We thank Pr. Bernard La Scola for helpful technical advices and interesting discussion on amoebal coculture and amoebal enrichment. We also thank Dr Vincent Thomas for his help in implementing the technique in our laboratory.

1. Amoebal Coculture
1.1 Sample preparation
<ol>
	<li>Environmental sample
	<ol>
		<li>Water samples 
		Filter the water sample (500 ml to 1 L) through a 0.22 &#956;m pore size membrane. Then, shake the membrane in Page&#39;s amoeba saline medium PAS (120 mg of NaCl, 4 mg of MgSO4&#8226;7H2O, 4 mg of CaCl2&#8226;2H2O, 142 mg of Na2HPO4, and 136 mg of KH2PO4 in 1 L of distilled water).</li>
		<li>Solid samples 
		Resuspend solid samples like soil or sand samples and semi-solid samples such as activated sludge in distilled water or PBS and filter them through a 0.22 &#956;m pore size membrane. Then, shake the membrane in PAS.</li>
		<li>Samples highly contaminated with endogenous amoebae and protozoa 
		First sediment the samples by low speed centrifugation (180 x g) for 10 min or filter it through a 5 &#956;m pore size membrane. Further process the supernatant (respectively Filtrate), as in 1.1.1. 
		Note: Other decontamination techniques might be used to further decontaminate environmental samples: Heat the sample at 50 &#176;C for 30 min or treat with acidic or basic solutions14.</li>
	</ol>
	</li>
	<li>Clinical sample 
	Process clinical samples depending on their physico-chemical properties. Filter or centrifuge liquids to remove large impurities. Resuspend solid samples. To use tissues, grind them, for instance by using a dounce homogeneiser or glass beads, and lyse the cells to free the intracellular bacteria.</li>
</ol>
1.2 Amoebae preparation
<ol>
	<li>Broth preparation 
	Prepare the following media: a rich media containing peptone, yeast extract and glucose (PYG; 100 g of proteose peptone, 10 g of yeast extract, 4.9 g of MgSO4&#8226;7H2O, 5 g of sodium citrate&#8226;2H2O, 0.1 g of Fe(NH4)2(SO4)2&#8226;6H2O, 1.7 g of KH2PO4, 1.97 g of Na2HPO4&#8226;7H2O, 45 g of glucose, and 0.295 g of CaCl2 in 5 L of distilled water) and a non-nutritive medium such as PAS for Acanthamoeba species.</li>
	<li>Amoebal culture
	<ol>
		<li>Cultivate amoebae (preferentially Acanthamoeba castellanii ATCC 30010 or A. polyphaga Linc-Ap1) at 25 &#176;C in cell culture flasks containing 30 ml of PYG medium.</li>
		<li>Harvest the amoebae by vigorous shaking of the flask and centrifuge the cell suspension for 10 min at 1,500 x g. Wash the pellet twice with PAS medium. Count the cells in a Kova slide and adjust the volume to obtain a suspension of 5 x 105 cells per ml.</li>
		<li>Transfer the amoebal suspension into microplates. Use 1 ml per well for 12- and 24-well plates, 500 &#956;l for 48-well plates and 300 &#956;l for 96-well plates. Incubate the microplate for at least 2 hr at 25 &#176;C. This allows sedimentation and attachment of the amoebae to the bottom of each well.</li>
	</ol>
	</li>
</ol>
1.3 Coculture
<ol>
	<li>Sample inoculation
	<ol>
		<li>Inoculate the plate from 2.3.3 with serial dilutions of the sample from 1.1 or 1.2, usually with 10-fold dilution series, starting with 100 &#956;l of undiluted sample.</li>
		<li>Centrifuge the microplate at 1,800 x g for 10 min to sediment on the amoebal lawn the microorganisms potentially present in the sample. This increases contact and phagocytosis of microorganisms by amoebae.</li>
		<li>Incubate the plates for 45 min at 25 &#176;C and wash three times with PAS by replacing the media with fresh PAS. Add 1 ml per well of PAS with or without addition of antibiotics (streptomycin, penicillin, gentamicin and/or vancomycin), depending on the bacterial species that are searched for.</li>
		<li>Incubate the microplate at 32 &#176;C in a humidified atmosphere to avoid encystment of the amoebae. Observe each well daily with a 20X objective to detect presence of bacteria invading and lysing amoebae.</li>
		<li>In the case of lysis, perform a subculture on fresh amoebae by inoculating 100 &#956;l of cocultures to a monolayer of about 105 amoebae/cm2. To specifically isolate a given bacterial species, inoculate also specific agar media designed for these bacteria (i.e. BCYE agar for Legionella spp.).</li>
		<li>In the absence of lysis, take 100 &#956;l of cocultures four to seven days after the first inoculation and inoculate a fresh amoebal culture of 900 &#956;l in a 24-well plate. If rapid lysis of amoebae is observed without proliferation of bacteria, a virus might be present. In this case, filter the supernatant at 0.22 &#956;m and use the filtered suspension to infect fresh amoebae.</li>
	</ol>
	</li>
</ol>
1.4 Bacterial isolation and characterization
<ol>
	<li>Bacterial staining 
	Perform cocultures directly on glass coverslips in 24-well microplates. Remove the medium and perform staining or immunofluorescence.
	<ol>
		<li>Modified Romanowsky staining
		<ol>
			<li>Let the coverslip dry. Immerse the coverslip five times in the fixative solution (2 mg/L Fast Green in methanol).</li>
			<li>Immerse the coverslip five times in the staining solution I (1.22 g/L Eosine G in phosphate buffer pH 6.6)</li>
			<li>Finally, immerse the coverslip 5 times in the staining solution II (1.1 g/L thiazine in phosphate buffer pH 6.6).</li>
			<li>Rinse the sample with distilled water. Let dry and observe by microscopy.</li>
		</ol>
		</li>
		<li>Ziehl-Neelsen staining
		<ol>
			<li>Let the coverslip dry. Cover the sample with Ziehl fuchsin. Heat the dye with a flame until vapors appear.</li>
			<li>Cool at room temperature for at least 5 min and rinse with distilled water. Cover the sample with 3% hydrochloric acid solution in isopropanol for 2 min and rinse with distilled water.</li>
			<li>Cover for 30 sec with methylene blue and rinse with distilled water. Let dry and observe by microscopy22.</li>
		</ol>
		</li>
		<li>Gimenez staining
		<ol>
			<li>Prepare a basic fuchsin stock solution by mixing 100 ml of 10% basic fuchsin (10 g of basic fuchsin in 100 ml 95% ethanol), 250 ml of 4% aqueous phenol and 650 ml of distilled water. Incubate at 37 &#176;C for 48 hr before use.</li>
			<li>Let the coverslip dry and fix by passing it through flame. Cover the sample with freshly filtered basic fuchsin (4 ml of basic fuchsin stock solution in 10 ml of 0.1 M sodium phosphate buffer, pH 7.45) for 2 min.</li>
			<li>Rinse the sample with water and incubate in malachite green (0.8% in distilled water) for 10 sec. Rinse again with water and repeat malachite green staining. Rinse again with water. Let the coverslip dry, mount it, and observe by microscopy23.</li>
		</ol>
		</li>
		<li>Immunofluorescence
		<ol>
			<li>Fix the coverslip by incubating in methanol for 5 min or with paraformaldehyde 4% for 10 min.</li>
			<li>Wash three times with PBS and incubate for 2 hr in blocking solution (5% BSA, 0.1% Saponin in PBS) at room temperature.</li>
			<li>Incubate the coverslip for 1 hr in blocking solution containing antibodies raised against the microorganism of interest.</li>
			<li>Wash again three times in PBS and incubate for 1 hr with a secondary antibody directed against the primary antibody and linked to a fluorophore. Wash three times with PBS, mount the coverslip and observe by fluorescence microscopy.</li>
		</ol>
		</li>
	</ol>
	</li>
	<li>DNA detection by PCR 
	Extract DNA from 100 to 200 &#956;l of amoebal coculture. Detect microorganisms with universal primers targeting the 16S rRNA gene or specific primers for species of interest such as mycobacteria 24, legionella25 or members of the Chlamydiales26.</li>
</ol>
2. Amoebal Enrichment
2.1. Sample preparation
Resuspend solid and semi-solid samples in PAS by vortexing. Centrifuge the suspension at low speed (180 x g) for 10 min. This allows enrichment of free-living amoebae in the pellet. The supernatant can be used for amoebal coculture and the pellet for amoebal enrichment21.
2.2. Medium preparation
<ol>
	<li>Add 1.5 g of agar to 100 ml of PAS and autoclave the medium 15 min at 121 &#176;C. Pour the warm medium in Petri dishes and let solidify at room temperature.</li>
	<li>Grow Escherichia coli (ATCC 25922) in LB or thioglycolate broth overnight at 37 &#176;C. Wash the bacteria twice with PBS and resuspend them in PAS medium. Dilute 10x in PAS and spread 2-3 ml of this dilution on a PAS agar plate and let dry.</li>
</ol>
2.3. Sample inoculation
Add a drop of sample (or a piece of filter) on one side of the plate and let it flow over the Petri dish to form a line in the center of the dish.
2.4. Amoebal growth and amoebal subculture
<ol>
	<li>Observe the Petri dish daily. If an amoebal migration front is detected, cut out a small piece of agar at the migration front and inoculate a fresh NNA Petri dish covered with a lawn of E. coli.</li>
	<li>Repeat the reinoculation several times depending on the purity of the sample, in order to have a pure culture of a given amoebal strain.</li>
</ol>
2.5. Amoebae and bacteria characterization
<ol>
	<li>Scrape the cells and resuspend them in PAS.</li>
	<li>Extract DNA and determine the identity of amoebae and/or bacterial endosymbionts by PCR and sequencing (16S rRNA amplification for bacteria, resp. 18S rRNA for the amoebae and sequencing, for example).</li>
	<li>Use these scraped cells in PAS to inoculate fresh amoebae and perform an amoebal coculture to detect bacteria possibly present in the sample.</li>
</ol>

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Natl. Acad. Sci. U.S.A. 106, 21848-21853 (2009).</li><li>Thomas, V., 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=Lausannevirus,+a+giant+amoebal+virus+encoding+histone+doublets.">Lausannevirus, a giant amoebal virus encoding histone doublets.</a> Environ. Microbiol. 13, 1454-1466 (2011).</li><li>Raoult, D., Renesto, P., Brouqui, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Laboratory+infection+of+a+technician+by+mimivirus.">Laboratory infection of a technician by mimivirus.</a> Ann. Internal Med. 144, 702-703 (2006).</li><li>Greub, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Parachlamydia+acanthamoebae,+an+emerging+agent+of+pneumonia.">Parachlamydia acanthamoebae, an emerging agent of pneumonia.</a> Clin. Microbiol. Infect. 15, 18-28 (2009).</li><li>Lamoth, F., Greub, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Amoebal+pathogens+as+emerging+causal+agents+of+pneumonia.">Amoebal pathogens as emerging causal agents of pneumonia.</a> FEMS Microbiol. Rev. 34, 260-280 (2010).</li><li>Lienard, J. G., Ashbolt, K., Sen, N. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ch.+6.">Ch. 6.</a> Environmental microbiology, current technology and water applications. , 143-162 (2011).</li><li>Boughalmi, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High-throughput+isolation+of+giant+viruses+of+the+Mimiviridae+and+Marseilleviridae+families+in+the+Tunisian+environment.">High-throughput isolation of giant viruses of the Mimiviridae and Marseilleviridae families in the Tunisian environment.</a> Environ. Microbiol. , (2012).</li><li>Ovrutsky, A. 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=Cooccurrence+of+Free-Living+Amoebae+and+Nontuberculous+Mycobacteria+in+Hospital+Water+Networks,+and+Preferential+Growth+of+Mycobacterium+avium+in+Acanthamoeba+lenticulata.">Cooccurrence of Free-Living Amoebae and Nontuberculous Mycobacteria in Hospital Water Networks, and Preferential Growth of Mycobacterium avium in Acanthamoeba lenticulata.</a> Appl. Environ. Microbiol. 79, 3185-3192 (2013).</li></ol>

The authors declare that they have no competing financial interests.

Amoebal coculture and amoebal enrichment are efficient methods that allowed the isolation of many new bacterial and amoebal species. Results obtained with these methods confirm the ubiquitous presence of both amoebae and amoeba-resisting bacteria in the environment, and most interestingly in manmade water networks that are considered to be controlled by chemical treatments such as chlorination and ozonation. Amoebal coculture and amoebal enrichment are essential tools to isolate and cultivate these potentially pathogenic...

Before the advent of molecular diagnosis, microorganisms present in environmental niches or in clinical samples were often detected by cultivating them on different selective media, mainly on agar in Petri dishes. The phenotype of the bacterial colonies and their metabolic activity then allowed bacterial classification at species level. Broth may also be used to increase the sensitivity of detection. However, both techniques do not allow the recovery of bacteria that grow slowly or not at all on these media. This is the reason why molecular approaches are so widely used nowadays. Nevertheless, detection of DNA provides no clue on the viability of the bacteria. Moreover, contrarily to culture, molecular approaches do not result in a strain that can be further characterized.
Studying pathogens that grow poorly on solid media or that need cells to grow is complicated. Most of these &#34;difficult to grow&#34; bacteria are fastidious intracellular bacteria, often discovered and characterized following large outbreaks as it was the case for Legionella pneumophila. This bacterium was characterized following an outbreak that occurred during an American Legion convention. As many as 182 persons were infected and 29 died due to a severe pneumonia1,2. It was later demonstrated that amoebae were the natural hosts of this bacterium and that their presence in the hotel air-conditioning system and water networks was at the origin of the outbreak of the so-called Legionnaire&#39;s disease3.
Amoebae are present worldwide and were isolated from soil, air, water and the nasal mucosa of human volunteers (reviewed in 4). These &#34;free-living&#34; amoebae are generally dividing autonomously in the environment but may occasionally invade permissive hosts5. Amoebae feed on various microorganisms through phagocytosis and subsequent lysosomal digestion by hydrolases6. Many facultative or obligate intracellular bacteria are able to resist digestion and thus infect and divide in amoebae as for example Legionella, Chlamydia-related bacteria or mycobacteria (reviewed in 7 and 8). Free-living amoebae likely represent an important potential reservoir for intracellular bacteria that have yet not been discovered. This led our group to implement in Lausanne two main techniques, called amoebal coculture and amoebal enrichment, which allowed different groups to isolate several new obligate intracellular microorganisms from various environmental samples9-15.
Since amoebae are professional phagocytes grazing on bacteria, a bacterium able to resist phagocytosis and to grow inside these protists might also colonize human phagocytes and be pathogenic towards humans. This was partially demonstrated for some Chlamydia-related bacteria, such as Waddlia chondrophila. W. chondrophila can grow not only in amoebae but also in several cell types such as mammalian epithelial cells, macrophages, and fish cell lines16-18. The amoebal coculture also appears relevant for detecting intracellular bacteria in clinical samples19,20, including stools which are heavily contaminated with different bacterial species21.
Here we describe the major steps of amoebal coculture and amoebal enrichment, including (a) treatment of environmental or clinical samples; (b) the growth of amoebae on axenic media and on a bacterial lawn of Escherichia coli and (c) the selection and characterization of intracellular bacteria.

<table border="1">
	<tbody>
		<tr>
			<td>Name of Reagent/ Equipment</td>
			<td>Company</td>
			<td>Catalog Number</td>
			<td>Comments/Description</td>
		</tr>
		<tr>
			<td>Glucose monohydrate</td>
			<td>Merck, Darmstadt, Germany</td>
			<td>108342</td>
			<td></td>
		</tr>
		<tr>
			<td>0.22 &#956;m pore size membrane</td>
			<td>Merck Millipore, Darmstadt, Germany</td>
			<td>SCVPU11RE</td>
			<td></td>
		</tr>
		<tr>
			<td>proteose peptone</td>
			<td>Becton-Dickinson, Franklin Lakes, NJ</td>
			<td>211693</td>
			<td></td>
		</tr>
		<tr>
			<td>yeast extract</td>
			<td>Becton-Dickinson, Franklin Lakes, NJ</td>
			<td>212750</td>
			<td></td>
		</tr>
		<tr>
			<td>Cell culture flasks</td>
			<td>Becton-Dickinson, Franklin Lakes, NJ</td>
			<td>353135</td>
			<td></td>
		</tr>
		<tr>
			<td>Kova slide</td>
			<td>Hycor, Indianapolis, IN</td>
			<td>87144</td>
			<td></td>
		</tr>
		<tr>
			<td>cell culture microplates</td>
			<td>Corning Inc, Corning, NY</td>
			<td>3524</td>
			<td></td>
		</tr>
		<tr>
			<td>Diff-Quik staining kit</td>
			<td>Siemens Healthcare diagn., Munich, Germany</td>
			<td>130832</td>
			<td></td>
		</tr>
		<tr>
			<td>Ziehl fuchsin</td>
			<td>Fluka, St-Louis, MI</td>
			<td>21820</td>
			<td></td>
		</tr>
		<tr>
			<td>basic fuchsin</td>
			<td>Sigma, St-Louis, MI</td>
			<td>857843</td>
			<td></td>
		</tr>
		<tr>
			<td>Phenol</td>
			<td>Sigma, St-Louis, MI</td>
			<td>P1037</td>
			<td>Corrosive and mutagenic</td>
		</tr>
		<tr>
			<td>malachite green oxalate</td>
			<td>Fluka, St-Louis, MI</td>
			<td>63160</td>
			<td></td>
		</tr>
		<tr>
			<td>Paraformaldehyde 16% solution</td>
			<td>Electron Microscopy Sciences, Hatfield, PA</td>
			<td>15710</td>
			<td></td>
		</tr>
		<tr>
			<td>Saponin</td>
			<td>Sigma, St-Louis, MI</td>
			<td>84510</td>
			<td></td>
		</tr>
	</tbody>
</table>

discovery of new intracellular pathogens by amoebal coculture and amoebal enrichment approaches

Intracellular pathogens such as legionella, mycobacteria and Chlamydia-like organisms are difficult to isolate because they often grow poorly or not at all on selective media that are usually used to cultivate bacteria. For this reason, many of these pathogens were discovered only recently or following important outbreaks. These pathogens are often associated with amoebae, which serve as host-cell and allow the survival and growth of the bacteria. We intend here to provide a demonstration of two techniques that allow isolation and characterization of intracellular pathogens present in clinical or environmental samples: the amoebal coculture and the amoebal enrichment. Amoebal coculture allows recovery of intracellular bacteria by inoculating the investigated sample onto an amoebal lawn that can be infected and lysed by the intracellular bacteria present in the sample. Amoebal enrichment allows recovery of amoebae present in a clinical or environmental sample. This can lead to discovery of new amoebal species but also of new intracellular bacteria growing specifically in these amoebae. Together, these two techniques help to discover new intracellular bacteria able to grow in amoebae. Because of their ability to infect amoebae and resist phagocytosis, these intracellular bacteria might also escape phagocytosis by macrophages and thus, be pathogenic for higher eukaryotes.

Using amoebal coculture and amoebal enrichment, a whole range of environmental and/or pathogenic bacteria were discovered (Table 1).
Amoebal coculture was used by our group and others to analyze environmental samples, water treatment plants and water distribution systems. A broad range of microorganisms could be isolated with this technique. The most common bacteria isolated by amoebal coculture are members of the Mycobacterium genus that could be recovered from water...

Watch this Scientific Journal Video about Discovery of New Intracellular Pathogens by Amoebal Coculture and Amoebal Enrichment Approaches at JoVE.com

Discovery of New Intracellular Pathogens by Amoebal Coculture and Amoebal Enrichment Approaches

Amoebal coculture is a cell culture system using adherent amoebae to selectively grow intracellular pathogens able to resist phagocytic cells such as amoebae and macrophages. It thus represents a key tool to discover new infectious agents. Amoebal enrichment allows discovery of new amoebal species and of their specific intracellular bacteria.

Intracellular pathogens such as legionella, mycobacteria and Chlamydia-like organisms are difficult to isolate because they often grow poorly or not at ...

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Immunology and Infection

14.4K Views.  University Hospital Center and University of Lausanne. Amoebal coculture is a cell culture system using adherent amoebae to selectively grow intracellular pathogens able to resist phagocytic cells such as amoebae and macrophages. It thus represents a key tool to discover new infectious agents. Amoebal enrichment allows discovery of new amoebal species and of their specific intracellular bacteria.

Video: Discovery of New Intracellular Pathogens by Amoebal Coculture and Amoebal Enrichment Approaches

Infection of Zebrafish Embryos with Intracellular Bacterial Pathogens

Zebrafish (Danio rerio) embryos are increasingly used as a model for studying the function of the vertebrate innate immune system in host-pathogen interactions 1. The major cell types of the innate immune system, macrophages and neutrophils, develop during the first days of embryogenesis prior to the maturation of lymphocytes that are required for adaptive immune responses. The ease of obtaining large numbers of embryos, their accessibility due to external development, the optical transparency of embryonic and larval stages, a wide range of genetic tools, extensive mutant resources and collections of transgenic reporter lines, all add to the versatility of the zebrafish model. Salmonella enterica serovar Typhimurium (S. typhimurium) and Mycobacterium marinum can reside intracellularly in macrophages and are frequently used to study host-pathogen interactions in zebrafish embryos. The infection processes of these two bacterial pathogens are interesting to compare because S. typhimurium infection is acute and lethal within one day, whereas M. marinum infection is chronic and can be imaged up to the larval stage 2, 3. The site of micro-injection of bacteria into the embryo (Figure 1) determines whether the infection will rapidly become systemic or will initially remain localized. A rapid systemic infection can be established by micro-injecting bacteria directly into the blood circulation via the caudal vein at the posterior blood island or via the Duct of Cuvier, a wide circulation channel on the yolk sac connecting the heart to the trunk vasculature. At 1 dpf, when embryos at this stage have phagocytically active macrophages but neutrophils have not yet matured, injecting into the blood island is preferred. For injections at 2-3 dpf, when embryos also have developed functional (myeloperoxidase-producing) neutrophils, the Duct of Cuvier is preferred as the injection site. To study directed migration of myeloid cells towards local infections, bacteria can be injected into the tail muscle, otic vesicle, or hindbrain ventricle 4-6. In addition, the notochord, a structure that appears to be normally inaccessible to myeloid cells, is highly susceptible to local infection 7. A useful alternative for high-throughput applications is the injection of bacteria into the yolk of embryos within the first hours after fertilization 8. Combining fluorescent bacteria and transgenic zebrafish lines with fluorescent macrophages or neutrophils creates ideal circumstances for multi-color imaging of host-pathogen interactions. This video article will describe detailed protocols for intravenous and local infection of zebrafish embryos with S. typhimurium or M. marinum bacteria and for subsequent fluorescence imaging of the interaction with cells of the innate immune system.

Transparent zebrafish embryos have proved useful model hosts to visualize and functionally study interactions between innate immune cells and intracellular bacterial pathogens, such as Salmonella typhimurium and Mycobacterium marinum. Micro-injection of bacteria and multi-color fluorescence imaging are essential techniques involved in the application of zebrafish embryo infection models.

Zebrafish (Danio rerio) embryos are increasingly used as a model for studying the function of the vertebrate innate immune system in host-pathogen ...

Single Cell Measurements of Vacuolar Rupture Caused by Intracellular Pathogens

Shigella flexneri are pathogenic bacteria that invade host cells entering into an endocytic vacuole. Subsequently, the rupture of this membrane-enclosed compartment allows bacteria to move within the cytosol, proliferate and further invade neighboring cells. Mycobacterium tuberculosis is phagocytosed by immune cells, and has recently been shown to rupture phagosomal membrane in macrophages. We developed a robust assay for tracking phagosomal membrane disruption after host cell entry of Shigella flexneri or Mycobacterium tuberculosis. The approach makes use of CCF4, a FRET reporter sensitive to &beta;-lactamase that equilibrates in the cytosol of host cells. Upon invasion of host cells by bacterial pathogens, the probe remains intact as long as the bacteria reside in membrane-enclosed compartments. After disruption of the vacuole, &beta;-lactamase activity on the surface of the intracellular pathogen cleaves CCF4 instantly leading to a loss of FRET signal and switching its emission spectrum. This robust ratiometric assay yields accurate information about the timing of vacuolar rupture induced by the invading bacteria, and it can be coupled to automated microscopy and image processing by specialized algorithms for the detection of the emission signals of the FRET donor and acceptor. Further, it allows investigating the dynamics of vacuolar disruption elicited by intracellular bacteria in real time in single cells. Finally, it is perfectly suited for high-throughput analysis with a spatio-temporal resolution exceeding previous methods. Here, we provide the experimental details of exemplary protocols for the CCF4 vacuolar rupture assay on HeLa cells and THP-1 macrophages for time-lapse experiments or end points experiments using Shigella flexneri as well as multiple mycobacterial strains such as Mycobacterium marinum, Mycobacterium bovis, and Mycobacterium tuberculosis.

We describe a method for tracking the endomembrane rupture elicited by the intracellular bacteria Shigella flexneri and Mycobacterium tuberculosis upon host cell invasion. Our assay makes use of CCF4, a host cytoplasmic FRET probe in live or fixed cells. This reporter is degraded by an enzyme activity present on the bacterial surface.

Shigella flexneri are pathogenic bacteria that invade host cells entering into an endocytic vacuole. Subsequently, the rupture of this membrane-enclosed ...

Monitoring Changes in Membrane Polarity, Membrane Integrity, and Intracellular Ion Concentrations in Streptococcus pneumoniae Using Fluorescent Dyes

Membrane depolarization and ion fluxes are events that have been studied extensively in biological systems due to their ability to profoundly impact cellular functions, including energetics and signal transductions. While both fluorescent and electrophysiological methods, including electrode usage and patch-clamping, have been well developed for measuring these events in eukaryotic cells, methodology for measuring similar events in microorganisms have proven more challenging to develop given their small size in combination with the more complex outer surface of bacteria shielding the membrane. During our studies of death-initiation in Streptococcus pneumoniae (pneumococcus), we wanted to elucidate the role of membrane events, including changes in polarity, integrity, and intracellular ion concentrations. Searching the literature, we found that very few studies exist. Other investigators had monitored radioisotope uptake or equilibrium to measure ion fluxes and membrane potential and a limited number of studies, mostly in Gram-negative organisms, had seen some success using carbocyanine or oxonol fluorescent dyes to measure membrane potential, or loading bacteria with cell-permeant acetoxymethyl (AM) ester versions of ion-sensitive fluorescent indicator dyes. We therefore established and optimized protocols for measuring membrane potential, rupture, and ion-transport in the Gram-positive organism S. pneumoniae. We developed protocols using the bis-oxonol dye DiBAC4(3) and the cell-impermeant dye propidium iodide to measure membrane depolarization and rupture, respectively, as well as methods to optimally load the pneumococci with the AM esters of the ratiometric dyes Fura-2, PBFI, and BCECF to detect changes in intracellular concentrations of Ca2+, K+, and H+, respectively, using a fluorescence-detection plate reader. These protocols are the first of their kind for the pneumococcus and the majority of these dyes have not been used in any other bacterial species. Though our protocols have been optimized for S. pneumoniae, we believe these approaches should form an excellent starting-point for similar studies in other bacterial species.

Monitoring Changes in Membrane Polarity, Membrane Integrity, and Intracellular Ion Concentrations in Streptococcus pneumoniae Using Fluorescent Dyes

Unlike that seen for eukaryotes, there is a paucity of studies that detail membrane depolarization and ion concentration changes in bacteria, primarily as their small size makes conventional methods of measurement difficult. Here, we detail protocols for monitoring such events in the significant Gram-positive pathogen Streptococcus pneumoniae utilizing fluorescence techniques.

Membrane depolarization and ion fluxes are events that have been studied extensively in biological systems due to their ability to profoundly impact ...

Application of Fluorescent Nanoparticles to Study Remodeling of the Endo-lysosomal System by Intracellular Bacteria

Fluorescent nanoparticles (NPs) with desirable chemical, optical and mechanical properties are promising tools to label intracellular organelles. Here, we introduce a method using gold-BSA-rhodamine NPs to label the endo-lysosomal system of eukaryotic cells and monitor manipulations of host cellular pathways by the intracellular pathogen Salmonella enterica. The NPs were readily internalized by HeLa cells and localized in late endosomes/lysosomes. Salmonella infection induced rearrangement of the vesicles and accumulation of NPs in Salmonella-induced membrane structures. We deployed the Imaris software package for quantitative analyses of confocal microscopy images. The number of objects and their size distribution in non-infected cells were distinct from the ones in Salmonella-infected cells, indicating extremely remodeling of the endo-lysosomal system by WT Salmonella.

This article describes methods for the synthesis and fluorescent labeling of nanoparticles (NPs). The NPs were applied in pulse-chase experiments to label the endo-lysosomal system of eukaryotic cells. Manipulation of the endo-lysosomal system by activities of the intracellular pathogen Salmonella enterica were followed by live cell imaging and quantified.

Fluorescent nanoparticles (NPs) with desirable chemical, optical and mechanical properties are promising tools to label intracellular organelles. Here, we ...

Biolistic Transformation of a Fluorescent Tagged Gene into the Opportunistic Fungal Pathogen Cryptococcus neoformans

The basidiomycete Cryptococcus neoformans, an invasive opportunistic pathogen of the central nervous system, is the most frequent cause of fungal meningitis worldwide resulting in more than 625,000 deaths per year worldwide.&#160;Although electroporation has been developed for the transformation of plasmids in Cryptococcus, only&#160;biolistic&#160;delivery provides&#160;an effective means to transform&#160;linear&#160;DNA&#160;that can be integrated into the genome by homologous recombination.&#160;
Acetate has been shown to be a major fermentation product during cryptococcal infection, but the significance of this is not yet known.&#160;A bacterial pathway composed of the enzymes xylulose-5-phosphate/fructose-6-phosphate phosphoketolase (Xfp) and acetate kinase (Ack) is one of three potential pathways for acetate production in C. neoformans. Here, we demonstrate the biolistic transformation of a construct, which has the gene encoding Ack fused to the fluorescent tag mCherry, into&#160;C. neoformans. We then confirm integration of the ACK-mCherry fusion into the&#160;ACK&#160;locus.

Biolistic Transformation of a Fluorescent Tagged Gene into the Opportunistic Fungal Pathogen Cryptococcus neoformans

Biolistic transformation is a method used to generate stable integration of DNA into the genome of the opportunistic pathogen Cryptococcus neoformans through homologous recombination. We will demonstrate biolistic transformation of a construct, which has the gene encoding acetate kinase fused to the fluorescent tag mCherry into&#160;C. neoformans.

The basidiomycete Cryptococcus neoformans, an invasive opportunistic pathogen of the central nervous system, is the most frequent cause of fungal ...

Identification of Rare Bacterial Pathogens by 16S rRNA Gene Sequencing and MALDI-TOF MS

There are a number of rare and, therefore, insufficiently described bacterial pathogens which are reported to cause severe infections especially in immunocompromised patients. In most cases only few data, mostly published as case reports, are available which investigate the role of such pathogens as an infectious agent. Therefore, in order to clarify the pathogenic character of such microorganisms, it is necessary to conduct epidemiologic studies which include large numbers of these bacteria. The methods used in such a surveillance study have to meet the following criteria: the identification of the strains has to be accurate according to the valid nomenclature, they should be easy to handle (robustness), economical in routine diagnostics and they have to generate comparable results among different laboratories. Generally, there are three strategies for identifying bacterial strains in a routine setting: 1) phenotypic identification characterizing the biochemical and metabolic properties of the bacteria, 2) molecular techniques such as 16S rRNA gene sequencing and 3) mass spectrometry as a novel proteome based approach. Since mass spectrometry and molecular approaches are the most promising tools for identifying a large variety of bacterial species, these two methods are described. Advances, limitations and potential problems when using these techniques are discussed.

Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) and molecular techniques (16S rRNA gene sequencing) permit the identification of rare bacterial pathogens in routine diagnostics. The goal of this protocol lies in the combination of both techniques which leads to more accurate and reliable data.

There are a number of rare and, therefore, insufficiently described bacterial pathogens which are reported to cause severe infections especially in ...

High-throughput Detection of Respiratory Pathogens in Animal Specimens by Nanoscale PCR

Nanoliter scale real-time PCR uses spatial multiplexing to allow multiple assays to be run in parallel on a single plate without the typical drawbacks of combining reactions together. We designed and evaluated a panel based on this principle to rapidly identify the presence of common disease agents in dogs and horses with acute respiratory illness. This manuscript describes a nanoscale diagnostic PCR workflow for sample preparation, amplification, and analysis of target pathogen sequences, focusing on procedures that are different from microliter scale reactions. In the respiratory panel presented, 18 assays were each set up in triplicate, accommodating up to 48 samples per plate. A universal extraction and pre-amplification workflow was optimized for high-throughput sample preparation to accommodate multiple matrices and DNA and RNA based pathogens. Representative data are presented for one RNA target (influenza A matrix) and one DNA target (equine herpesvirus 1). The ability to quickly and accurately test for a comprehensive, syndrome-based group of pathogens is a valuable tool for improving efficiency and ergonomics of diagnostic testing and for acute respiratory disease diagnosis and management.

High-throughput testing of DNA and RNA based pathogens by nanoscale PCR is described using a syndromic canine and equine respiratory PCR panel.

Nanoliter scale real-time PCR uses spatial multiplexing to allow multiple assays to be run in parallel on a single plate without the typical drawbacks of ...

Visualizing Intracellular SNARE Trafficking by Fluorescence Lifetime Imaging Microscopy

Soluble N-ethylmaleimide sensitive fusion protein (NSF) attachment protein receptor (SNARE) proteins are key for membrane trafficking, as they catalyze membrane fusion within eukaryotic cells. The SNARE protein family consists of about 36 different members. Specific intracellular transport routes are catalyzed by specific sets of 3 or 4 SNARE proteins that thereby contribute to the specificity and fidelity of membrane trafficking. However, studying the precise function of SNARE proteins is technically challenging, because SNAREs are highly abundant and functionally redundant, with most SNAREs having multiple and overlapping functions. In this protocol, a new method for the visualization of SNARE complex formation in live cells is described. This method is based on expressing SNARE proteins C-terminally fused to fluorescent proteins and measuring their interaction by F&#246;rster resonance energy transfer (FRET) employing fluorescence lifetime imaging microscopy (FLIM). By fitting the fluorescence lifetime histograms with a multicomponent decay model, FRET-FLIM allows (semi-)quantitative estimation of the fraction of the SNARE complex formation at different vesicles. This protocol has been successfully applied to visualize SNARE complex formation at the plasma membrane and at endosomal compartments in mammalian cell lines and primary immune cells, and can be readily extended to study SNARE functions at other organelles in animal, plant, and fungal cells.

This protocol describes a new method allowing for the quantitative visualization of complex formation of SNARE proteins, based on F&#246;rster resonance energy transfer, and fluorescence lifetime imaging microscopy.

Soluble N-ethylmaleimide sensitive fusion protein (NSF) attachment protein receptor (SNARE) proteins are key for membrane trafficking, as they catalyze ...

Zika Virus Specific Diagnostic Epitope Discovery

High-density peptide microarrays allow screening of more than six thousand peptides on a single standard microscopy slide. This method can be applied for drug discovery, therapeutic target identification, and developing of diagnostics. Here, we present a protocol to discover specific Zika virus (ZIKV) diagnostic peptides using a high-density peptide microarray. A human serum sample validated for ZIKV infection was incubated with a high-density peptide microarray containing the entire ZIKV protein translated into 3,423 unique 15 linear amino acid (aa) residues with a 14-aa residue overlap printed in duplicate. Staining with different secondary antibodies within the same array, we detected peptides that bind to Immunoglobulin M (IgM) and Immunoglobulin G (IgG) antibodies present in serum. These peptides were selected for further validation experiments. In this protocol, we describe the strategy followed to design, process, and analyze a high-density peptide microarray.

In this protocol, we describe a technique to discover Zika virus specific diagnostic peptides using a high-density peptide microarray. This protocol can readly be adapted for other emerging infectious diseases.

High-density peptide microarrays allow screening of more than six thousand peptides on a single standard microscopy slide. This method can be applied for ...

Human Colonoid Monolayers to Study Interactions Between Pathogens, Commensals, and Host Intestinal Epithelium

Human 3-dimensional (3D) enteroid or colonoid cultures derived from crypt base stem cells are currently the most advanced ex vivo model of the intestinal epithelium. Due to their closed structures and significant supporting extracellular matrix, 3D cultures are not ideal for host-pathogen studies. Enteroids or colonoids can be grown as epithelial monolayers on permeable tissue culture membranes to allow manipulation of both luminal and basolateral cell surfaces and accompanying fluids. This enhanced luminal surface accessibility facilitates modeling bacterial-host epithelial interactions such as the mucus-degrading ability of enterohemorrhagic E. coli (EHEC) on colonic epithelium. A method for 3D culture fragmentation, monolayer seeding, and transepithelial electrical resistance (TER) measurements to monitor the progress towards confluency and differentiation are described. Colonoid monolayer differentiation yields secreted mucus that can be studied by the immunofluorescence or immunoblotting techniques. More generally, enteroid or colonoid monolayers enable a physiologically-relevant platform to evaluate specific cell populations that may be targeted by pathogenic or commensal microbiota.

Here, we present a protocol to culture human enteroid or colonoid monolayers that have intact barrier function to study host epithelial-microbiota interactions at the cellular and biochemical level.

Human 3-dimensional (3D) enteroid or colonoid cultures derived from crypt base stem cells are currently the most advanced ex vivo model of the intestinal ...