be used to analyze the activities of host-encoding factors.

Video: Using a Bacterial Pathogen to Probe for Cellular and Organismic-level Host Responses

Invasion of Human Cells by a Bacterial Pathogen

Here we will describe how we study the invasion of human endothelial cells by bacterial pathogen Staphylococcus aureus . The general protocol can be applied to the study of cell invasion by virtually any culturable bacterium. The stages at which specific aspects of invasion can be studied, such as the role of actin rearrangement or caveolae, will be highlighted. Host cells are grown in flasks and when ready for use are seeded into 24-well plates containing Thermanox coverslips. Using coverslips allows subsequent removal of the cells from the wells to reduce interference from serum proteins deposited onto the sides of the wells (to which S. aureus would attach). Bacteria are grown to the required density and washed to remove any secreted proteins (e.g. toxins). Coverslips with confluent layers of endothelial cells are transferred to new 24-well plates containing fresh culture medium before the addition of bacteria. Bacteria and cells are then incubated together for the required amount of time in 5% CO2 at 37&deg;C. For S. aureus this is typically between 15-90 minutes. Thermanox coverslips are removed from each well and dip-washed in PBS to remove unattached bacteria. If total associated bacteria (adherent and internalised) are to be quantified, coverslips are then placed in a fresh well containing 0.5% Triton X-100 in PBS. Gentle pipetting leads to complete cell lysis and bacteria are enumerated by serial dilution and plating onto agar. If the number of bacteria that have invaded the cells is needed, coverslips are added to wells containing 500 &mu;l tissue culture medium supplemented with gentamicin and incubation continued for 1 h, which will kill all external bacteria. Coverslips can then be washed, cells lysed and bacteria enumerated by plating onto agar as described above. If the experiment requires direct visualisation, coverslips can be fixed and stained for light, fluorescence or confocal microscopy or prepared for electron microscopy.

A general protocol for the study of invasion of host cells by a bacterial pathogen, focusing on Staphylococcus aureus and human endothelial cells.

Here we will describe how we study the invasion of human endothelial cells by bacterial pathogen Staphylococcus aureus . The general protocol can be ...

Use of the EpiAirway Model for Characterizing Long-term Host-pathogen Interactions

Nontypeable Haemophilus influenzae (NTHi) are human-adapted Gram-negative bacteria that can cause recurrent and chronic infections of the respiratory mucosa 1; 2. To study the mechanisms by which these organisms survive on and inside respiratory tissues, a model in which successful long-term co-culture of bacteria and human cells can be performed is required. We use primary human respiratory epithelial tissues raised to the air-liquid interface, the EpiAirway model (MatTek, Ashland, MA). These are non-immortalized, well-differentiated, 3-dimensional tissues that contain tight junctions, ciliated and nonciliated cells, goblet cells that produce mucin, and retain the ability to produce cytokines in response to infection. 
This biologically relevant in vitro model of the human upper airway can be used in a number of ways; the overall goal of this method is to perform long-term co-culture of EpiAirway tissues with NTHi and quantitate cell-associated and internalized bacteria over time. As well, mucin production and the cytokine profile of the infected co-cultures can be determined. This approach improves upon existing methods in that many current protocols use submerged monolayer or Transwell cultures of human cells, which are not capable of supporting bacterial infections over extended periods3. For example, if an organism can replicate in the overlying media, this can result in unacceptable levels of cytotoxicity and loss of host cells, arresting the experiment. The EpiAirway model allows characterization of long-term host-pathogen interactions. Further, since the source for the EpiAirway is normal human tracheo-bronchial cells rather than an immortalized line, each is an excellent representation of actual human upper respiratory tract tissue, both in structure and in function4.
For this method, the EpiAirway tissues are weaned off of anti-microbial and anti-fungal compounds for 2 days prior to delivery, and all procedures are performed under antibiotic-free conditions. This necessitates special considerations, since both bacteria and primary human tissues are used in the same biosafety cabinet, and are co-cultured for extended periods.

This method allows characterization of extended bacterial co-culture with EpiAirways, primary human respiratory epithelial tissue grown at the air-liquid interface, a biologically relevant in vitro model. The approach can be used with any microbe that is amenable to long-term co-culture.

Nontypeable Haemophilus influenzae  (NTHi) are human-adapted Gram-negative bacteria that can cause recurrent and chronic infections of the respiratory ...

Visualization of Bacterial Toxin Induced Responses Using Live Cell Fluorescence Microscopy

Bacterial toxins bind to cholesterol in membranes, forming pores that allow for leakage of cellular contents and influx of materials from the external environment. The cell can either recover from this insult, which requires active membrane repair processes, or else die depending on the amount of toxin exposure and cell type1. In addition, these toxins induce strong inflammatory responses in infected hosts through activation of immune cells, including macrophages, which produce an array of pro-inflammatory cytokines2. Many Gram positive bacteria produce cholesterol binding toxins which have been shown to contribute to their virulence through largely uncharacterized mechanisms.
Morphologic changes in the plasma membrane of cells exposed to these toxins include their sequestration into cholesterol-enriched surface protrusions, which can be shed into the extracellular space, suggesting an intrinsic cellular defense mechanism3,4. This process occurs on all cells in the absence of metabolic activity, and can be visualized using EM after chemical fixation4. In immune cells such as macrophages that mediate inflammation in response to toxin exposure, induced membrane vesicles are suggested to contain cytokines of the IL-1 family and may be responsible both for shedding toxin and disseminating these pro-inflammatory cytokines5,6,7. A link between IL-1&beta; release and a specific type of cell death, termed pyroptosis has been suggested, as both are caspase-1 dependent processes8. To sort out the complexities of this macrophage response, which includes toxin binding, shedding of membrane vesicles, cytokine release, and potentially cell death, we have developed labeling techniques and fluorescence microscopy methods that allow for real time visualization of toxin-cell interactions, including measurements of dysfunction and death (Figure 1). Use of live cell imaging is necessary due to limitations in other techniques. Biochemical approaches cannot resolve effects occurring in individual cells, while flow cytometry does not offer high resolution, real-time visualization of individual cells. The methods described here can be applied to kinetic analysis of responses induced by other stimuli involving complex phenotypic changes in cells.

Methods for purifying the cholesterol binding toxin streptolysin O from recombinant E. coli and visualization of toxin binding to live eukaryotic cells are described. Localized delivery of toxin induces rapid and complex changes in targeted cells revealing novel aspects of toxin biology.

Bacterial toxins bind to cholesterol in membranes, forming pores that allow for leakage of cellular contents and influx of materials from the external ...

The Citrobacter rodentium Mouse Model: Studying Pathogen and Host Contributions to Infectious Colitis

This protocol outlines the steps required to produce a robust model of infectious disease and colitis, as well as the methods used to characterize Citrobacter rodentium infection in mice. C. rodentium is a gram negative, murine specific bacterial pathogen that is closely related to the clinically important human pathogens enteropathogenic E. coli and enterohemorrhagic E. coli. Upon infection with C. rodentium, immunocompetent mice suffer from modest and transient weight loss and diarrhea. Histologically, intestinal crypt elongation, immune cell infiltration, and goblet cell depletion are observed. Clearance of infection is achieved after 3 to 4 weeks. Measurement of intestinal epithelial barrier integrity, bacterial load, and histological damage at different time points after infection, allow the characterization of mouse strains susceptible to infection.
The virulence mechanisms by which bacterial pathogens colonize the intestinal tract of their hosts, as well as specific host responses that defend against such infections are poorly understood. Therefore the C. rodentium model of enteric bacterial infection serves as a valuable tool to aid in our understanding of these processes. Enteric bacteria have also been linked to Inflammatory Bowel Diseases (IBDs). It has been hypothesized that the maladaptive chronic inflammatory responses seen in IBD patients develop in genetically susceptible individuals following abnormal exposure of the intestinal mucosal immune system to enteric bacteria. Therefore, the study of models of infectious colitis offers significant potential for defining potentially pathogenic host responses to enteric bacteria. C. rodentium induced colitis is one such rare model that allows for the analysis of host responses to enteric bacteria, furthering our understanding of potential mechanisms of IBD pathogenesis; essential in the development of novel preventative and therapeutic treatments.

The Citrobacter rodentium Mouse Model: Studying Pathogen and Host Contributions to Infectious Colitis

Citrobacter rodentium infection provides a valuable model to study enteric bacterial infections as well as host immune responses and colitis in mice. This protocol outlines the measurement of barrier integrity, pathogen load and histological damage allowing for the thorough characterization of pathogen and host contributions to murine infectious colitis.

This protocol  outlines the steps required to produce a robust model of infectious disease and  colitis, as well as the methods used to characterize ...

A Comparative Approach to Characterize the Landscape of Host-Pathogen Protein-Protein Interactions

Significant efforts were gathered to generate large-scale comprehensive protein-protein interaction network maps. This is instrumental to understand the pathogen-host relationships and was essentially performed by genetic screenings in yeast two-hybrid systems. The recent improvement of protein-protein interaction detection by a Gaussia luciferase-based fragment complementation assay now offers the opportunity to develop integrative comparative interactomic approaches necessary to rigorously compare interaction profiles of proteins from different pathogen strain variants against a common set of cellular factors.
This paper specifically focuses on the utility of combining two orthogonal methods to generate protein-protein interaction datasets: yeast two-hybrid (Y2H) and a new assay, high-throughput Gaussia princeps protein complementation assay (HT-GPCA) performed in mammalian cells.
A large-scale identification of cellular partners of a pathogen protein is performed by mating-based yeast two-hybrid screenings of cDNA libraries using multiple pathogen strain variants. A subset of interacting partners selected on a high-confidence statistical scoring is further validated in mammalian cells for pair-wise interactions with the whole set of pathogen variants proteins using HT-GPCA. This combination of two complementary methods improves the robustness of the interaction dataset, and allows the performance of a stringent comparative interaction analysis. Such comparative interactomics constitute a reliable and powerful strategy to decipher any pathogen-host interplays.

This article focuses on the identification of high-confident interaction datasets between host and pathogen proteins using a combination of two orthogonal methods: yeast two-hybrid followed by a high-throughput interaction assay in mammalian cells called HT-GPCA.

Significant efforts were gathered to generate  large-scale comprehensive protein-protein interaction network maps. This is  instrumental to understand the ...

Imaging InlC Secretion to Investigate Cellular Infection by the Bacterial Pathogen Listeria monocytogenes

Bacterial intracellular pathogens can be conceived as molecular tools to dissect cellular signaling cascades due to their capacity to exquisitely manipulate and subvert cell functions which are required for the infection of host target tissues. Among these bacterial pathogens, Listeria monocytogenes is a Gram positive microorganism that has been used as a paradigm for intracellular parasitism in the characterization of cellular immune responses, and which has played instrumental roles in the discovery of molecular pathways controlling cytoskeletal and membrane trafficking dynamics. In this article, we describe a robust microscopical assay for the detection of late cellular infection stages of L. monocytogenes based on the fluorescent labeling of InlC, a secreted bacterial protein which accumulates in the cytoplasm of infected cells; this assay can be coupled to automated high-throughput small interfering RNA screens in order to characterize cellular signaling pathways involved in the up- or down-regulation of infection.

Imaging InlC Secretion to Investigate Cellular Infection by the Bacterial Pathogen Listeria monocytogenes

Listeria monocytogenes is a Gram positive bacterial pathogen frequently used as a major model for the study of intracellular parasitism. Imaging late L. monocytogenes infection stages within the context of small-interfering RNA screens allows for the global study of cellular pathways required for bacterial infection of target host cells.

Bacterial intracellular  pathogens can be conceived as molecular tools to dissect cellular signaling  cascades due to their capacity to exquisitely ...

Isolation of Salmonella typhimurium-containing Phagosomes from Macrophages

Salmonella typhimurium is a facultative intracellular bacterium that causes gastroenteritis in humans. After invasion of the lamina propria, S. typhimurium bacteria are quickly detected and phagocytized by macrophages, and contained in vesicles known as phagosomes in order to be degraded. Isolation of S. typhimurium-containing phagosomes have been widely used to study how S. typhimurium infection alters the process of phagosome maturation to prevent bacterial degradation. Classically, the isolation of bacteria-containing phagosomes has been performed by sucrose gradient centrifugation. However, this process is time-consuming, and requires specialized equipment and a certain degree of dexterity. Described here is a simple and quick method for the isolation of S. typhimurium-containing phagosomes from macrophages by coating the bacteria with biotin-streptavidin-conjugated magnetic beads. Phagosomes obtained by this method can be suspended in any buffer of choice, allowing the utilization of isolated phagosomes for a broad range of assays, such as protein, metabolite, and lipid analysis. In summary, this method for the isolation of S. typhimurium-containing phagosomes is specific, efficient, rapid, requires minimum equipment, and is more versatile than the classical method of isolation by sucrose gradient-ultracentrifugation.

Isolation of Salmonella typhimurium-containing Phagosomes from Macrophages

We describe here a simple and quick method for the isolation of Salmonella typhimurium-containing phagosomes from macrophages by coating the bacteria with biotin and streptavidin.

Salmonella typhimurium is a facultative intracellular bacterium that causes gastroenteritis in humans. After invasion of the lamina propria, S. ...

Evaluation of Host-Pathogen Responses and Vaccine Efficacy in Mice

Vaccines are a 20th century medical marvel. They have dramatically reduced the morbidity and mortality caused by infectious diseases and contributed to a striking increase in life expectancy around the globe. Nonetheless, determining vaccine efficacy remains a challenge. Emerging evidence suggests that the current acellular vaccine (aPV) for Bordetella pertussis (B. pertussis) induces suboptimal immunity. Therefore, a major challenge is designing a next-generation vaccine that induces protective immunity without the adverse side effects of a whole-cell vaccine (wPV). Here we describe a protocol that we used to test the efficacy of a promising, novel adjuvant that skews immune responses to a protective Th1/Th17 phenotype and promotes a better clearance of a B. pertussis challenge from the murine respiratory tract. This article describes the protocol for mouse immunization, bacterial inoculation, tissue harvesting, and analysis of immune responses. Using this method, within our model, we have successfully elucidated crucial mechanisms elicited by a promising, next-generation acellular pertussis vaccine. This method can be applied to any infectious disease model in order to determine vaccine efficacy.

Here we present an elegant protocol for in vivo evaluation of vaccine effectiveness and host immune responses. This protocol can be adapted for vaccine models that study viral, bacterial, or parasitic pathogens.

Vaccines are a 20th century medical marvel. They have dramatically reduced the morbidity and mortality caused by infectious diseases and contributed to a ...

Opsonophagocytic Killing Assay to Assess Immunological Responses Against Bacterial Pathogens

A key aspect of the immune response to bacterial colonization of the host is phagocytosis. An opsonophagocytic killing assay (OPKA) is an experimental procedure in which phagocytic cells are co-cultured with bacterial units. The immune cells will phagocytose and kill the bacterial cultures in a complement-dependent manner. The efficiency of the immune-mediated cell killing is dependent on a number of factors and can be used to determine how different bacterial cultures compare with regard to resistance to cell death. In this way, the efficacy of potential immune-based therapeutics can be assessed against specific bacterial strains and/or serotypes. In this protocol, we describe a simplified OPKA that utilizes basic culture conditions and cell counting to determine bacterial cell viability after co-culture with treatment conditions and HL-60 immune cells. This method has been successfully utilized with a number of different pneumococcal serotypes, capsular and acapsular strains, and other bacterial species. The advantages of this OPKA protocol are its simplicity, versatility (as this assay is not limited to antibody treatments as opsonins), and minimization of time and reagents to assess basic experimental groups.

This opsonophagocytic killing assay is used to compare the ability of phagocytic immune cells to respond to and kill bacteria based on different treatments and/or conditions. Classically, this assay serves as the gold&#160;standard for assessing effector functions of antibodies raised against a bacterium as opsonin.

A key aspect of the immune response to bacterial colonization of the host is phagocytosis. An opsonophagocytic killing assay (OPKA) is an experimental ...

A Precise Pathogen Delivery and Recovery System for Murine Models of Secondary Bacterial Pneumonia

Secondary bacterial pneumonias following influenza infections consistently rank within the top ten leading causes of death in the United States. To date, murine models of co-infection have been the primary tool developed to explore the pathologies of both the primary and secondary infections. Despite the prevalence of this model, considerable discrepancies regarding instillation procedures, dose volumes, and efficacies are prevalent among studies. Furthermore, these efforts have been largely incomplete in addressing how the pathogen may be directly influencing disease progression post-infection. Herein we provide a precise method of pathogen delivery, recovery, and analysis to be used in murine models of secondary bacterial pneumonia. We demonstrate that intratracheal instillation enables an efficient and accurate delivery of controlled volumes directly and evenly into the lower respiratory tract. Lungs can be excised to recover and quantify the pathogen burden. Following excision of the infected lungs, we describe a method to extract high quality pathogen RNA for subsequent transcriptional analysis. This procedure benefits from being a non-surgical method of delivery without the use of specialized laboratory equipment and provides a reproducible strategy to investigate pathogen contributions to secondary bacterial pneumonia.

Here, we present methods to improve secondary bacterial pneumonia studies by providing a non-invasive route of instillation into the lower respiratory tract followed by pathogen recovery and transcript analysis. These procedures are reproducible and can be performed without specialized equipment such as cannulas, guide wires, or fiber optic cables.

Secondary bacterial pneumonias following influenza infections consistently rank within the top ten leading causes of death in the United States. To date, ...