Research reported in this manuscript was supported by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health under award number R01AI099122 to J.E.K. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. We would like to thank Jennifer Smith, David Wrobel, Su Chiang, Doug Flood, Sean Johnston, Jennifer Nale, Stewart Rudnicki, Paul Yan, Richard Siu, and Rachel Warden from the ICCB-Longwood Screening Facility and/or the National Screening Laboratory for the New England Regional Centers of Excellence in Biodefense and Emerging Infectious Diseases (supported by U54AI057159) for their assistance in development and performance of high-throughput screening assays. We also would like to thank Kenneth P. Smith for helpful comments on the manuscript.

1. Real Time Intracellular Growth and Eukaryotic Cell Cytotoxicity Assay
<ol>
	<li>Preparing Host Cells (J774A.1 Cells)
	<ol>
		<li>Culture J774A.1 Mus musculus macrophage-like cells in suspension in RPMI 1640 with 9% iron-supplemented calf serum. Initially passage in tissue culture flasks. After cells have become confluent in a 75 cm2 tissue culture flask in 15 ml of medium, split by scraping and dilution to 65 ml with the same type of medium, of which 15 ml is returned to the tissue culture flask...

<ol>
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C., Lorian, V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ch.+9.">Ch. 9.</a> Antimicrobial combinations. In: Antibiotics in Laboratory Medicin. , 330-396 (1996).</li><li>Jones, R. E., Zheng, W., McKew, J. C., Chen, C. Z. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+alternative+direct+compound+dispensing+method+using+the+HP+D300+digital+dispenser.">An alternative direct compound dispensing method using the HP D300 digital dispenser.</a> J Lab Autom. 18 (5), 367-374 (2013).</li><li>Odds, F. 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R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Two+distinct+defects+in+intracellular+growth+complemented+by+a+single+genetic+locus+in+Legionella+pneumophila.">Two distinct defects in intracellular growth complemented by a single genetic locus in Legionella pneumophila.</a> Mol Microbiol. 7 (1), 7-19 (1993).</li><li>Vogel, J. P., Isberg, R. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cell+biology+of+Legionella+pneumophila.">Cell biology of Legionella pneumophila.</a> Curr Opin Microbiol. 2 (1), 30-34 (1999).</li><li>Kirby, J. E., Isberg, R. 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R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Conjugative+transfer+by+the+virulence+system+of+Legionella+pneumophila.">Conjugative transfer by the virulence system of Legionella pneumophila.</a> Science. 279 (5352), 873-876 (1998).</li><li>Song, H., Fares, M., Maguire, K. R., Sid&#233;n, A., Pot&#225;cov&#225;, Z. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cytotoxic+Effects+of+Tetracycline+Analogues+(Doxycycline,+Minocycline+and+COL-3)+in+Acute+Myeloid+Leukemia+HL-60+Cells.">Cytotoxic Effects of Tetracycline Analogues (Doxycycline, Minocycline and COL-3) in Acute Myeloid Leukemia HL-60 Cells.</a> PLoS ONE. 9 (12), e114457 (2014).</li><li>Isberg, R. R., Falkow, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+single+genetic+locus+encoded+by+Yersinia+pseudotuberculosis+permits+invasion+of+cultured+animal+cells+by+Escherichia+coli+K-12.">A single genetic locus encoded by Yersinia pseudotuberculosis permits invasion of cultured animal cells by Escherichia coli K-12.</a> Nature. 317 (6034), 262-264 (1985).</li><li>Niles, A. L., Moravec, R. A., Riss, T. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Update+on+in+vitro+cytotoxicity+assays+for+drug+development.">Update on in vitro cytotoxicity assays for drug development.</a> Expert Opin Drug Discov. 3 (6), 655-669 (2008).</li><li>Niles, A. L., Moravec, R. A., Riss, T. 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We describe real-time assays for simultaneous detection of intracellular bacterial growth and host cell cytotoxicity. There are several critical steps in the protocol. First, for robust assay performance, there must be sufficient spectral separation between bacterial and cytotoxicity readouts. Such separation is intrinsic for combinations of luciferase operon reporters and fluorescent DNA-binding dyes. However, based on our experience (Table 1-3, Figure 2), use of dual, fluorescent reado...

Pathogens that grow or reside temporarily in intracellular compartments are difficult to therapeutically eradicate. Obligate or relatively obligate intracellular pathogens such as Legionella pneumophila, Coxiella burnetii, Brucella spp., Francisella tularensis, and Mycobacterium spp. often require prolonged courses of antimicrobial therapy for cure that may range from months to even years. Furthermore, extracellular pathogens may transiently occupy intracellular niches and in this way escape clearance by normal courses of antimicrobial therapy and later emerge to start new rounds of virulent infection. Staphylococcus aureus1 and uropathogenic Enterobacteriaceae2,3 infections are two increasingly recognized examples. Therefore, a fundamental drug discovery goal is to identify novel antimicrobials that penetrate into intracellular compartments. Optimal therapy to quickly eradicate intracellular organisms and prevent development of resistance through sub-inhibitory antimicrobial exposure is especially desirable.
To this end, we developed a high-throughput screening technology to identify intracellular-penetrant antimicrobials targeting the intracellular growth of the model pathogen, Legionella pneumophila.4 Previous clinical observations indicate that standard antimicrobial susceptibility testing did not accurately predict in vivo therapeutic efficacy against this organism.5 Specifically, this was because major classes of antimicrobials such as &#946;-lactams and aminoglycosides, although highly effective against axenically grown Legionella, do not sufficiently penetrate into the intracellular compartments where Legionella resides.5,6 Later evidence suggested that technically more complex intracellular growth assays effectively predicted clinical efficacy.7 Unfortunately, these assays were extremely laborious endpoints assays, requiring infected macrophages, treated with antimicrobials, to be lysed at different times points for colony forming unit enumeration. Such assays are impractical to do on a large scale and are unsuitable for high-throughput drug discovery.
Therefore, we developed technology for real-time determination of intracellular bacterial growth.6 This was accomplished through use of a bacterial strain modified through integration of either a bacterial luciferase operon8 (first generation assay, described previously)4 or fluorescent protein9 reporters (second generation, orthogonal assay, described here) into the bacterial chromosome. In this way, luminescent or fluorescent signal provides a surrogate, real-time readout of bacterial number.
However, these attributes do not address a major confounder in intracellular infection assays, off-target effects on host cells. In particular, the death of the host cell inherently limits intracellular growth and leads to false positive identification of antimicrobial effect. As many compounds in screening libraries are eukaryotic cell toxic, such false positives would overwhelm true antimicrobials, necessitating a large number of follow-up, endpoint cytotoxicity assays for resolution.
Thus, it was of great interest to be able to assess eukaryotic cell viability and intracellular growth simultaneously. Notably, a characteristic of non-viable eukaryotic cells is loss of cell membrane integrity. Probes that test the permeability of the cell membrane may therefore be used to assess cell viability. We previously characterized the ability of a series of putatively cell membrane-impermeant, fluorescent, DNA-binding dyes to access and stain nuclear DNA of dead cells.4 On binding nuclear DNA, these dyes display a large increase in quantum fluorescent yield resulting in increased signal over background solution fluorescence. As such, these dyes provided a quantitative readout of eukaryotic cell death.4 Notably, we found that several were non-toxic themselves during prolonged co-incubation with J774 macrophages. When added during initial infection, they provided a real-time, fluorescent readout of eukaryotic cell death that can be measured by a microplate fluorimeter or observed microscopically.
Therefore, by combining use of a bacterial reporter and non-toxic, membrane-impermeant, DNA-binding dyes, we were able to develop a simple, non-destructive, real-time assay to measure both bacterial load and eukaryotic cell cytotoxicity simultaneously. This assay has allowed us to screen in 384-well plate format ~10,000 known bioactives including ~250 antimicrobials and &#62;240,000 small molecules with functionally uncharacterized activity for the ability to inhibit intracellular growth of Legionella pneumophila, while at the same time generating eukaryotic cell cytotoxicity data for each compound.6 Our analysis of known antimicrobials against intracellular growth of Legionella was the most comprehensive exploration of this type to date.6
Based on the efficiency of our assay format, we also subsequently explored the potentially synergistic effects of known antimicrobials when used in combination. One of the most common synergy tests, the so-called checkerboard assay, is standardly performed by assessing combinatorial effects of two-fold serial dilutions of two or more antimicrobials.10 In these assays, synergy is defined by the observation of greater effect when two or more antimicrobials are applied together than the sum of the effects of each applied separately. Of note, heretofore, only focused and selective synergy testing was performed against intracellular Legionella pneumophila because of the great effort involved in traditional endpoint assays multiplied by the combinatorial permutations required.
To facilitate synergy testing, we made use of our real-time intracellular growth/eukaryotic cytotoxicity assay in combination with automated digital dispensing technology6. This automation permitted us to dispense serial dilutions of compounds dissolved in DMSO or aqueous solution alone or in combination in 384-well format.11 Furthermore, such robust liquid handling technology permitted us to easily perform higher resolution, square-root-of-two (rather than the standard, lower resolution, doubling) dilution combinations to achieve higher levels of specificity in our two-dimensional, checkerboard synergy analysis. This resolution was especially valuable in addressing concerns in the synergy field about reproducibility when using two-fold dilution series12. Lastly, our assay was quantitative and also therefore measured gradations of inhibition. As a result, the assay captured the entirety of inhibitory information, expressible in isocontour isobolograms in which isocontours connect combinatorial concentrations with similar levels of growth inhibition.6 This plotting strategy allowed visualization of combinatorial dose-response curves. To illustrate our methodology, we describe our protocol for performing these assays and show representative results.

<table border="0" cellpadding="0" cellspacing="0" width="1458">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:423px;">J774A.1 cells</td>
			<td style="width:248px;">American Type Culture Collection</td>
			<td style="width:161px;">TIB-67</td>
			<td style="width:627px;">Host cell</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:423px;">ACES</td>
			<td style="width:248px;">Sigma-Aldrich</td>
			<td style="width:161px;">A9758&#160;</td>
			<td style="width:627px;">For making buffered charcoal yeast extract agar and buffered yeast extract medium</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:423px;">Yeast extract, ultrafiltered</td>
			<td style="width:248px;">Becton-Dickinson/Difco</td>
			<td style="width:161px;">210929</td>
			<td style="width:627px;">For making buffered charcoal yeast extract agar and buffered yeast extract medium; lower grades may cause impaired growth and/or alter sensitivity of Legionella to growth inhibitors</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:423px;">Alpha-ketoglutaric acid, monopotassium salt</td>
			<td style="width:248px;">Sigma-Aldrich</td>
			<td style="width:161px;">K2000</td>
			<td style="width:627px;">For making buffered charcoal yeast extract agar and buffered yeast extract medium</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:423px;">Sodium pyruvate</td>
			<td style="width:248px;">Sigma-Aldrich</td>
			<td style="width:161px;">P5280</td>
			<td style="width:627px;">For making buffered charcoal yeast extract agar and buffered yeast extract medium</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:423px;">Potassium phosphate, dibasic</td>
			<td style="width:248px;">Thermo Fisher Scientific</td>
			<td style="width:161px;">P288-500</td>
			<td style="width:627px;">For making buffered charcoal yeast extract agar and buffered yeast extract medium</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:423px;">L-cysteine</td>
			<td style="width:248px;">Sigma-Aldrich</td>
			<td style="width:161px;">C-7755</td>
			<td style="width:627px;">For making buffered charcoal yeast extract agar and buffered yeast extract medium</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:423px;">Ammonium iron(III) citrate</td>
			<td style="width:248px;">Sigma-Aldrich</td>
			<td style="width:161px;">F5879</td>
			<td style="width:627px;">For making buffered charcoal yeast extract agar and buffered yeast extract medium; ferric pyrophosphate may be used instead but is more difficult to weigh accurately</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:423px;">Potassium hydroxide solution, concentrated</td>
			<td style="width:248px;">Thermo Fisher Scientific</td>
			<td style="width:161px;">SP236-500</td>
			<td style="width:627px;">For making buffered charcoal yeast extract agar and buffered yeast extract medium</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:423px;">Deonized water</td>
			<td style="width:248px;">N/A</td>
			<td style="width:161px;">N/A</td>
			<td style="width:627px;">For making buffered charcoal yeast extract agar and buffered yeast extract medium</td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:423px;">Thymidine (tissue culture grade)</td>
			<td style="width:248px;">Sigma-Aldrich</td>
			<td style="width:161px;">T1895</td>
			<td style="width:627px;">For supplementing both RPMI 1640 and buffered yeast extract agar/medium &#8212; lower grade thymidine may be used for the latter, but may cause impaired cell growth and/or cell death in RPMI 1640</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:423px;">RPMI 1640, standard formulation</td>
			<td style="width:248px;">Corning via Thermo Fisher Scientific</td>
			<td style="width:161px;">10-040-CV</td>
			<td style="width:627px;">For growing J774A.1 cells prior to plating; includes 2 mM L-glutamine</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:423px;">RPMI 1640 lacking phenol red</td>
			<td style="width:248px;">Corning via Thermo Fisher Scientific</td>
			<td style="width:161px;">17-105-CV</td>
			<td style="width:627px;">For plating J774A.1 cells in 384 well dishes (not suitable for growth prior to plating); also lacks L-glutamine &#8212; supplement to 2 mM before use</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:423px;">L-glutamine, 200 mM in 0.85% NaCl (tissue culture grade)</td>
			<td style="width:248px;">HyClone via Thermo Fisher Scientific</td>
			<td style="width:161px;">SH30034.02</td>
			<td style="width:627px;">For supplementing RPMI 1640 lacking L-glutamine, to 2 mM final concentration</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:423px;">Iron-supplemented calf serum</td>
			<td style="width:248px;">Gemini Bioproducts</td>
			<td style="width:161px;">100-510</td>
			<td style="width:627px;">For supplementing RPMI 1640, to 9.1% final concentration</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:423px;">Trypan Blue solution</td>
			<td style="width:248px;">Sigma-Aldrich</td>
			<td style="width:161px;">T8154</td>
			<td style="width:627px;">For staining for J774A.1 cell death determination while counting cell density</td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:423px;">SYTOX Green, 5 mM solution in DMSO</td>
			<td style="width:248px;">Thermo Fisher Scientific</td>
			<td style="width:161px;">S7020</td>
			<td style="width:627px;">For staining for J774A.1 cell death determination by fluorescence reading or epifluorescence microscopy (in conjunction with orange-red or far red fluorescent bacteria). Use at 125 nM final concentration.</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:423px;">GelRed, 10000X solution in water</td>
			<td style="width:248px;">Biotium</td>
			<td style="width:161px;">41003</td>
			<td style="width:627px;">For staining for J774A.1 cell death determination by epifluorescence microscopy (in conjunction with green fluorescent bacteria). Use Gel Red&#160; at 1X final concentration.&#160;&#160;</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:423px;">Cell culture incubator</td>
			<td style="width:248px;">Thermo Fisher Scientific</td>
			<td style="width:161px;">13-255-26</td>
			<td style="width:627px;">For incubation of J774A.1 cells (both before and after infection); can also be used for incubation of bacteria, or a standard atmosphere incubator can be used instead)</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:423px;">Orbital shaker</td>
			<td style="width:248px;">BellCo Glass</td>
			<td style="width:161px;">7744-01010</td>
			<td style="width:627px;">For shaking incubation of J774A.1 cells before infection; fits inside cell culture incubator; includes shaker base 7744-01000 and tray 7740-01010 (these are also available separately)</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:423px;">Shaker flasks (250 ml)</td>
			<td style="width:248px;">ChemGlass Life Sciences</td>
			<td style="width:161px;">CLS-2038-04</td>
			<td style="width:627px;">For shaking incubation of J774A.1 cells before infection</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:423px;">Shaker clamps for flasks (250 ml)</td>
			<td style="width:248px;">BellCo Glass</td>
			<td style="width:161px;">7744-16250</td>
			<td style="width:627px;">For shaking incubation of J774A.1 cells before infection</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:423px;">Shaker flasks (1000 ml)</td>
			<td style="width:248px;">ChemGlass Life Sciences</td>
			<td style="width:161px;">CLS-2038-07</td>
			<td style="width:627px;">For shaking incubation of J774A.1 cells before infection</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:423px;">Shaker clamps for flasks (1000 ml)</td>
			<td style="width:248px;">BellCo Glass</td>
			<td style="width:161px;">7744-16100</td>
			<td style="width:627px;">For shaking incubation of J774A.1 cells before infection</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:423px;">Sponge foam caps for flasks (250 ml - 1000 ml)</td>
			<td style="width:248px;">ChemGlass Life Sciences</td>
			<td style="width:161px;">CLS-1490-038</td>
			<td style="width:627px;">For shaking incubation of J774A.1 cells before infection; reduces risk of contamination relative to standard metal caps</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:423px;">MultiDrop Combi programmable multichannel peristaltic pump</td>
			<td style="width:248px;">Thermo Fisher Scientific</td>
			<td style="width:161px;">5840300</td>
			<td style="width:627px;">For dispensing J774A.1 cells, medium, and bacterial suspension containing fluorophores to large numbers of 384 well dishes</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:423px;">Combi standard bore manifold</td>
			<td style="width:248px;">Thermo Fisher Scientific</td>
			<td style="width:161px;">24072670</td>
			<td style="width:627px;">Default predispense volume of 20 ml is insufficient to compensate for settling &#8212; increase to 80 ml</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:423px;">White 384 well dishes treated for tissue culture</td>
			<td style="width:248px;">Corning</td>
			<td style="width:161px;">3570</td>
			<td style="width:627px;">For reading luminescence and fluorescence; Greiner catalog # 781080 also tested successfully</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:423px;">DMSO (tissue culture grade, in sealed ampoules)</td>
			<td style="width:248px;">Sigma-Aldrich</td>
			<td style="width:161px;">D2650</td>
			<td style="width:627px;">For dissolving positive control and test compounds</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:423px;">Azithromycin</td>
			<td style="width:248px;">Sigma-Aldrich</td>
			<td style="width:161px;">PHR1088</td>
			<td style="width:627px;">Antibiotic positive control</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:423px;">Saponin (from Quillaja bark)</td>
			<td style="width:248px;">Sigma-Aldrich</td>
			<td style="width:161px;">S-4521</td>
			<td style="width:627px;">Cytoxicity positive control</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:423px;">Multichannel pipettor</td>
			<td style="width:248px;">Thermo Fisher Scientific</td>
			<td style="width:161px;">Finnpipette</td>
			<td style="width:627px;">For transfer of fixed amounts of positive control compounds; pipettor must have digital dispensing with detents to enable repetitive fixed volume dispensing</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:423px;">Epson pin transfer robot</td>
			<td style="width:248px;">Epson/ICCB-L</td>
			<td style="width:161px;">(Custom equipment)</td>
			<td style="width:627px;">For transfer of fixed amounts of test compounds from library arrays</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:423px;">&#160;D300 digital dispensing system</td>
			<td style="width:248px;">Hewlett-Packard via Tecan</td>
			<td style="width:161px;">D300</td>
			<td style="width:627px;">For transfer of variable amounts of test compounds ranging from 11 picoliters to 10 microliters</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:423px;">T8+ cartridges for D300 digital dispensing system</td>
			<td style="width:248px;">Hewlett-Packard via Tecan</td>
			<td style="width:161px;">T8+</td>
			<td style="width:627px;">For dispensing test compounds</td>
		</tr>
		<tr height="126">
			<td height="126" style="height:126px;width:423px;">EnVision multi-mode plate reader</td>
			<td style="width:248px;">Perkin-Elmer</td>
			<td style="width:161px;">(Contact manufacturer)</td>
			<td style="width:627px;">For optimal detection of SYTOX Green fluorescence, use excitation filter 485/14, emission filter 535/25, and dichroic mirror 505 nm, with selection of minimum gain and transmittance, and &#8220;high concentration mode. For luminescence detection, use the &#34;USLUM&#34; protocol for high-sensitivity detection. For mNeptune2 detection, use excitation filter 600/8, emission filter 665/7.5, and dichroic mirror 658 nm, with selection of gain and transmittance to achieve the highest maximum signal possible without saturating the photomultiplier.</td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:423px;">Epifluorescence microscope with computer-connected digital camera</td>
			<td style="width:248px;">Nikon</td>
			<td style="width:161px;">Ti</td>
			<td style="width:627px;">For live cell imaging; any standard fluorescent microscope can substitute, with phase contrast or DIC optics, capable of imaging green (fluorescein), orange-red to red (Texas Red), and far-red (Cy5) fluorescence, with 100X oil objective for highest resolution</td>
		</tr>
		<tr height="84">
			<td height="84" style="height:84px;width:423px;">Glass-bottom tissue culture dishes</td>
			<td style="width:248px;">MatTek Corporation</td>
			<td style="width:161px;">P35G-1.5-20-C</td>
			<td style="width:627px;">For live cell imaging. Dishes such as the MatTek allow microscopic visualization at 600X or 1000X magnification through use of an inverted epifluorescent or confocal microscope.&#160; These specific dishes are 3.5 cm nominal diameter, 3.3 cm inside diameter, with 20 mm diameter #1.5 thickness cover slips inserted into the bottoms.</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:423px;">Photoshop CS6</td>
			<td style="width:248px;">Adobe</td>
			<td style="width:161px;"></td>
			<td style="width:627px;">Adobe photoshop or similar programs can be used to pseudocolor and merge light microscopic and fluorescent images.</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:423px;">Mathematica 10</td>
			<td style="width:248px;">Wolfam</td>
			<td style="width:161px;"></td>
			<td style="width:627px;">For generation of two-dimensioonal isocontour isobolograms and three-dimensional surface isobolograms.</td>
		</tr>
	</tbody>
</table>

high throughput, real-time, dual-readout testing of intracellular antimicrobial activity and eukaryotic cell cytotoxicity

Traditional measures of intracellular antimicrobial activity and eukaryotic cell cytotoxicity rely on endpoint assays. Such endpoint assays require several additional experimental steps prior to readout, such as cell lysis, colony forming unit determination, or reagent addition. When performing thousands of assays, for example, during high-throughput screening, the downstream effort required for these types of assays is considerable. Therefore, to facilitate high-throughput antimicrobial discovery, we developed a real-time assay to simultaneously identify inhibitors of intracellular bacterial growth and assess eukaryotic cell cytotoxicity. Specifically, real-time intracellular bacterial growth detection was enabled by marking bacterial screening strains with either a bacterial lux operon (1st generation assay) or fluorescent protein reporters (2nd generation, orthogonal assay). A non-toxic, cell membrane-impermeant, nucleic acid-binding dye was also added during initial infection of macrophages. These dyes are excluded from viable cells. However, non-viable host cells lose membrane integrity permitting entry and fluorescent labeling of nuclear DNA (deoxyribonucleic acid). Notably, DNA binding is associated with a large increase in fluorescent quantum yield that provides a solution-based readout of host cell death. We have used this combined assay to perform a high-throughput screen in microplate format, and to assess intracellular growth and cytotoxicity by microscopy. Notably, antimicrobials may demonstrate synergy in which the combined effect of two or more antimicrobials when applied together is greater than when applied separately. Testing for in vitro synergy against intracellular pathogens is normally a prodigious task as combinatorial permutations of antibiotics at different concentrations must be assessed. However, we found that our real-time assay combined with automated, digital dispensing technology permitted facile synergy testing. Using these approaches, we were able to systematically survey action of a large number of antimicrobials alone and in combination against the intracellular pathogen, Legionella pneumophila.

Microplate intracellular growth assay
Figure 1 diagrams the assay steps. The automated steps shown can be performed manually. However, throughput is greatly facilitated using liquid handling systems.
Figure 2 shows representative results from a 384-well microplate, dual-readout, real-time intracellular growth and eukaryotic cell cytoto...

Watch this Scientific Journal Video about High Throughput, Real-time, Dual-readout Testing of Intracellular Antimicrobial Activity and Eukaryotic Cell Cytotoxicity at JoVE.com

High Throughput, Real-time, Dual-readout Testing of Intracellular Antimicrobial Activity and Eukaryotic Cell Cytotoxicity

A high throughput, real-time assay was developed to simultaneously identify (1) eukaryotic cell-penetrant antimicrobials targeting an intracellular bacterial pathogen, and (2) assess eukaryotic cell cytotoxicity. A variation on the same technology was thereafter combined with digital dispensing technology to enable facile, high-resolution, dose-response, and two- and three-dimensional synergy studies.

Traditional measures of intracellular antimicrobial activity and eukaryotic cell cytotoxicity rely on endpoint assays. Such endpoint assays require ...

The overall goal of this protocol is to use a single combination real-time assay to identify specific small molecule inhibitors of intracellular bacterial growth that are non-toxic to host cells. This method can help answer key questions in the antimicrobial discovery field. Specifically, what types of compounds can penetrate into intracellular compartments and kill pathogens without harming the host cell?The main advantages of this technique are the bacterial growth mammalian cell toxicity are detected simultaneously using non-destructive, real-time assays. Generally, individuals new to this method will struggle with the scalability that it affords. Assaying greater than ten thousand compounds in a session requires a whole new set of techniques and equipment.In addition to Lucius, demonstrating a communal commitment to academic antimicrobial discovery and translational diagnostic microbiology are post-doctoral fellows, KP Smith, Yoon-Suk Kang, Jennifer Tsang, Thea Brennan-Krohn, and undergraduate Kat Truelson. To prepare host cells, culture J774A. 1 macrophage is in suspension in RPMI 1640, with nine percent iron supplemented calf serum.Initially passage cells in tissue culture flasks. After cells have become confluent in a 75 square centimeter tissue culture flask in 15 milliliters of medium, split the cells by scraping and diluting them to 65 milliliters with the same type of medium. Return 15 milliliters to the tissue culture flask, and transfer 50 milliliters to a 250 milliliter bacterial shaker flask.Aerate by setting rotation speed at approximately 120 revolutions per minute. For consistent growth, incubate at exactly five percent carbon dioxide and 37 degrees Celsius. Harvest the cells when they reach a density in the range of two point five million cells per milliliter, to five million cells per milliliter.Ensure dead cell percentage does not exceed 25 percent, as dead cells will increase background noise in cytotoxicity assays. It's critical to prevent cell settling in reservoirs when you're dispensing large volumes of macrophages and bacteria with liquid handlers. Swirl reservoirs every few minutes while dispensing to avoid non-uniformity and assay plate wells.Plate the cells in white tissue culture treated, 384 well microplates at 50, 000 cells in 30 microliters of tissue culture medium per well. Incubate microplates overnight to achieve ninety percent confluence on the day of the experiment. Prepare patches of bacteria for experiments, by spreading organisms thickly on a new BCYE plate and incubating one day to obtain confluent growth.Re-suspend the organisms in the same tissue culture medium used for the J774A. 1 cells. To perform the macrophage infection, add test compounds of interest, including screening compounds, and positive and negative controls for bacterial growth inhibition in eukaryotic cell lysis.Stock solutions should be dissolved at greater than or equal to 500x in DMSO or an aqueous solution, to allow sufficient dilution of the vehicle. Dilute luminescent bacteria to a target of two point five million CFU per millileter in tissue culture medium. Then, add appropriate non-toxic membrane impermeant nucleic acid finding dye at two point five x final assay concentration.Add 20 microliters of this mixture to each culture well. The final assay volume is 50 microliters and the final bacterial concentration should be one million CFU per milliliter for the lux epron reporter, or four million CFU per milliliter for the fluorescent protein reporter. Incubate at 37 degrees Celsius, for one to three days in five percent carbon dioxide at 100 percent relative humidity to prevent evaporative edge effects.To avoid temperature associated edge effects when reading assay results, thermally equilibrilate microplates prior to luminescence reading by placement in a single layer on a lab bench with lids ajar for approximately 20 minutes. Read bacterial growth and eukaryotic cell toxicity on a microplate luminometer and flourometer as appropriate for the reporters being used. Return microplates to the incubator if real-time readout at later time points is desired.Analyze the data as described in the text protocol. For dose response and synergy testing experiments, prepare macrophages in bacteria as before. Just prior to macrophage infection, or axenic incubation, use an automated liquid handling system to facilitate single dose response in combinatorial synergy testing set up through direct automated addition of antimicrobial dilutions according to manufacturers protocol.Add antimicrobials of experimental interest in a serial doubling dilution series. The goal is to span, on the high end, a concentration that completely eliminates growth, and on the low end, a concentration that shows no obvious activity. Shown here, are representative results over time for bacterial luminescence and cytotoxicity associated fluorescence.Note the contrasting effects of antimicrobial treatment and eukaryotic cell cytotoxic detergent. Dual IC50 and CC50 dose response determination in the same screening wells was used to determine selectivity for the antibiotic Doxycycline. Bacterial replication was inhibited by intermediate concentrations of antibiotic.However, cytotoxicity was observed at high concentrations consistent with the selectivity of approximately 100. The same assay format was used to test two dimensional dose response for combinations of Minocycline and Azithromycin. Isocontours connect points of equal intracellular growth inhibition.Here, concave isocontours suggested strong synergistic effects for the two drugs. Digital dispensing robotics for assay setup real-time readout, and high-throughput format enabled combinatorial triple synergy testing. Here, observation of a distinctly concave surface suggests a high degree of synergistic effect for combinations of Minocycline, Azithromycin, and Rifampin against intracellular growth of legionella pheumophila.After watching this video, you should have a good understanding of how to combine either fluorescent or luminescent assay read-out with real-time, cytotoxicity testing in high-throughput assay format. Following this procedure, other methods like confocal microscope can be applied answer questions about biological event in the whole cell, which are also sited with their antimicrobe activity or whole cell cytotoxicity. Though we studied the effects on legionella replication, the same techniques can also be applied to other intracellular pathogens such as Brucella, and microbacteria.We first conceived to this protocol when trying to figure out an assay simple and reliable enough to use in a very high-throughput screening format. Don't forget that working with bacterial pathogens, cell lines, and robotic equipment has some inherent risks and appropriate precautions should be taken, such as use of appropriate personal protective equipment while performing this procedure.

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Research

JoVE Journal

Immunology and Infection

7.8K visualizações.  Beth Israel Deaconess Medical Center. The overall goal of this protocol is to use a single combination real-time assay to identify specific small molecule inhibitors of intracellular bacterial growth that are non-toxic to host cells. This method can help answer key questions in the antimicrobial discovery field. Specifically, what types of compounds can penetrate into intracellular compartments and kill pathogens without harming the host cell?The main advantages of this technique are the bacterial growth mammalian cell tox...