This work has been supported by Elizabeth E. Kennedy Research Award.

1. Preparation of Producer Strain
<ol>
	<li>Streak a pneumococcal strain to be tested for bacteriocin production on a 5% sheep blood tryptic soy agar plate from -80 &#176;C freezer stocks. 
	NOTE: The use of blood plates for initial growth of the strain to be tested for inhibition greatly increases the reproducibility of the assay. Additionally, other non-pneumococcal strains that produce bacteriocins can be used although growth conditions may need to be modified for a specific organism. We have used Streptococcus mitis and Lactococcus lactis in the overlay assay successfully.</li>
	<li>Incubate the plate overnight (O/N) at 37 &#176;C with 5% CO2.</li>
	<li>After incubation of the producer strain, prepare the tryptic soy agar (TSA) plate by pipetting 3,000 to 4,000 units of catalase onto plates containing 25 ml of TSA and spread the catalase solution using sterile glass beads. Let the plate dry for about 10&#160;min&#160;under a biological safety cabinet.</li>
	<li>Collect a visible quantity of bacteria onto a pipette tip. Stab the pipette tip into the dried TSA plate. 
	NOTE: More than one producer strain can be stabbed into a single TSA plate. It is important to space out the stabs so that resulting halos do not overlap.
	<ol>
		<li>If possible, include known bacteriocin producer as a positive control and the strain to be used in the overlay as a negative control. 
		NOTE: Positive and negative controls are have been previously published and are available upon request10.</li>
	</ol>
	</li>
	<li>Incubate TSA plate containing multiple stabs at 37 &#176;C with 5% CO2 for 6 hr.</li>
</ol>
2. Making Glycerol Stocks of the Overlay Strain
<ol>
	<li>Prepare glycerol stocks (cultures grown to mid-exponential phase and then stored at -80 &#176;C after the addition of glycerol) prior to the day of the overlay assay. Inoculate 5-10 colonies of pneumococcal strain to be tested for sensitivity or pheromone secretion in Todd-Hewitt medium with 0.5% yeast extract (THY). 
	NOTE: Construction of BlpC inducible reporters has been previously described2 and strains are available upon request.</li>
	<li>Incubate 5-10 colonies in glass tubes with 5 ml of THY with tightly closed lids in a 37 &#176;C water bath without shaking.</li>
	<li>Incubate cultures at 37 &#176;C until they reach an OD620 of 0.3 to 0.5. 
	NOTE: This will take approximately 4-5 hr depending on the strain used.
	<ol>
		<li>Gently invert the tube a few times prior to measuring the OD.</li>
	</ol>
	</li>
	<li>If the experiment cannot be performed the same day or the strain will be used multiple times in the future, make glycerol stocks and resume the experiment at a later date. For glycerol stocks, add glycerol to cultures to a final concentration of 20%. Aliquot cultures into 1.5 ml microcentrifuge tubes and store at -80 &#176;C. NOTE: Samples can be stored for months at -80 &#176;C. If not making glycerol stocks, use samples directly for overlay assay.</li>
</ol>
3. Overlay Assay
<ol>
	<li>Just prior to overlay application, mix the overlay components. In a 15 ml conical tube, add 5 ml of THY, 3,000-4,000 U of catalase, and 200 &#181;l of the overlay strain broth culture that was either grown that day or a glycerol stock of the culture that was thawed at room temperature. If using the reporter strain, add 50 &#181;l of X-gal (40 mg/ml) to the overlay mixture. Use one conical tube per plate.</li>
	<li>Equilibrate overlay mixture at room temperature prior to addition of molten TSA.</li>
	<li>Remove TSA plate with stabbed strain from incubator. Melt solid TSA in microwave and keep at 55 &#176;C water bath until ready to use. Add 3 ml of molten TSA with 1.5% agar cooled to 55 &#176;C to overlay mixture.
	<ol>
		<li>Prepare the overlay mixture immediately before pipetting, the mixture will begin to solidify very quickly. NOTE: If the overlay begins to solidify before plating, the results will be uninterpretable.</li>
	</ol>
	</li>
	<li>Mix the overlay mixture by pipetting up and down several times with a 5 ml pipet being careful not to introduce bubbles into the mixture. Slowly pipette overlay mixture directly on to the stabbed TSA plate. Keep the plate on the benchtop for few minutes allowing the agar to harden.
	<ol>
		<li>Do not rotate the plate to distribute the overlay mixture, this will pull growth from the stabbed culture into the overlay.</li>
	</ol>
	</li>
	<li>Carefully place TSA plate with overlay into 37 &#176;C incubator containing 5% CO2 O/N (approximately 16-18 hr).</li>
	<li>Observe the plates after overnight growth. The plates should appear opaque from growth of the overlay strain except in areas where inhibition or pheromone signaling has occurred. These will appear as either clear or blue zones around the stabbed strain, respectively. 
	NOTE: Although measurements of the diameter of blue or clearing can be determined for quantitative assessment, differences in the diameter can also vary depending on the amount of bacteria that was stabbed into the plate. The overlay assay is a qualitative assay, any quantitative assessment should be interpreted with caution. Any visible clearing as compared to the negative control is regarded as activity.</li>
</ol>

<ol>
	<li>Dawid, S., Roche, A. M., Weiser, J. N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+blp+bacteriocins+of+Streptococcus+pneumoniae+mediate+intraspecies+competition+both+in+vitro+and+in+vivo.">The blp bacteriocins of Streptococcus pneumoniae mediate intraspecies competition both in vitro and in vivo.</a> Infect Immun. 75 (1), 443-451 (2007).</li><li>Sawa, N., 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=Isolation+and+characterization+of+enterocin+W,+a+novel+two-peptide+lantibiotic+produced+by+Enterococcus+faecalis+NKR-4-1.">Isolation and characterization of enterocin W, a novel two-peptide lantibiotic produced by Enterococcus faecalis NKR-4-1.</a> Appl Environ Microbiol. 78 (3), 900-903 (2012).</li><li>Kochan, T. J., Dawid, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+HtrA+protease+of+Streptococcus+pneumoniae+controls+density-dependent+stimulation+of+the+bacteriocin+blp+locus+via+disruption+of+pheromone+secretion.">The HtrA protease of Streptococcus pneumoniae controls density-dependent stimulation of the bacteriocin blp locus via disruption of pheromone secretion.</a> J Bacteriol. 195 (7), 1561-1572 (2013).</li><li>Lux, T., Nuhn, M., Hakenbeck, R., Reichmann, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Diversity+of+bacteriocins+and+activity+spectrum+in+Streptococcus+pneumoniae.">Diversity of bacteriocins and activity spectrum in Streptococcus pneumoniae.</a> J Bacteriol. 189 (21), 7741-7751 (2007).</li><li>Reichmann, P., Hakenbeck, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Allelic+variation+in+a+peptide-inducible+two-component+system+of+Streptococcus+pneumoniae.">Allelic variation in a peptide-inducible two-component system of Streptococcus pneumoniae.</a> FEMS Microbiol Lett. 190 (2), 231-236 (2000).</li><li>Saizieu, A., 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=Microarray-based+identification+of+a+novel+Streptococcus+pneumoniae+regulon+controlled+by+an+autoinduced+peptide.">Microarray-based identification of a novel Streptococcus pneumoniae regulon controlled by an autoinduced peptide.</a> J Bacteriol. 182 (17), 4696-4703 (2000).</li><li>Barbour, A., Philip, K., Muniandy, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Enhanced+production,+purification,+characterization+and+mechanism+of+action+of+salivaricin+9+lantibiotic+produced+by+Streptococcus+salivarius+NU10.">Enhanced production, purification, characterization and mechanism of action of salivaricin 9 lantibiotic produced by Streptococcus salivarius NU10.</a> PLoS One. 8 (10), 77751 (2013).</li><li>Wladyka, B., 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=Isolation,+biochemical+characterization,+and+cloning+of+a+bacteriocin+from+the+poultry-associated+Staphylococcus+aureus+strain+CH-91.">Isolation, biochemical characterization, and cloning of a bacteriocin from the poultry-associated Staphylococcus aureus strain CH-91.</a> Appl Microbiol Biotechnol. 97 (16), 7229-7239 (2013).</li><li>Shea, E. 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J., Dawid, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+HtrA+protease+of+Streptococcus+pneumoniae+controls+density-dependent+stimulation+of+the+bacteriocin+blp+locus+via+disruption+of+pheromone+secretion.">The HtrA protease of Streptococcus pneumoniae controls density-dependent stimulation of the bacteriocin blp locus via disruption of pheromone secretion.</a> J Bacteriol. 195, 1561-1572 (2013).</li><li>Widdick, D. A., 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=Cloning+and+engineering+of+the+cinnamycin+biosynthetic+gene+cluster+from+Streptomyces+cinnamoneus+cinnamoneus+DSM+40005.">Cloning and engineering of the cinnamycin biosynthetic gene cluster from Streptomyces cinnamoneus cinnamoneus DSM 40005.</a> Proc Natl Acad Sci U S A. 100 (7), 4316-4321 (2003).</li><li>Begley, M., Cotter, P. D., Hill, C., Ross, R. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+of+a+novel+two-peptide+lantibiotic,+lichenicidin,+following+rational+genome+mining+for+LanM+proteins.">Identification of a novel two-peptide lantibiotic, lichenicidin, following rational genome mining for LanM proteins.</a> Appl Environ Microbiol. 75 (17), 5451-5460 (2009).</li></ol>

The authors have nothing to disclose.

This overlay assay is a rapid way to determine the range of activity for bacteriocin producers and to demonstrate competitive interactions that may occur among pneumococcal strains. The overlay assay can be adapted to use for screening multiple strains for bacteriocin production on a single plate. We have successfully screened large strain collections with this assay by using a 48-pin replicator to inoculate SBA plates from one half of a 96-well plate. After overnight incubation, growth is transferred to the TSA plate us...

Streptococcus pneumoniae, a common colonizer of the polymicrobial community of the nasopharynx, is able to compete with other pneumococci and closely related species through the production of bacterially produced antimicrobial peptides (bacteriocins). Every fully-sequenced pneumococcal strain examined to date contains a version of the bacteriocin-like peptide locus, blp. Bacteriocin production by pneumococcus has been demonstrated to be important in the outcome of both in vitro and in vivo competition1-4. Competitive dynamics are influenced by the expression of diverse bacteriocins along with cognate immunity proteins in response to a specific peptide pheromone. Induction of the blp locus is controlled by a quorum sensing system in which a peptide pheromone, BlpC, binds to the sensor kinase, BlpH, and initiates a signaling cascade resulting in the transcription of the blp locus5,6. There are four allelic variations of BlpC that each bind to its cognate BlpH6. For the cell to survive the effects of its own bacteriocin, the genes that encode cognate immunity proteins are transcribed on the same operon as each of the bacteriocin genes. Killing occurs if a competitor strain is not able to upregulate the blp locus in response to exogenous pheromone or, if the strain lacks the specific immunity gene required for protection. The transporter complex, BlpAB is required for the secretion and processing of the peptide pheromone and the bacteriocin peptides2,4. Recently, it has been shown that a significant proportion of pneumococcal strains are &#8220;cheaters&#8221; meaning they have a conserved mutation in the blpA gene which renders them unable to secrete pheromones and bacteriocins1,2. These strains are able to respond to exogenous BlpC2 secreted by neighboring strains allowing for the production of immunity proteins.
Although, crude preparations of bacteriocins from supernatants can be prepared from producer strains using biochemical methods steps to achieve purity, this approach is not useful for screening large collections of isolates and if the level of bacteriocin expression is low in broth grown cultures2,7-9. The overlay assay is used as a rapid way to investigate the competitive dynamics between strains that may exist in vitro. To do so, a pneumococcal strain is pre-inoculated onto an agar plate and allowed to grow to achieve local bacterial concentrations sufficient for induction of the blp locus. A second strain is then inoculated into a molten soft agar solution which is then applied over the pre-inoculated strain to test for sensitivity. To evaluate for activity of the blp locus (independent of inhibitory activity), strains can be overlaid with a series of three previously described BlpC reporter strains. These strains were constructed to contain one of three different blpH alleles that respond to the three most common BlpC pheromones secreted by the pneumococci. The reporter strains have an integrated lacZ gene that is under the control of a BlpH dependent promoter and carry a deletion in the blpC gene that prevents self-stimulation10,11.

<table border="0" cellpadding="0" cellspacing="0" width="753">
	<tbody>
		<tr height="42">
			<td height="42" style="height:42px;width:212px;">Name of Material/ Equipment</td>
			<td style="width:71px;">Company</td>
			<td style="width:119px;">Catalog Number</td>
			<td style="width:351px;">Comments/Description</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:212px;">Trypticase Soy Agar with 5% Sheep Blood</td>
			<td style="width:71px;">Fisher</td>
			<td style="width:119px;">B21261X&#160;</td>
			<td>For growth from freezer cultures</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:212px;">Catalase</td>
			<td style="width:71px;">Sigma</td>
			<td style="width:119px;">C100-500mg</td>
			<td>4,741 Units per plate</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:212px;">Todd Hewitt Broth + Yeast Extract (THY)</td>
			<td style="width:71px;">Fisher</td>
			<td style="width:119px;">DF0492-17-6&#160;</td>
			<td>30 g of THB, 5 g yeast extract, 1 L ddH20 autoclave</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:212px;">Trypticase Soy Broth + Agar plates (TSA)</td>
			<td style="width:71px;">Fisher</td>
			<td style="width:119px;">B11768&#160;</td>
			<td>30 g of TS, 15 g agar, 1 L ddH20 autoclave</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:212px;">5-Bromo-4-chloro-3-indolyl &#946;-D-galactopyranoside (X-gal)</td>
			<td style="width:71px;">Sigma</td>
			<td style="width:119px;">B4252-50MG</td>
			<td>Dissolve in dimethylformamide</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:212px;">Petri dishes</td>
			<td style="width:71px;">Fisher</td>
			<td>FB0875712</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:212px;">Spectrophometer</td>
			<td style="width:71px;"></td>
			<td style="width:119px;"></td>
			<td>Measures the OD620 of cultures</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:212px;">37 &#176;C water bath</td>
			<td style="width:71px;"></td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:212px;">37 &#176;C incubator with 5% CO2</td>
			<td style="width:71px;"></td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:212px;">15 ml conical tube</td>
			<td style="width:71px;"></td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
	</tbody>
</table>

using the overlay assay to qualitatively measure bacterial production of and sensitivity to pneumococcal bacteriocins

Streptococcus pneumoniae colonizes the highly diverse polymicrobial community of the nasopharynx where it must compete with resident organisms. We have shown that bacterially produced antimicrobial peptides (bacteriocins) dictate the outcome of these competitive interactions. All fully-sequenced pneumococcal strains harbor a bacteriocin-like peptide (blp) locus. The blp locus encodes for a range of diverse bacteriocins and all of the highly conserved components needed for their regulation, processing, and secretion. The diversity of the bacteriocins found in the bacteriocin immunity region (BIR) of the locus is a major contributor of pneumococcal competition. Along with the bacteriocins, immunity genes are found in the BIR and are needed to protect the producer cell from the effects of its own bacteriocin. The overlay assay is a quick method for examining a large number of strains for competitive interactions mediated by bacteriocins. The overlay assay also allows for the characterization of bacteriocin-specific immunity, and detection of secreted quorum sensing peptides. The assay is performed by pre-inoculating an agar plate with a strain to be tested for bacteriocin production followed by application of a soft agar overlay containing a strain to be tested for bacteriocin sensitivity. A zone of clearance surrounding the stab indicates that the overlay strain is sensitive to the bacteriocins produced by the pre-inoculated strain. If no zone of clearance is observed, either the overlay strain is immune to the bacteriocins being produced or the pre-inoculated strain does not produce bacteriocins. To determine if the blp locus is functional in a given strain, the overlay assay can be adapted to evaluate for peptide pheromone secretion by the pre-inoculated strain. In this case, a series of four lacZ-reporter strains with different pheromone specificity are used in the overlay.

There are two possible outcomes in the overlay assay. It should be possible to see growth of the stabbed strain after overnight incubation. In Figure 1A, the overlay strain is sensitive to the bacteriocins being produced. A zone of clearance can be visualized surrounding the stabbed strain. Additionally, swirling of the stabbed strain into the overlay mixture is possible and can be seen in the Figure 1A. In Figure 1B, the overlay strain is immune to the bacteriocins bein...

Watch this Scientific Journal Video about Using the Overlay Assay to Qualitatively Measure Bacterial Production of and Sensitivity to Pneumococcal Bacteriocins at JoVE.com

Using the Overlay Assay to Qualitatively Measure Bacterial Production of and Sensitivity to Pneumococcal Bacteriocins

Competition in Streptococcus pneumoniae is mediated by bacteriocins, small antimicrobial peptides with inhibitory activity towards pneumococcus and other related species.&#160; Here we describe an optimized bacterial overlay assay that allows for the characterization of bacteriocin activity and inhibitory spectrum, bacteriocin-specific immunity, and detection of secreted quorum sensing peptides.

Streptococcus pneumoniae colonizes the highly diverse polymicrobial community of the nasopharynx where it must compete with resident organisms.  We have ...

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JoVE Journal

Immunology and Infection

13.4K vistas.  University of Michigan. Competition in Streptococcus pneumoniae is mediated by bacteriocins, small antimicrobial peptides with inhibitory activity towards pneumococcus and other related species.  Here we describe an optimized bacterial overlay assay that allows for the characterization of bacteriocin activity and inhibitory spectrum, bacteriocin-specific immunity, and detection of secreted quorum sensing peptides. 

Video: Using the Overlay Assay to Qualitatively Measure Bacterial Production of and Sensitivity to Pneumococcal Bacteriocins

Using Luciferase to Image Bacterial Infections in Mice

Imaging is a valuable technique that can be used to monitor biological processes. In particular, the presence of cancer cells, stem cells, specific immune cell types, viral pathogens, parasites and bacteria can be followed in real-time within living animals 1-2. Application of bioluminescence imaging to the study of pathogens has advantages as compared to conventional strategies for analysis of infections in animal models3-4. Infections can be visualized within individual animals over time, without requiring euthanasia to determine the location and quantity of the pathogen. Optical imaging allows comprehensive examination of all tissues and organs, rather than sampling of sites previously known to be infected. In addition, the accuracy of inoculation into specific tissues can be directly determined prior to carrying forward animals that were unsuccessfully inoculated throughout the entire experiment. Variability between animals can be controlled for, since imaging allows each animal to be followed individually. Imaging has the potential to greatly reduce animal numbers needed because of the ability to obtain data from numerous time points without having to sample tissues to determine pathogen load3-4.
This protocol describes methods to visualize infections in live animals using bioluminescence imaging for recombinant strains of bacteria expressing luciferase. The click beetle (CBRLuc) and firefly luciferases (FFluc) utilize luciferin as a substrate5-6. The light produced by both CBRluc and FFluc has a broad wavelength from 500 nm to 700 nm, making these luciferases excellent reporters for the optical imaging in living animal models7-9. This is primarily because wavelengths of light greater than 600 nm are required to avoid absorption by hemoglobin and, thus, travel through mammalian tissue efficiently. Luciferase is genetically introduced into the bacteria to produce light signal10. Mice are pulmonary inoculated with bioluminescent bacteria intratracheally to allow monitoring of infections in real time. After luciferin injection, images are acquired using the IVIS Imaging System. During imaging, mice are anesthetized with isoflurane using an XGI-8 Gas Anethesia System. Images can be analyzed to localize and quantify the signal source, which represents the bacterial infection site(s) and number, respectively. After imaging, CFU determination is carried out on homogenized tissue to confirm the presence of bacteria. Several doses of bacteria are used to correlate bacterial numbers with luminescence. Imaging can be applied to study of pathogenesis and evaluation of the efficacy of antibacterial compounds and vaccines.

Methods for bioluminescence imaging of bacterial infections in living animals are decribed. Pathogens are modified to express luciferase allowing optical whole body imaging of infections in live animals. Animal models can be infected with luciferase expressing pathogens and the resulting course of disease visualized in real-time by bioluminescence imaging.

Imaging is a valuable technique that can be used to monitor biological processes.  In particular, the presence of cancer cells, stem cells, specific ...

A Functional Whole Blood Assay to Measure Viability of Mycobacteria, using Reporter-Gene Tagged BCG or M.Tb (BCG lux/M.Tb lux)

Functional assays have long played a key role in measuring of immunogenicity of a given vaccine. This is conventionally expressed as serum bactericidal titers. Studies of serum bactericidal titers in response to childhood vaccines have enabled us to develop and validate cut-off levels for protective immune responses and such cut-offs are in routine use. No such assays have been taken forward into the routine assessment of vaccines that induce primarily cell-mediated immunity in the form of effector T cell responses, such as TB vaccines. In the animal model, the performance of a given vaccine candidate is routinely evaluated in standardized bactericidal assays, and all current novel TB-vaccine candidates have been subjected to this step in their evaluation prior to phase 1 human trials. The assessment of immunogenicity and therefore likelihood of protective efficacy of novel anti-TB vaccines should ideally undergo a similar step-wise evaluation in the human models now, including measurements in bactericidal assays.
Bactericidal assays in the context of tuberculosis vaccine research are already well established in the animal models, where they are applied to screen potentially promising vaccine candidates. Reduction of bacterial load in various organs functions as the main read-out of immunogenicity. However, no such assays have been incorporated into clinical trials for novel anti-TB vaccines to date.
Although there is still uncertainty about the exact mechanisms that lead to killing of mycobacteria inside human macrophages, the interaction of macrophages and T cells with mycobacteria is clearly required. The assay described in this paper represents a novel generation of bactericidal assays that enables studies of such key cellular components with all other cellular and humoral factors present in whole blood without making assumptions about their relative individual contribution. The assay described by our group uses small volumes of whole blood and has already been employed in studies of adults and children in TB-endemic settings. We have shown immunogenicity of the BCG vaccine, increased growth of mycobacteria in HIV-positive patients, as well as the effect of anti-retroviral therapy and Vitamin D on mycobacterial survival in vitro. Here we summarise the methodology, and present our reproducibility data using this relatively simple, low-cost and field-friendly model.
Note: Definitions/Abbreviations
BCG lux = M. bovis BCG, Montreal strain, transformed with shuttle plasmid pSMT1 carrying the luxAB genes from Vibrio harveyi, under the control of the mycobacterial GroEL (hsp60) promoter. 
CFU = Colony Forming Unit (a measure of mycobacterial viability).

A Functional Whole Blood Assay to Measure Viability of Mycobacteria, using Reporter-Gene Tagged BCG or M.Tb BCG lux/M.Tb lux

We describe an alternative approach to the enumeration of mycobacteria in vitro, which uses reporter-gene tagged mycobacteria instead of colony-forming units (CFU). &#x201C;Survival&#x201D; of organisms as well as host response-markers are measured simultaneously, providing a low-cost, versatile and functional system for studies of host/pathogen interactions in the context of tuberculosis.

Functional assays have long played a key role in measuring of immunogenicity of a given vaccine. This is conventionally expressed as serum bactericidal ...

A Visual Assay to Monitor T6SS-mediated Bacterial Competition

Type VI secretion systems (T6SSs) are molecular nanomachines allowing Gram-negative bacteria to transport and inject proteins into a wide variety of target cells1,2. The T6SS is composed of 13 core components and displays structural similarities with the tail-tube of bacteriophages3. The phage uses a tube and a puncturing device to penetrate the cell envelope of target bacteria and inject DNA. It is proposed that the T6SS is an inverted bacteriophage device creating a specific path in the bacterial cell envelope to drive effectors and toxins to the surface. The process could be taken further and the T6SS device could perforate other cells with which the bacterium is in contact, thus injecting the effectors into these targets. The tail tube and puncturing device parts of the T6SS are made with Hcp and VgrG proteins, respectively4,5.
The versatility of the T6SS has been demonstrated through studies using various bacterial pathogens. The Vibrio cholerae T6SS can remodel the cytoskeleton of eukaryotic host cells by injecting an "evolved" VgrG carrying a C-terminal actin cross-linking domain6,7. Another striking example was recently documented using Pseudomonas aeruginosa which is able to target and kill bacteria in a T6SS-dependent manner, therefore promoting the establishment of bacteria in specific microbial niches and competitive environment8,9,10.
In the latter case, three T6SS-secreted proteins, namely Tse1, Tse2 and Tse3 have been identified as the toxins injected in the target bacteria (Figure 1). The donor cell is protected from the deleterious effect of these effectors via an anti-toxin mechanism, mediated by the Tsi1, Tsi2 and Tsi3 immunity proteins8,9,10. This antimicrobial activity can be monitored when T6SS-proficient bacteria are co-cultivated on solid surfaces in competition with other bacterial species or with T6SS-inactive bacteria of the same species8,11,12,13.
The data available emphasized a numerical approach to the bacterial competition assay, including time-consuming CFU counting that depends greatly on antibiotic makers. In the case of antibiotic resistant strains like P. aeruginosa, these methods can be inappropriate. Moreover, with the identification of about 200 different T6SS loci in more than 100 bacterial genomes14, a convenient screening tool is highly desirable. We developed an assay that is easy to use and requires standard laboratory material and reagents. The method offers a rapid and qualitative technique to monitor the T6SS-dependent bactericidal/bacteriostasis activity by using a reporter strain as a prey (in this case Escherichia coli DH5&alpha;) allowing a-complementation of the lacZ gene. Overall, this method is graphic and allows rapid identification of T6SS-related phenotypes on agar plates. This experimental protocol may be adapted to other strains or bacterial species taking into account specific conditions such as growth media, temperature or time of contact.

We describe a qualitative assay to monitor bacterial competition mediated by the Pseudomonas aeruginosa type VI secretion system (T6SS). The assay relies on the survival/killing of Escherichia coli target cells carrying a lacZ-reporter. This technique is adjustable to assess the bactericidal/bacteriostasis activity of T6SS-proficient microorganisms.

Type VI secretion systems (T6SSs) are molecular  nanomachines allowing Gram-negative bacteria to transport and inject proteins  into a wide variety of ...

Using Click Chemistry to Measure the Effect of Viral Infection on Host-Cell RNA Synthesis

Many RNA viruses have evolved the ability to inhibit host cell transcription as a means to circumvent cellular defenses. For the study of these viruses, it is therefore important to have a quick and reliable way of measuring transcriptional activity in infected cells. Traditionally, transcription has been measured either by incorporation of radioactive nucleosides such as 3H-uridine followed by detection via autoradiography or scintillation counting, or incorporation of halogenated uridine analogs such as 5-bromouridine (BrU) followed by detection via immunostaining. The use of radioactive isotopes, however, requires specialized equipment and is not feasible in a number of laboratory settings, while the detection of BrU can be cumbersome and may suffer from low sensitivity.
The recently developed click chemistry, which involves a copper-catalyzed triazole formation from an azide and an alkyne, now provides a rapid and highly sensitive alternative to these two methods. Click chemistry is a two step process in which nascent RNA is first labeled by incorporation of the uridine analog 5-ethynyluridine (EU), followed by detection of the label with a fluorescent azide. These azides are available as several different fluorophores, allowing for a wide range of options for visualization.
This protocol describes a method to measure transcriptional suppression in cells infected with the Rift Valley fever virus (RVFV) strain MP-12 using click chemistry. Concurrently, expression of viral proteins in these cells is determined by classical intracellular immunostaining. Steps 1 through 4 detail a method to visualize transcriptional suppression via fluorescence microscopy, while steps 5 through 8 detail a method to quantify transcriptional suppression via flow cytometry. This protocol is easily adaptable for use with other viruses.

This method describes the use of click chemistry to measure changes in host cell transcription after infection with the Rift Valley fever virus (RVFV) strain MP-12. Results can be visualized qualitatively via fluorescence microscopy or obtained quantitatively through flow cytometry. This method is adaptable for use with other viruses.

Many RNA viruses have evolved the ability to inhibit host cell transcription as a means to circumvent cellular defenses. For the study of these viruses, ...

Investigating the Effects of Probiotics on Pneumococcal Colonization Using an In Vitro Adherence Assay

Adherence of Streptococcus pneumoniae (the pneumococcus) to the epithelial lining of the nasopharynx can result in colonization and is considered a prerequisite for pneumococcal infections such as pneumonia and otitis media. In vitro adherence assays can be used to study the attachment of pneumococci to epithelial cell monolayers and to investigate potential interventions, such as the use of probiotics, to inhibit pneumococcal&#160;colonization.&#160;The protocol described here is used to investigate the effects of the probiotic Streptococcus salivarius on the adherence of pneumococci to the human epithelial cell line CCL-23 (sometimes referred to as HEp-2 cells). The assay involves three main steps: 1) preparation of epithelial and bacterial cells, 2) addition of bacteria to epithelial cell monolayers, and 3) detection of adherent pneumococci by viable counts (serial dilution and plating) or quantitative real-time PCR (qPCR). This technique is relatively straightforward and does not require specialized equipment other than a tissue culture setup. The assay can be used to test other probiotic species and/or potential inhibitors of pneumococcal colonization and can be easily modified to address other scientific questions regarding pneumococcal adherence and invasion.

Investigating the Effects of Probiotics on Pneumococcal Colonization Using an In Vitro Adherence Assay

In vitro adherence assays can be used to study the attachment of Streptococcus pneumoniae to epithelial cell monolayers and to investigate potential interventions such as the use of probiotics for inhibiting pneumococcal colonization.

Adherence of Streptococcus pneumoniae (the pneumococcus) to the epithelial lining of the nasopharynx can result in colonization and is considered a ...

Cell-based Flow Cytometry Assay to Measure Cytotoxic Activity

Cytolytic activity of CD8+ T cells is rarely evaluated. We describe here a new cell-based assay to measure the capacity of antigen-specific CD8+ T cells to kill CD4+ T cells loaded with their cognate peptide. Target CD4+ T cells are divided into two populations, labeled with two different concentrations of CFSE. One population is pulsed with the peptide of interest (CFSE-low) while the other remains un-pulsed (CFSE-high). Pulsed and un-pulsed CD4+ T cells are mixed at an equal ratio and incubated with an increasing number of purified CD8+ T cells. The specific killing of autologous target CD4+ T cells is analyzed by flow cytometry after coculture with CD8+ T cells containing the antigen-specific effector CD8+ T cells detected by peptide/MHCI tetramer staining. The specific lysis of target CD4+ T cells measured at different effector versus target ratios, allows for the calculation of lytic units, LU30/106 cells. This simple and straightforward assay allows for the accurate measurement of the intrinsic capacity of CD8+ T cells to kill target CD4+ T cells.

This protocol describes a sensitive, cell-based cytotoxicity assay. By enumerating the decrease in frequency of live target CD4+ T cells in the presence of an increasing number of effector CD8+ T cells, this assay allows for the direct assessment of cytolytic activity of antigen-specific CD8+ T cells.

Cytolytic activity of CD8+ T cells is rarely evaluated. We describe here a new cell-based assay to measure the capacity of antigen-specific CD8+ T cells ...

Capsular Serotyping of Streptococcus pneumoniae Using the Quellung Reaction

There are over 90 different capsular serotypes of Streptococcus pneumoniae (the pneumococcus). As well as being a tool for understanding pneumococcal epidemiology, capsular serotyping can provide useful information for vaccine efficacy and impact studies.&#160;The Quellung reaction is the gold standard method for pneumococcal capsular serotyping. The method involves testing a pneumococcal cell suspension with pooled and specific antisera directed against the capsular polysaccharide. The antigen-antibody reactions are observed microscopically. The protocol has three main steps: 1) preparation of a bacterial cell suspension, 2) mixing of cells and antisera on a glass slide, and 3) reading the Quellung reaction using a microscope. The Quellung reaction is reasonably simple to perform and can be applied wherever a suitable microscope and antisera are available.

Capsular Serotyping of Streptococcus pneumoniae Using the Quellung Reaction

The Quellung reaction is the gold standard technique for serotyping Streptococcus pneumoniae. This technique utilizes a microscope and specific pneumococcal antisera and is commonly used in reference and research laboratories worldwide.

There are over 90 different capsular serotypes of Streptococcus pneumoniae (the pneumococcus). As well as being a tool for understanding pneumococcal ...

Capsular Serotyping of Streptococcus pneumoniae by Latex Agglutination

Latex agglutination reagents are widely used in microbial diagnosis, identification and serotyping. Streptococcus pneumoniae (the pneumococcus) is a major cause of morbidity and mortality world-wide. Current vaccines target the pneumococcal capsule, and there are over 90 capsular serotypes. Serotyping pneumococcal isolates is therefore important for assessing the impact of vaccination programs and for epidemiological purposes. The World Health Organization has recommended latex agglutination as an alternative method to the &#8216;gold standard&#8217; Quellung test for serotyping pneumococci. Latex agglutination is a relatively simple, quick and inexpensive method; and is therefore suitable for resource-poor settings as well as laboratories with high-volume workloads. Latex agglutination reagents can be prepared in-house utilizing commercially-sourced antibodies that are passively attached to latex particles. This manuscript describes a method of production and quality control of latex agglutination reagents, and details a sequential testing approach which is time- and cost-effective. 
This method of production and quality control may also be suitable for other testing purposes.

Capsular Serotyping of Streptococcus pneumoniae by Latex Agglutination

Latex agglutination testing is a simple, rapid and inexpensive method for serotyping Streptococcus pneumoniae, and has also been widely applied in diagnostic microbiology. This manuscript describes the in-house production of latex agglutination reagents, quality control procedures and the application of this technique to pneumococcal serotyping.

Latex agglutination reagents are widely used in microbial diagnosis, identification and serotyping. Streptococcus pneumoniae (the pneumococcus) is a major ...

Methods to Inhibit Bacterial Pyomelanin Production and Determine the Corresponding Increase in Sensitivity to Oxidative Stress

Pyomelanin is an extracellular red-brown pigment produced by several bacterial and fungal species. This pigment is derived from the tyrosine catabolism pathway and contributes to increased oxidative stress resistance. Pyomelanin production in Pseudomonas aeruginosa is reduced in a dose dependent manner through treatment with 2-[2-nitro-4-(trifluoromethyl)benzoyl]-1,3-cyclohexanedione (NTBC). We describe a titration method using multiple concentrations of NTBC to determine the concentration of drug that will reduce or abolish pyomelanin production in bacteria. The titration method has an easily quantifiable outcome, a visible reduction in pigment production with increasing drug concentrations. We also describe a microtiter plate method to assay antibiotic minimum inhibitory concentration (MIC) in bacteria. This method uses a minimum of resources and can easily be scaled up to test multiple antibiotics in one microtiter plate for one strain of bacteria. The MIC assay can be adapted to test the affects of non-antibiotic compounds on bacterial growth at specific concentrations. Finally, we describe a method for testing bacterial sensitivity to oxidative stress by incorporating H2O2 into agar plates and spotting multiple dilutions of bacteria onto the plates. Sensitivity to oxidative stress is indicated by reductions in colony number and size for the different dilutions on plates containing H2O2 compared to a no H2O2 control. The oxidative stress spot plate assay uses a minimum of resources and low concentrations of H2O2. Importantly, it also has good reproducibility. This spot plate assay could be adapted to test bacterial sensitivity to various compounds by incorporating the compounds in agar plates and characterizing the resulting bacterial growth.

Bacterial pyomelanin production results in increased resistance to oxidative stress and virulence. We report on techniques that can be used to determine inhibition of pyomelanin production and assay the resulting increase in sensitivity to oxidative stress in bacteria, as well as determine antibiotic minimum inhibitory concentration (MIC).

Pyomelanin is an extracellular red-brown pigment produced by several bacterial and fungal species. This pigment is derived from the tyrosine catabolism ...

Use of the Soft-agar Overlay Technique to Screen for Bacterially Produced Inhibitory Compounds

The soft-agar overlay technique was originally developed over 70 years ago and has been widely used in several areas of microbiological research, including work with bacteriophages and bacteriocins, proteinaceous antibacterial agents. This approach is relatively inexpensive, with minimal resource requirements. This technique consists of spotting supernatant from a donor strain (potentially harboring a toxic compound(s)) onto a solidified soft agar overlay that is seeded with a bacterial test strain (potentially sensitive to the toxic compound(s)). We utilized this technique to screen a library of Pseudomonas syringae strains for intraspecific killing. By combining this approach with a precipitation step and targeted gene deletions, multiple toxic compounds produced by the same strain can be differentiated. The two antagonistic agents commonly recovered using this technique are bacteriophages and bacteriocins. These two agents can be differentiated using two simple additional tests. Performing a serial dilution on a supernatant containing bacteriophage will result in individual plaques becoming less in number with greater dilution, whereas serial dilution of a supernatant containing bacteriocin will result a clearing zone that becomes uniformly more turbid with greater dilution. Additionally, a bacteriophage will produce a clearing zone when spotted onto a fresh soft agar overlay seeded with the same strain, whereas a bacteriocin will not produce a clearing zone when transferred to a fresh soft agar lawn, owing to the dilution of the bacteriocin.

We describe a simple method for screening bacterial cultures for the production of compounds inhibitory towards other bacteria.