This work was supported by internal funding from the Faculty of Medicine, Universidade Cato&#769;lica Portuguesa, and external funding from Funda&#231;&#227;o para a Ci&#234;ncia e a Tecnologia (FCT), under the grants UIDP/04279/2020, UIDB/04279/2020, and EXPL/SAU-INF/0742/2021.

NOTE: The protocol described here is for BCG but can be applied to any Mycobacteria. BCG can be used as a surrogate bacterium for TB experiments when BSL3 facilities are not available22. The following procedures using BCG should be performed under a biosafety level 2 (BSL2) laboratory and follow the appropriate biosafety guidelines and good laboratory practices for the manipulation of hazard group 2 microorganisms.
1. Culture media preparation
<ol>
	<li>Prepare Middlebrook 7H9 broth supplemented with 10% (v/v) oleic acid, albumin, dextrose, and catalase (OADC) enrichment, according to the supplier&#39;s instructions. Supplement the broth with 0.05% (v/v) of tyloxapol. 
	NOTE: Tyloxapol is a non-ionic liquid polymer that has been used as a surfactant to prevent bacterial clump formation16.</li>
	<li>Prepare Middlebrook 7H10 solid medium supplemented with 10% (v/v) OADC enrichment according to the supplier&#39;s instructions.</li>
	<li>Distribute 40 mL of medium per square Petri dish (120 mm x 120 mm). Allow the plates to dry to minimize condensation at the surface of the agar. 
	NOTE: This specific size of petri dish is fundamental to allow direct transposal of at least 96 droplets from a 96-well plate. Effective drying of the plates will later facilitate the plating of small droplets of bacterial suspension and prevent the droplets from spreading.</li>
	<li>Prepare either Roswell Park Memorial Institute Medium (RPMI 1640) or Dulbecco&#39;s Modified Eagle Medium (DMEM) to produce the infection medium. In either case, supplement the medium with 10% fetal calf serum, 1% L-glutamine, and 1 mM sodium pyruvate. Do not add penicillin and streptomycin to the medium.</li>
</ol>
2. Sample preparation
<ol>
	<li>Obtain samples from a variety of sources. Typically, to quantify CFU to evaluate the efficacy of a TB vaccine, acquire samples from vaccinated and unvaccinated animal tissues. For example, mouse lung and spleen11&#160;or macaque lung, thoracic and peripheral lymph nodes, spleen, liver, skin, blood, bone marrow, and bronchoalveolar lavage wash23. Alternatively, obtain samples from in vitro cultures of macrophages/dendritic cells/neutrophils infected with BCG18,19,20, 24,25,26.</li>
</ol>
3. Production of BCG culture
NOTE: For in vivo studies of TB vaccines, the aim is to improve the efficacy of BCG. Therefore, BCG-vaccinated groups are usually used as control. BCG strains used for human vaccination are ideal for testing in animal models. In this case, a culture of BCG must be reconstituted according to the supplier&#39;s instructions27. However, a BCG culture for in vivo studies can also be produced in-house11. The production of unicellular, uniform, and high-quality BCG culture for in vitro infection protocols has been produced very successfully in several studies11, 16, 18,19,20, 26, 28, 29, using the following protocol, which can also be used for animal challenge studies.
<ol>
	<li>Culture 50 mL of BCG in 7H9 broth, at 37 &#176;C, with agitation at 200 rpm. Vary the volume according to the needs of the experiment.</li>
	<li>Every day, for 8-10 days, collect 100 &#181;L of the culture and dilute it by adding 900 &#181;L of PBS in a 1 mL cuvette. Then proceed by measuring the optical density of bacteria (OD at &#955;=600 nm; OD600) in a spectrophotometer. Draw a growth curve from those values. Identify the mid-log phase of the culture (when the OD is doubling consistently per unit of time).</li>
	<li>Prepare a subsequent culture and incubate until reaching the mid/late log growth phase as in steps 3.1 and 3.2. Use the values obtained in the previous step as guidance. Ensure that the culture does not reach the stationary growth phase (when the OD starts stabilizing) to maintain a good quality culture of viable bacteria.</li>
	<li>Collect the culture at the mid/late log growth phase. Centrifuge at 3000 x g for 10 min. Remove the supernatant.</li>
	<li>Add 10 mL of PBS to wash the bacteria. Centrifuge at 3000 x g for 10 min. Remove the supernatant.</li>
	<li>Resuspend the bacteria with 5 mL of infection media. Place the tube in an ultrasound bath for 15 min, full power at 80 Hz.</li>
	<li>Centrifuge at 1000 x g for 10 min. Collect the supernatant avoiding the pellet as it is rich in bacterial clumps that should be avoided in a high-quality BCG culture and discard it.</li>
	<li>Measure the OD of the supernatant. Here, cultures at the exponential growth phase, with an OD600 of 0.1, are equivalent to 1 x 107 CFU/mL. 
	NOTE: Each laboratory should produce its own BCG growth curves before starting experiments to establish a linear regression between OD600&#160;and CFU using the spectrophotometer. Please note that spectrophotometers have different light path distances, which can vary the readings obtained for the same sample.</li>
	<li>Carry out simple calculations to establish the number of bacteria to add to each host cell culture. The number of bacteria per host cell is the Multiplicity of Infection (MOI). Use an MOI of 10 bacteria per host cell, which is the most common MOI used for BCG infection experiments.</li>
</ol>
4. Micro-colony forming unit assay
NOTE: After an in vivo or in vitro infection experiment is completed, the enumeration of bacteria can be performed by mCFU. For in vivo studies, samples must be first homogenized in a bead beater or another tissue homogenizer. For in vitro cultures of macrophages/dendritic cells/neutrophils infected with BCG, samples must be lysed using a non-ionic detergent (e.g., 0.05% solution of non-ionic, non-denaturing detergent).
<ol>
	<li>Serial dilutions using a 96-well plate: perform serial 10-fold dilutions of the lysates, in a sterile 96-well plate according to the scheme in Figure 1A. Distribute the lysates on rows A and E. For each plate, the maximum number of samples and/or replicates is 24.</li>
	<li>Add 180 &#181;L of dH2O to the remaining wells to perform the serial dilution.</li>
	<li>Using a 12-channel pipette, resuspend the lysates in row A and transfer 20 &#181;L to row B (20 &#181;L lysate + 180 &#181;L dH2O). Homogenize well. Sequentially repeat this step for rows B and C until reaching the last dilution in row D. 
	NOTE: We usually perform three dilutions (100, 101, 102, 103), thus using 4 rows of the plate (A-D or E-H) for each set of 12 samples and/or replicates.</li>
	<li>Micro droplet plating: use a 0.5-10 &#181;L (thin tips are preferred) multichannel pipette to transfer 5 &#181;L from each row of the 96-well plate to the solid medium square plate, according to Figure 1B.</li>
	<li>While slowly pipetting the 5 &#181;L droplets, allow them to slightly touch the agar. This will help to take off the droplet from the tip towards the agar and reduce the possibility of retention of the liquid inside the tip.</li>
	<li>Allow the droplets to dry, close the agar plate, and incubate it at 37 &#176;C while monitoring bacterial growth. Optionally, incubate the agar plates in a sealed plastic bag to prevent the plates from drying.</li>
	<li>Micro-colony counting: following approximately 6-10 days of incubation, check for individual colonies, visible to the naked eye (Figure 2).</li>
	<li>Count the colonies using the lowest magnification objective (4x or lower) of an inverted optical microscope or magnifying glass. Counts should be performed in the dilutions where the number of colonies is lower than 300 and higher than 30. Alternatively, use a camera to take a picture of the droplet to manually count colonies on the computer or use software such as ImageJ to automate colony counting.</li>
	<li>To express cell numbers in CFU/mL, use the following equation: 
	<img alt="Equation 1" src="/files/ftp_upload/65447/65447eq01.jpg" style="margin: auto;" /> 
	Where C = number of colonies counted, V = volume plated in &#181;L, and Dil = dilution where the colonies were counted (100, 101, 102, 103). For example, if 30 colonies were counted in a 5 &#181;L droplet in dilution 102, then: 
	<img alt="Equation 2" src="/files/ftp_upload/65447/65447eq02.jpg" style="margin: auto;" /></li>
</ol>
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/65447/65447fig01.jpg" /> 
Figure 1.&#160;Schematic representation of the mCFU protocol. (A) Serial 10-fold dilutions of the BCG-containing lysates in a 96-well plate. (B) Square Petri dish containing solid culture medium and overlayed by 96 droplets of 5 &#181;L each. Droplets are pipetted directly from the 96-well plate using a multichannel pipette. Created with BioRender.com. <a href="https://www.jove.com/files/ftp_upload/65447/65447fig01large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/65447/65447fig02.jpg" /> 
Figure 2.&#160;Micro-colony forming units of BCG following 10 days of incubation. On the left, a photo of a square Petri dish overlayed by 96 droplets of 5 &#181;L each, as previously represented in Figure 1B. On the right, individual photos of 3 droplets correspond to an original lysate (100) and two dilutions (101, 102). Photos were taken using a DSRL camera equipped with an 18-55 mm zoom lens (plate) or a 105 mm macro lens (droplets). <a href="https://www.jove.com/files/ftp_upload/65447/65447fig02large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
5. Micro-colony forming unit counting in Fiji (ImageJ)
NOTE: The mCFU method allows CFU quantification of large sets of samples. Pictures of the droplets may be recorded for posterior analysis to facilitate colony counting. Several photographic devices can produce images with sufficient quality for this purpose. These include digital cameras, webcams, camera-attached microscopes and magnifying glasses, and cell phones. Free image analysis software such as ImageJ offers the possibility of manual or automated colony counting in those images. To demonstrate both methods, Fiji will be used, which is a distribution of ImageJ that packages several tools for scientific image analysis30. Fiji can be downloaded from&#160;https://fiji.sc/.
<ol>
	<li>Manual counting method
	<ol>
		<li>Open the image containing the mCFU in Fiji. Select Plugins &#62; Analyze &#62; Cell Counter.</li>
		<li>On the Cell Counter menu, select Initialize and then select a counter (e.g., Type 1).</li>
		<li>Proceed by clicking on each colony. Each click will be shown on the picture and will update the counter (Figure 3). To undo accidental clicks, select Delete.</li>
		<li>Register the value displayed on the counter. Click the Reset button to reset the count and open a new image to count additional samples. 
		NOTE: Further instructions on this plugin can be found at&#160;https://imagej.net/plugins/cell-counter.</li>
	</ol>
	</li>
	<li>Automated counting method
	<ol>
		<li>Open the image containing the mCFU in Fiji. Select Image &#62; Type &#62; 8 -bit. This will convert the image to an 8-bit gray-scale image.</li>
		<li>Select the Oval tool in the tool bar and draw an oval around the area with the colonies (Figure 4A). The oval may be adjusted after being drawn.</li>
		<li>Select Edit &#62; Clear Outside, to remove any interference from the outside area (Figure 4B). Select Image &#62; Adjust &#62; Threshold.</li>
		<li>Move the sliders in the threshold menu until the colonies appear in red and background noise is minimized (Figure 4C).</li>
		<li>Select Apply and exit the threshold window. A black-and-white image is generated (Figure 4D).</li>
		<li>Select Analyze &#62; Analyze Particles. In the analyze particles window, specify the range for colony area (between 1 and infinity, measured in squared pixels) and circularity (between 0 and 1, where 1 is a perfect circle; Figure 4E).</li>
		<li>Select Outlines in the show popup menu. Check Display Results for detailed measurements for each colony in the results window. Check Clear Results to erase any previous measurements. Check the Summarize box to display the summarized results of the measurements (Figure 4E).</li>
		<li>Initiate the analyzer by selecting OK. A new window appears, displaying all the outlined colonies that were detected and counted. The results window displays the details for each colony, and the summarized results window shows the total colonies counted (Figure 4F). 
		&#8203;NOTE: The settings for size and circularity will vary with the image&#39;s resolution and magnification and the colonies&#39; size and shape. Repeat the process several times until the best settings are found that detect all colonies. Further instructions on the analyze particles plugin can be found at&#160;https://imagej.nih.gov/ij/docs/menus/analyze.html#ap.</li>
	</ol>
	</li>
</ol>
<img alt="Figure 3" class="xfigimg" src="/files/ftp_upload/65447/65447fig03.jpg" /> 
Figure 3.&#160;A manual method for counting mCFU using the cell counter plugin on Fiji software. The blue dots indicate colonies already clicked on by the user. The menu on the right displays the number of colonies counted so far (the count is 41). <a href="https://www.jove.com/files/ftp_upload/65447/65447fig03large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 4" class="xfigimg" src="/files/ftp_upload/65447/65447fig04.jpg" /> 
Figure 4.&#160;An automated method for counting mCFU using Fiji software. (A, B) The region of interest with the colonies is selected using the oval selection tool, and the outside area is removed using the clear outside command. (C, D) A black-and-white image of the colonies is generated using the threshold tool. (E, F) The number of colonies is quantified using the analyze particles tool. <a href="https://www.jove.com/files/ftp_upload/65447/65447fig04large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

Accelerating Tuberculosis Determination Using the Micro-CFU Method

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E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Characterizing+the+BCG-Induced+Macrophage+and+Neutrophil+Mechanisms+for+Defense+Against+Mycobacterium+tuberculosis.">Characterizing the BCG-Induced Macrophage and Neutrophil Mechanisms for Defense Against Mycobacterium tuberculosis.</a> Frontiers in immunology. 11, 1202 (2020).</li><li>Pires, D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Interference+of+Mycobacterium+tuberculosis+with+the+endocytic+pathways+on+macrophages+and+dendritic+cells+from+healthy+donors:+role+of+cathepsins.">Interference of Mycobacterium tuberculosis with the endocytic pathways on macrophages and dendritic cells from healthy donors: role of cathepsins.</a> Drug Discovery Today. 15 (23-24), 1112-1112 (2010).</li><li>Betts, G., 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=Optimising+Immunogenicity+with+Viral+Vectors:+Mixing+MVA+and+HAdV-5+Expressing+the+Mycobacterial+Antigen+Ag85A+in+a+Single+Injection.">Optimising Immunogenicity with Viral Vectors: Mixing MVA and HAdV-5 Expressing the Mycobacterial Antigen Ag85A in a Single Injection.</a> PLoS ONE. 7 (12), e50447 (2012).</li><li>Tanner, 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=The+influence+of+haemoglobin+and+iron+on+in+vitro+mycobacterial+growth+inhibition+assays.">The influence of haemoglobin and iron on in vitro mycobacterial growth inhibition assays.</a> Scientific reports. 7 (1), 43478 (2017).</li><li>McNeill, E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Regulation+of+mycobacterial+infection+by+macrophage+Gch1+and+tetrahydrobiopterin.">Regulation of mycobacterial infection by macrophage Gch1 and tetrahydrobiopterin.</a> Nature communications. 9 (1), 5409 (2018).</li><li>Schindelin, J., 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=Fiji:+an+open-source+platform+for+biological-image+analysis.">Fiji: an open-source platform for biological-image analysis.</a> Nature Methods. 9 (7), 676-682 (2012).</li><li>Pereira, M., Vale, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Saquinavir:+From+HIV+to+COVID-19+and+Cancer+Treatment.">Saquinavir: From HIV to COVID-19 and Cancer Treatment.</a> Biomolecules. 12 (7), 944 (2022).</li><li>Pires, D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Repurposing+Saquinavir+for+Host-Directed+Therapy+to+Control+Mycobacterium+Tuberculosis+Infection.">Repurposing Saquinavir for Host-Directed Therapy to Control Mycobacterium Tuberculosis Infection.</a> Frontiers in immunology. 12, 647728 (2021).</li><li>Pires, D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Liposomal+Delivery+of+Saquinavir+to+Macrophages+Overcomes+Cathepsin+Blockade+by+Mycobacterium+tuberculosis+and+Helps+Control+the+Phagosomal+Replicative+Niches.">Liposomal Delivery of Saquinavir to Macrophages Overcomes Cathepsin Blockade by Mycobacterium tuberculosis and Helps Control the Phagosomal Replicative Niches.</a> International journal of molecular sciences. 24 (2), (2023).</li><li>Maartens, G., Wilkinson, R. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tuberculosis.">Tuberculosis.</a> The Lancet. 370 (9604), 2030-2043 (2007).</li><li>Matarazzo, L., Bettencourt, P. J. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=mRNA+vaccines:+a+new+opportunity+for+malaria,+tuberculosis+and+HIV.">mRNA vaccines: a new opportunity for malaria, tuberculosis and HIV.</a> Frontiers in Immunology. 14, 1172691 (2023).</li><li>Young, D., Dye, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Development+and+Impact+of+Tuberculosis+Vaccines.">The Development and Impact of Tuberculosis Vaccines.</a> Cell. 124 (4), 683-687 (2006).</li><li>Kommareddi, S., Abramowsky, C. R., Swinehart, G. L., Hrabak, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nontuberculous+mycobacterial+infections:+Comparison+of+the+fluorescent+auramine-o+and+Ziehl-Neelsen+techniques+in+tissue+diagnosis.">Nontuberculous mycobacterial infections: Comparison of the fluorescent auramine-o and Ziehl-Neelsen techniques in tissue diagnosis.</a> Human Pathology. 15 (11), 1085-1089 (1984).</li><li>Sabiiti, W., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+Tuberculosis+Molecular+Bacterial+Load+Assay+(TB-MBLA).">A Tuberculosis Molecular Bacterial Load Assay (TB-MBLA).</a> Journal of visualized experiments: JoVE. (158), e60460 (2020).</li><li>Somosko&#776;vi, 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=Comparison+of+Recoveries+of+Mycobacterium+tuberculosis+Using+the+Automated+BACTEC+MGIT+960+System,+the+BACTEC+460+TB+System,+and+Lo&#776;wenstein-Jensen+Medium.">Comparison of Recoveries of Mycobacterium tuberculosis Using the Automated BACTEC MGIT 960 System, the BACTEC 460 TB System, and Lo&#776;wenstein-Jensen Medium.</a> Journal of Clinical Microbiology. 38 (6), 2395-2397 (2000).</li><li>Tanner, 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=The+in+vitro+direct+mycobacterial+growth+inhibition+assay+(MGIA)+for+the+early+evaluation+of+TB+vaccine+candidates+and+assessment+of+protective+immunity:+a+protocol+for+non-human+primate+cells.">The in vitro direct mycobacterial growth inhibition assay (MGIA) for the early evaluation of TB vaccine candidates and assessment of protective immunity: a protocol for non-human primate cells.</a> F1000Research. 10, 257 (2021).</li></ol>

DP and PJGB declare that the study was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

TB is an important public health problem with increasing importance, particularly in low and middle-income countries. The disruption of healthcare settings to diagnose and treat TB during the COVID-19 pandemic caused a negative impact on the incidence of new cases1. In addition, the multi-drug and extensively-drug resistant M.tb strains, and the co-infection of M.tb and HIV must be urgently addressed to control this epidemic1,3...

Tuberculosis (TB) is the leading cause of death worldwide by a single infectious agent, bacterium Mycobacterium tuberculosis (M.tb), killing more people than any other pathogen. In 2021, TB was responsible for 1.6 million deaths and was surpassed by COVID-19 during the 2019-2021 pandemic1. Moreover, according to the World Health Organization&#180;s global TB report of 2022, the COVID-19 pandemic was responsible for an increase in new TB cases. The WHO also reports large drops in the number of people diagnosed with TB during this period, which could increase further the number of TB cases1.
The Bacillus Calmette-Gu&#233;rin (BCG) is a live-attenuated strain of the pathogenic Mycobacterium bovis, used for the first time as a vaccine more than 100 years ago. This is the only vaccine against TB and is the oldest licensed vaccine in the world still in use2,3. Currently, there are 12 vaccines in different phases of clinical trials4, and dozens of vaccines are under pre-clinical development5,6. Pre-clinical assessment of vaccines against TB includes the evaluation of the safety and immunogenicity7, which can be obtained in diverse animal models such as zebrafish, mice, guinea pigs, rabbits, cattle, and non-human primates8,9,10. Additionally, assessing the capacity of a vaccine to induce protection against M.tb infection and/or transmission, i.e., the vaccine efficacy, requires an M.tb challenge in vivo5,11. Interestingly, BCG vaccination induces non-specific effects that affect the survival of other bacterial and viral pathogens12,13&#160;through the mechanism of trained immunity14. To quantify the viable bacterial burden in an infected animal, the method of choice is the enumeration of bacterial colonies through the colony-forming units (CFU) assay5,15. CFU is a unit that estimates the number of microorganisms (bacteria or fungi) that form colonies under specific growth conditions. CFUs originate from viable and replicative microorganisms, and the absolute number of living microorganisms within each colony is difficult to estimate. It is uncertain whether a colony has originated from one or more microorganisms. The CFU unit reflects this uncertainty, hence a great variability can be observed in replicates of the same sample. This time-consuming assay requires specialized technicians trained to work in a biosafety level 3 (BSL3) facility, substantial laboratory and incubator space, takes from 4 to 6 weeks to conclude, and is prone to contamination.
In this study, we describe an optimized method for colony enumeration, the micro-CFU (mCFU), and offer a simple and rapid solution to analyze the results15,16,17,18,19,20. The mCFU assay requires tenfold fewer reagents, reduces the incubation period threefold, taking 1 to 2 weeks to conclude, reduces lab space and reagent cost, and minimizes the health and safety risks associated with working with large numbers of M.tb. We propose that this method should be universally adopted for pre-clinical studies of vaccine efficacy determination, ultimately leading to time reduction in the development of vaccines against TB. Finally, this optimized method of CFU enumeration has been used to quantify not only Mycobacteria but also other bacteria, such as Escherichia coli and Ralstonia solanacearum21.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>96-well plates</td>
			<td>VWR</td>
			<td>734-2781</td>
			<td></td>
		</tr>
		<tr>
			<td>DSLR 15-55 mm lens</td>
			<td>Nikon</td>
			<td>AF-P DX NIKKOR 18-55mm f/3.5-5.6G VR</td>
			<td></td>
		</tr>
		<tr>
			<td>DSLR camera</td>
			<td>Nikon</td>
			<td>D3400</td>
			<td></td>
		</tr>
		<tr>
			<td>DSLR macro lens</td>
			<td>Sigma</td>
			<td>MACRO 105mm F2.8 EX DG OS HSM</td>
			<td></td>
		</tr>
		<tr>
			<td>Fetal calf serum</td>
			<td>Gibco</td>
			<td>10270106</td>
			<td></td>
		</tr>
		<tr>
			<td>Fiji Software</td>
			<td></td>
			<td>https://fiji.sc/</td>
			<td>Fiji is an open-source software supported by several laboratories, institutions, and individuals. All the required plugins are included.</td>
		</tr>
		<tr>
			<td>Igepal CA-630</td>
			<td>Sigma-Aldrich</td>
			<td>18896</td>
			<td></td>
		</tr>
		<tr>
			<td>L-glutamine</td>
			<td>Gibco</td>
			<td>25030-081</td>
			<td></td>
		</tr>
		<tr>
			<td>Middlebrook 7H10</td>
			<td>BD</td>
			<td>262710</td>
			<td></td>
		</tr>
		<tr>
			<td>Middlebrook 7H9</td>
			<td>BD</td>
			<td>271310</td>
			<td></td>
		</tr>
		<tr>
			<td>Multichannel pipette (0.5 - 10 &#181;l)</td>
			<td>Gilson</td>
			<td>FA10013</td>
			<td></td>
		</tr>
		<tr>
			<td>Multichannel pipette (20 - 200 &#181;l)</td>
			<td>Gilson</td>
			<td>FA10011</td>
			<td></td>
		</tr>
		<tr>
			<td>Mycobacterium bovis BCG&#160;</td>
			<td>American Type Culture Collection</td>
			<td>ATCC35734</td>
			<td>strain TMC 1011 [BCG Pasteur]</td>
		</tr>
		<tr>
			<td>OADC enrichment</td>
			<td>BD</td>
			<td>211886</td>
			<td></td>
		</tr>
		<tr>
			<td>Phosphate buffered saline (PBS)</td>
			<td>NZYTech</td>
			<td>MB25201</td>
			<td></td>
		</tr>
		<tr>
			<td>RPMI 1640 medium</td>
			<td>Gibco</td>
			<td>21875091</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium pyruvate</td>
			<td>Gibco</td>
			<td>11360-070</td>
			<td></td>
		</tr>
		<tr>
			<td>Spectrophotometer UV-6300PC</td>
			<td>VWR</td>
			<td>634-6041</td>
			<td></td>
		</tr>
		<tr>
			<td>Square Petri dish 120 x 120 mm</td>
			<td>Corning</td>
			<td>BP124-05</td>
			<td></td>
		</tr>
		<tr>
			<td>Tyloxapol</td>
			<td>Sigma-Aldrich</td>
			<td>T8761</td>
			<td></td>
		</tr>
		<tr>
			<td>Ultrasound bath Elma P 30 H</td>
			<td>VWR</td>
			<td>142-0051</td>
			<td></td>
		</tr>
	</tbody>
</table>

micro-colony forming unit assay for efficacy evaluation of vaccines against tuberculosis

Tuberculosis (TB), the leading cause of death worldwide by an infectious agent, killed 1.6 million people in 2022, only being surpassed by COVID-19 during the 2019-2021 pandemic. The disease is caused by the bacterium Mycobacterium tuberculosis (M.tb). The Mycobacterium bovis strain Bacillus Calmette-Gu&#233;rin (BCG), the only TB vaccine, is the oldest licensed vaccine in the world, still in use. Currently, there are 12 vaccines in clinical trials and dozens of vaccines under pre-clinical development. The method of choice used to assess the efficacy of TB vaccines in pre-clinical studies is the enumeration of bacterial colonies by the colony-forming units (CFU) assay. This time-consuming assay takes 4 to 6 weeks to conclude, requires substantial laboratory and incubator space, has high reagent costs, and is prone to contamination. Here we describe an optimized method for colony enumeration, the micro-CFU (mCFU), that offers a simple and rapid solution to analyze M.tb vaccine efficacy results. The mCFU assay requires tenfold fewer reagents, reduces the incubation period threefold, taking 1 to 2 weeks to conclude, reduces lab space and reagent cost, and minimizes the health and safety risks associated with working with large numbers of M.tb. Moreover, to evaluate the efficacy of a TB vaccine, samples may be obtained from a variety of sources, including tissues from vaccinated animals infected with Mycobacteria. We also describe an optimized method to produce a unicellular, uniform, and high-quality mycobacterial culture for infection studies. Finally, we propose that these methods should be universally adopted for pre-clinical studies of vaccine efficacy determination, ultimately leading to time reduction in the development of vaccines against TB.

The mCFU assay described here increases the amount of information that can be retrieved from a single Petri dish to at least 96-fold. Figure 5&#160;depicts a comparison of two drug-delivery methods for the repurposed use of saquinavir (SQV)31,32&#160;as a host-directed drug to treat tuberculosis. In this assay, four different strains of Mycobacterium tuberculosis were used to infect primary human macrophages. M. tubercul...

Watch this Scientific Journal Video about Optimizing CFU Determination for Efficient Assessment of TB Vaccine Efficacy and Antigen Presentation Analysis at JoVE.com

Author Spotlight: Optimizing CFU Determination for Efficient Assessment of TB Vaccine Efficacy and Antigen Presentation Analysis 

The determination of colony-forming units (CFU) is the gold-standard technique for quantifying bacteria, including Mycobacterium tuberculosis which can take weeks to form visible colonies. Here we describe a micro-CFU for CFU determination with increased time efficiency, reduced lab space and reagent cost, and scalability to medium and high throughput experiments.

Micro-Colony Forming Unit Assay for Efficacy Evaluation of Vaccines Against Tuberculosis

Tuberculosis (TB), the leading cause of death worldwide by an infectious agent, killed 1.6 million people in 2022, only being surpassed by COVID-19 during ...

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2.0K Views.  Universidade Católica Portuguesa. The determination of colony-forming units (CFU) is the gold-standard technique for quantifying bacteria, including Mycobacterium tuberculosis which can take weeks to form visible colonies. Here we describe a micro-CFU for CFU determination with increased time efficiency, reduced lab space and reagent cost, and scalability to medium and high throughput experiments.

Video: Author Spotlight: Optimizing CFU Determination for Efficient Assessment of TB Vaccine Efficacy and Antigen Presentation Analysis 

Rapid Point-of-Care Assay of Enoxaparin Anticoagulant Efficacy in Whole Blood

There is the need for a clinical assay to determine the extent to which a patient's blood is effectively anticoagulated by the low-molecular-weight-heparin (LMWH), enoxaparin. There are also urgent clinical situations where it would be important if this could be determined rapidly. The present assay is designed to accomplish this. We only assayed human blood samples that were spiked with known concentrations of enoxaparin. The essential feature of the present assay is the quantification of the efficacy of enoxaparin in a patient's blood sample by degrading it to complete inactivity with heparinase. Two blood samples were drawn into Vacutainer tubes (Becton-Dickenson; Franklin Lakes, NJ) that were spiked with enoxaparin; one sample was digested with heparinase for 5 min at 37 &deg;C, the other sample represented the patient's baseline anticoagulated status. The percent shortening of clotting time in the heparinase-treated sample, as compared to the baseline state, yielded the anticoagulant contribution of enoxaparin. We used the portable, battery operated Hemochron 801 apparatus for measurements of clotting times (International Technidyne Corp., Edison, NJ). The apparatus has 2 thermostatically controlled (37 &deg;C) assay tube wells. We conducted the assays in two types of assay cartridges that are available from the manufacturer of the instrument. One cartridge was modified to increase its sensitivity. We removed the kaolin from the FTK-ACT cartridge by extensive rinsing with distilled water, leaving only the glass surface of the tube, and perhaps the detection magnet, as activators. We called this our minimally activated assay (MAA). The use of a minimally activated assay has been studied by us and others. 2-4 The second cartridge that was studied was an activated partial thromboplastin time (aPTT) assay (A104). This was used as supplied from the manufacturer. The thermostated wells of the instrument were used for both the heparinase digestion and coagulation assays. The assay can be completed within 10 min. The MAA assay showed robust changes in clotting time after heparinase digestion of enoxaparin over a typical clinical concentration range. At 0.2 anti-Xa I.U. of enoxaparin per ml of blood sample, heparinase digestion caused an average decrease of 9.8% (20.4 sec) in clotting time; at 1.0 I.U. per ml of enoxaparin there was a 41.4% decrease (148.8 sec). This report only presents the experimental application of the assay; its value in a clinical setting must still be established.

Demonstration of a rapid quantitative assay of the inhibition of blood coagulation by the low-molecular-weight-heparin, enoxaparin. The contribution of enoxaparin is assessed by removing its influence through digestion with heparinase. A fuller description of the assay is detailed in our published paper.1 The assay still requires clinical confirmation.

There is the need for a clinical assay to determine the extent to which a patient's blood is effectively anticoagulated by the ...

Cytotoxic Efficacy of Photodynamic Therapy in Osteosarcoma Cells In Vitro

In recent years, there has been the difficulty in finding more effective therapies against cancer with less systemic side effects. Therefore Photodynamic Therapy is a novel approach for a more tumor selective treatment.
Photodynamic Therapy (PDT) that makes use of a nontoxic photosensitizer (PS), which, upon activation with light of a specific wavelength in the presence of oxygen, generates oxygen radicals that elicit a cytotoxic response1. Despite its approval almost twenty years ago by the FDA, PDT is nowadays only used to treat a limited number of cancer types (skin, bladder) and nononcological diseases (psoriasis, actinic keratosis)2.
The major advantage of the use of PDT is the ability to perform a local treatment, which prevents systemic side effects. Moreover, it allows the treatment of tumors at delicate sites (e.g. around nerves or blood vessels). Here, an intraoperative application of PDT is considered in osteosarcoma (OS), a tumor of the bone, to target primary tumor satellites left behind in tumor surrounding tissue after surgical tumor resection. The treatment aims at decreasing the number of recurrences and at reducing the risk for (postoperative) metastasis.
In the present study, we present in vitro PDT procedures to establish the optimal PDT settings for effective treatment of widely used OS cell lines that are used to reproduce the human disease in well established intratibial OS mouse models. The uptake of the PS mTHPC was examined with a spectrophotometer and phototoxicity was provoked with laser light excitation of mTHPC at 652 nm to induce cell death assessed with a WST-1 assay and by the counting of surviving cells. The established techniques enable us to define the optimal PDT settings for future studies in animal models. They are an easy and quick tool for the evaluation of the efficacy of PDT in vitro before an application in vivo.

Cytotoxic Efficacy of Photodynamic Therapy in Osteosarcoma Cells In Vitro

The protocol reported here allows the evaluation of the efficacy of photodynamic therapy (PDT) in cell lines and the optimization of the PDT settings before applying the therapy in animal models.

In recent years, there has been the difficulty in finding more effective therapies against cancer with less systemic side effects. Therefore Photodynamic ...

Non-invasive Assessment of the Efficacy of New Therapeutics for Intestinal Pathologies Using Serial Endoscopic Imaging of Live Mice

Animal models of inflammatory bowel disease (IBD) and colorectal cancer (CRC) have provided significant insight into the cell intrinsic and extrinsic mechanisms that contribute to the onset and progression of intestinal diseases. The identification of new molecules that promote these pathologies has led to a flurry of activity focused on the development of potential new therapies to inhibit their function. As a result, various pre-clinical mouse models with an intact immune system and stromal microenvironment are now heavily used. Here we describe three experimental protocols to test the efficacy of new therapeutics in pre-clinical models of (1) acute mucosal damage, (2) chronic colitis and/or colitis-associated colon cancer, and (3) sporadic colorectal cancer. We also outline procedures for serial endoscopic examination that can be used to document the therapeutic response of an individual tumor and to monitor the health of individual mice. These protocols provide complementary experimental platforms to test the effectiveness of therapeutic compounds shown to be well tolerated by mice.

We describe methods for longitudinal monitoring of the efficacy of therapeutics for the treatment of colonic pathologies in mice using a rigid endoscope. This protocol can be readily used for the characterization of the therapeutic response of an individual tumor in live mice and also for monitoring potential disease relapse.

Animal models of inflammatory bowel disease (IBD) and colorectal cancer (CRC) have provided significant insight into the cell intrinsic and extrinsic ...

Evaluation of the Efficacy of the H. pylori Protein HP-NAP as a Therapeutic Tool for Treatment of Bladder Cancer in an Orthotopic Murine Model

Bladder cancer is one of the most common malignancies of the urogenital tract. Intravesical injection of Bacillus Calmette-Gu&#233;rin (BCG) is the gold standard treatment for the high-grade non-muscle invasive bladder cancer (NMIBC). However, since the treatment-related side effects are relevant, newer biological response modifiers with a better benefit/side effects ratio are needed.
The tumour microenvironment can influence both tumour development and therapy efficacy. In order to obtain a good model, it is desirable to implant tumour cells in the organ from which the cancer originates.
In this protocol, we describe a method for establishing a tumour in the bladder cavity of female mice and subsequent delivery of therapeutic agents; the latter are exemplified by our use of Helicobacter pylori neutrophil activating protein (HP-NAP). A preliminary chemical burn of the mucosa, followed by the injection of mouse urothelial carcinoma cell line MB49 via urethral catheterization, enables the cells to attach to the bladder mucosa. After a period, required to allow an initial proliferation of the cells, mice are treated with HP-NAP, administrated again via catheterization. The anti-tumour activity of HP-NAP is evaluated comparing the tumour volume, the extent of necrosis and the degree of vascularization between vehicle- and HP-NAP-treated animals.

Evaluation of the Efficacy of the H. pylori Protein HP-NAP as a Therapeutic Tool for Treatment of Bladder Cancer in an Orthotopic Murine Model

Here the method to establish a syngeneic mouse model of orthotopic bladder tumour to evaluate the anti-tumour efficacy of the bacterial protein HP-NAP is described.

Bladder cancer is one of the most common malignancies of the urogenital tract. Intravesical injection of Bacillus Calmette-Gu&#233;rin (BCG) is the gold ...

Quantitative Fundus Autofluorescence for the Evaluation of Retinal Diseases

The retinal pigment epithelium (RPE) is juxtaposed to the overlying sensory retina, and supports the function of the visual system. Among the tasks performed by the RPE are phagocytosis and processing of outer photoreceptor segments through lysosome-derived organelles. These degradation products, stored and referred to as lipofuscin granules, are composed partially of bisretinoids, which have broad fluorescence absorption and emission spectra that can be detected clinically as fundus autofluorescence with confocal scanning laser ophthalmoscopy (cSLO). Lipofuscin accumulation is associated with increasing age, but is also found in various patterns in both acquired and inherited degenerative diseases of the retina. Thus, studying its pattern of accumulation and correlating such patterns with changes in the overlying sensory retina are essential to understanding the pathophysiology and progression of retinal disease. Here, we describe a technique employed by our lab and others that uses cSLO in order to quantify the level of RPE lipofuscin in both healthy and diseased eyes.

The retinal pigment epithelium (RPE) supports the sensory retina through recycling visual cycle byproducts, which accumulate as lipofuscin. These products are autofluorescent and can be qualitatively imaged in vivo. Here, we describe a method to quantitatively image RPE lipofuscin using confocal scanning laser ophthalmoscopy.

The retinal pigment epithelium (RPE) is juxtaposed to the overlying sensory retina, and supports the function of the visual system. Among the tasks ...

Synthesis, Characterization, and Application of Superparamagnetic Iron Oxide Nanoprobes for Extrapulmonary Tuberculosis Detection

A molecular imaging probe comprising superparamagnetic iron oxide (SPIO) nanoparticles and Mycobacterium tuberculosis surface antibody (MtbsAb) was synthesized to enhance imaging sensitivity for extrapulmonary tuberculosis (ETB). An SPIO nanoprobe was synthesized and conjugated with MtbsAb. The purified SPIO-MtbsAb nanoprobe was characterized using TEM and NMR. To determine the targeting ability of the probe, SPIO-MtbsAb nanoprobes were incubated with Mtb for in vitro imaging assays and injected into Mtb-inoculated mice for in vivo investigation with magnetic resonance (MR). The contrast enhancement reduction on magnetic resonance imaging (MRI) of Mtb and THP1 cells showed proportional to the SPIO-MtbsAb nanoprobe concentration. After 30 min of intravenous SPIO-MtbsAb nanoprobe injection into Mtb-infected mice, the signal intensity of the granulomatous site was enhanced by 14-fold in the T2-weighted MR images compared with that in mice receiving PBS injection. The MtbsAb nanoprobes can be used as a novel modality for ETB detection.

To improve serological diagnostic tests for Mycobacterium tuberculosis antigens, we developed superparamagnetic iron oxide nanoprobes to detect extrapulmonary tuberculosis.

A molecular imaging probe comprising superparamagnetic iron oxide (SPIO) nanoparticles and Mycobacterium tuberculosis surface antibody (MtbsAb) was ...

Rapid Evaluation of Toxicity of Chemical Compounds Using Zebrafish Embryos

The zebrafish is a widely used vertebrate model organism for the disease and phenotype-based drug discovery. The zebrafish generates many offspring, has transparent embryos and rapid external development. Zebrafish embryos can, therefore, also be used for the rapid evaluation of toxicity of the drugs that are precious and available in small quantities. In the present article, a method for the efficient screening of the toxicity of chemical compounds using 1-5-day post fertilization embryos is described. The embryos are monitored by stereomicroscope to investigate the phenotypic defects caused by the exposure to different concentrations of compounds. Half-maximal lethal concentrations (LC50) of the compounds are also determined. The present study required 3-6 mg of an inhibitor compound, and the whole experiment takes about 8-10 h to be completed by an individual in a laboratory having basic facilities. The current protocol is suitable for testing any compound to identify intolerable toxic or off-target effects of the compound in the early phase of drug discovery and to detect subtle toxic effects that may be missed in the cell culture or other animal models. The method reduces procedural delays and costs of drug development.

Zebrafish embryos are used for evaluating the toxicity of chemical compounds. They develop externally and are sensitive to chemicals, allowing detection of subtle phenotypic changes. The experiment only requires a small amount of compound, which is directly added to the plate containing embryos, making the testing system efficient and cost-effective.

The zebrafish is a widely used vertebrate model organism for the disease and phenotype-based drug discovery. The zebrafish generates many offspring, has ...

Biotribological Testing and Analysis of Articular Cartilage Sliding against Metal for Implants

Osteochondral defects in middle-aged patients might be treated with focal metallic implants. First developed for defects in the knee joint, implants are now available for the shoulder, hip, ankle and the first metatarsalphalangeal joint. While providing pain reduction and clinical improvement, progressive degenerative changes of the opposing cartilage are observed in many patients. The mechanisms leading to this damage are not fully understood. This protocol describes a tribological experiment to simulate a metal-on-cartilage pairing and comprehensive analysis of the articular cartilage. Metal implant material is tested against bovine osteochondral cylinders as a model for human articular cartilage. By applying different loads and sliding speeds, physiological loading conditions can be imitated. To provide a comprehensive analysis of the effects on the articular cartilage, histology, metabolic activity and gene expression analysis are described in this protocol. The main advantage of tribological testing is that loading parameters can be adjusted freely to simulate in vivo conditions. Furthermore, different testing solutions might be used to investigate the influence of lubrication or pro-inflammatory agents. By using gene expression analysis for cartilage-specific genes and catabolic genes, early changes in the metabolism of articular chondrocytes in response to mechanical loading might be detected.

This protocol describes the preparation, biotribological testing, and analysis of osteochondral cylinders sliding against metal implant material. Outcome measures included in this protocol are metabolic activity, gene expression and histology.

Osteochondral defects in middle-aged patients might be treated with focal metallic implants. First developed for defects in the knee joint, implants are ...

Near Infrared Photoimmunotherapy for Mouse Models of Pleural Dissemination

The efficacy of photoimmunotherapy can be evaluated more accurately with an orthotopic mouse model than with a subcutaneous one. A pleural dissemination model can be used for the evaluation of treatment methods for intrathoracic diseases such as lung cancer or malignant pleural mesothelioma.
Near-infrared photoimmunotherapy (NIR-PIT) is a recently developed cancer treatment strategy that combines the specificity of tumor-targeting antibodies with toxicity caused by a photoabsorber (IR700Dye) after exposure to NIR light. The efficacy of NIR-PIT has been reported using various antibodies; however, only a few reports have shown the therapeutic effect of this strategy in an orthotopic model. In the present study, we demonstrate an example of efficacy evaluation of the pleural disseminated lung cancer model, which was treated using NIR-PIT.

Near-infrared photoimmunotherapy (NIR-PIT) is an emerging cancer therapeutic strategy that utilizes an antibody-photoabsorber (IR700Dye) conjugate and NIR light to destroy cancer cells. Here, we present a method to evaluate the antitumor effect of NIR-PIT in a mouse model of pleural disseminated lung cancer and malignant pleural mesothelioma using bioluminescence imaging.

The efficacy of photoimmunotherapy can be evaluated more accurately with an orthotopic mouse model than with a subcutaneous one. A pleural dissemination ...

Large Animal Model for Evaluating the Efficacy of the Gene Therapy in Ischemic Heart

Coronary artery disease is one of the significant causes of mortality and morbidity worldwide. Despite the progression of current therapeutics, a considerable proportion of coronary artery disease patients remain symptomatic. Gene therapy-mediated therapeutic angiogenesis offers a novel therapeutic method for improving myocardial perfusion and relieving symptoms. Gene therapy with different angiogenic factors has been studied in few clinical trials. Due to the novelty of the method, the progress of myocardial gene therapy is a continuous path from bench to bedside. Therefore, large animal models are needed for evaluating the safety and efficacy. The more the large animal model identifies the original disease and the endpoints used in clinics, the more predictable outcomes are from clinical trials. Here, we introduce a large animal model for evaluating the efficacy of the gene therapy in the ischemic porcine heart. We use clinically relevant imaging methods such as ultrasound imaging and 15H2O-PET. For targeting the gene transfers into the desired area, electroanatomical mapping is used. The aim of this method is: (1) to mimic chronic coronary artery disease, (2) to induce therapeutic angiogenesis at hypoxic areas of the heart, and (3) to evaluate the safety and efficacy of the gene therapy by using relevant endpoints.

Myocardial gene therapy for ischemic heart disease holds great promise for future therapeutics. Here, we introduce a large animal model for evaluating the efficacy of gene therapy in the ischemic heart.