The authors wish to acknowledge Mark Rodgers for outlining the infection procedures and L. Eoin Carney and Brian Lopresti for guidance in establishing these imaging procedures. Funding for this work has been provided by The Bill and Melinda Gates Foundation (J.L.F., P.L.L.), National Institutes of Health, National Institutes of Allergy and Infectious Diseases R01 AI111871 (P.L.L.), National Heart Lung and Blood Institute R01 HL106804 (J.L.F.), R01 HL110811.

<ol>
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E., Kallenius, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tuberculosis+and+HIV+co-infection.">Tuberculosis and HIV co-infection.</a> PLoS Pathog. 8 (2), e1002464 (2012).</li><li>Keane, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=TNF-blocking+agents+and+tuberculosis:+new+drugs+illuminate+an+old+topic.">TNF-blocking agents and tuberculosis: new drugs illuminate an old topic.</a> Rheumatology (Oxford). 44 (6), 714-720 (2005).</li><li>Lin, P. L., 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=PET+CT+Identifies+Reactivation+Risk+in+Cynomolgus+Macaques+with+Latent+M.+tuberculosis.">PET CT Identifies Reactivation Risk in Cynomolgus Macaques with Latent M. tuberculosis.</a> PLoS Pathog. 12 (7), e1005739 (2016).</li><li>Flynn, J. L., Klein, E., Dick, T., Leong, V. D. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> A color atlas of comparative pulmonary tuberculosis histopathology. , 83-106 (2011).</li><li>Signore, A., Mather, S. J., Piaggio, G., Malviya, G., Dierckx, R. 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T., 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=PET/CT+imaging+reveals+a+therapeutic+response+to+oxazolidinones+in+macaques+and+humans+with+tuberculosis.">PET/CT imaging reveals a therapeutic response to oxazolidinones in macaques and humans with tuberculosis.</a> Sci Transl Med. 6 (265), (2014).</li><li>Coleman, M. T., 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=Early+Changes+by+(18)Fluorodeoxyglucose+positron+emission+tomography+coregistered+with+computed+tomography+predict+outcome+after+Mycobacterium+tuberculosis+infection+in+cynomolgus+macaques.">Early Changes by (18)Fluorodeoxyglucose positron emission tomography coregistered with computed tomography predict outcome after Mycobacterium tuberculosis infection in cynomolgus macaques.</a> Infect Immun. 82 (6), 2400-2404 (2014).</li><li>Lin, P. L., 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=Radiologic+Responses+in+Cynomolgus+Macaques+for+Assessing+Tuberculosis+Chemotherapy+Regimens.">Radiologic Responses in Cynomolgus Macaques for Assessing Tuberculosis Chemotherapy Regimens.</a> Antimicrob Agents Chemother. 57 (9), 4237-4244 (2013).</li><li>Diedrich, C. 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=Reactivation+of+latent+tuberculosis+in+cynomolgus+macaques+infected+with+SIV+is+associated+with+early+peripheral+T+cell+depletion+and+not+virus+load.">Reactivation of latent tuberculosis in cynomolgus macaques infected with SIV is associated with early peripheral T cell depletion and not virus load.</a> PLoS One. 5 (3), e9611 (2010).</li><li>Lin, P. L., 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+multistage+vaccine+H56+boosts+the+effects+of+BCG+to+protect+cynomolgus+macaques+against+active+tuberculosis+and+reactivation+of+latent+Mycobacterium+tuberculosis+infection.">The multistage vaccine H56 boosts the effects of BCG to protect cynomolgus macaques against active tuberculosis and reactivation of latent Mycobacterium tuberculosis infection.</a> J Clin Invest. 122 (1), 303-314 (2012).</li><li>Lin, P. L., 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=CD4+T+cell+depletion+exacerbates+acute+Mycobacterium+tuberculosis+while+reactivation+of+latent+infection+is+dependent+on+severity+of+tissue+depletion+in+cynomolgus+macaques.">CD4 T cell depletion exacerbates acute Mycobacterium tuberculosis while reactivation of latent infection is dependent on severity of tissue depletion in cynomolgus macaques.</a> AIDS Res Hum Retroviruses. 28 (12), 1693-1702 (2012).</li><li>Mattila, J. T., Diedrich, C. R., Lin, P. L., Phuah, J., Flynn, J. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Simian+immunodeficiency+virus-induced+changes+in+T+cell+cytokine+responses+in+cynomolgus+macaques+with+latent+Mycobacterium+tuberculosis+infection+are+associated+with+timing+of+reactivation.">Simian immunodeficiency virus-induced changes in T cell cytokine responses in cynomolgus macaques with latent Mycobacterium tuberculosis infection are associated with timing of reactivation.</a> J Immunol. 186 (6), 3527-3537 (2011).</li><li>Scanga, C. A., Flynn, J. A., Kaufmann, S. H. E., Rubin, E. J., Zumla, A. <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. , 243-258 (2015).</li><li>Kita, Y., 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=Development+of+therapeutic+and+prophylactic+vaccine+against+Tuberculosis+using+monkey+and+transgenic+mice+models.">Development of therapeutic and prophylactic vaccine against Tuberculosis using monkey and transgenic mice models.</a> Hum Vaccin. 7, 108-114 (2011).</li><li>Langermans, J. 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=Divergent+effect+of+bacillus+Calmette-Guerin+(BCG)+vaccination+on+Mycobacterium+tuberculosis+infection+in+highly+related+macaque+species:+implications+for+primate+models+in+tuberculosis+vaccine+research.">Divergent effect of bacillus Calmette-Guerin (BCG) vaccination on Mycobacterium tuberculosis infection in highly related macaque species: implications for primate models in tuberculosis vaccine research.</a> Proc Natl Acad Sci U S A. 98 (20), 11497-11502 (2001).</li><li>Okada, 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=Novel+prophylactic+and+therapeutic+vaccine+against+tuberculosis.">Novel prophylactic and therapeutic vaccine against tuberculosis.</a> Vaccine. 27 (25-26), 3267-3270 (2009).</li><li>Reed, S. 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=Defined+tuberculosis+vaccine,+Mtb72F/AS02A,+evidence+of+protection+in+cynomolgus+monkeys.">Defined tuberculosis vaccine, Mtb72F/AS02A, evidence of protection in cynomolgus monkeys.</a> Proc Natl Acad Sci U S A. 106 (7), 2301-2306 (2009).</li><li>Capuano, S. 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=Experimental+Mycobacterium+tuberculosis+infection+of+cynomolgus+macaques+closely+resembles+the+various+manifestations+of+human+M.+tuberculosis+infection.">Experimental Mycobacterium tuberculosis infection of cynomolgus macaques closely resembles the various manifestations of human M. tuberculosis infection.</a> Infect Immun. 71 (10), 5831-5844 (2003).</li><li>Srinivas, S. 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=A+recovery+coefficient+method+for+partial+volume+correction+of+PET+images.">A recovery coefficient method for partial volume correction of PET images.</a> Ann Nucl Med. 23 (4), 341-348 (2009).</li><li>Kumar, 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=Role+of+modern+imaging+techniques+for+diagnosis+of+infection+in+the+era+of+18F-fluorodeoxyglucose+positron+emission+tomography.">Role of modern imaging techniques for diagnosis of infection in the era of 18F-fluorodeoxyglucose positron emission tomography.</a> Clin Microbiol Rev. 21 (1), 209-224 (2008).</li><li>Martin, C. 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=Digitally+Barcoding+Mycobacterium+tuberculosis+Reveals+In+Vivo+Infection+Dynamics+in+the+Macaque+Model+of+Tuberculosis.">Digitally Barcoding Mycobacterium tuberculosis Reveals In Vivo Infection Dynamics in the Macaque Model of Tuberculosis.</a> MBio. 8 (3), (2017).</li><li>Lin, P. L., 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=Metronidazole+prevents+reactivation+of+latent+Mycobacterium+tuberculosis+infection+in+macaques.">Metronidazole prevents reactivation of latent Mycobacterium tuberculosis infection in macaques.</a> Proc Natl Acad Sci U S A. 109 (35), 14188-14193 (2012).</li><li>Lin, P. L., 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=Tumor+necrosis+factor+neutralization+results+in+disseminated+disease+in+acute+and+latent+Mycobacterium+tuberculosis+infection+with+normal+granuloma+structure+in+a+cynomolgus+macaque+model.">Tumor necrosis factor neutralization results in disseminated disease in acute and latent Mycobacterium tuberculosis infection with normal granuloma structure in a cynomolgus macaque model.</a> Arthritis Rheum. 62 (2), 340-350 (2010).</li><li>Phuah, 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=Effects+of+B+Cell+Depletion+on+Early+Mycobacterium+tuberculosis+Infection+in+Cynomolgus+Macaques.">Effects of B Cell Depletion on Early Mycobacterium tuberculosis Infection in Cynomolgus Macaques.</a> Infect Immun. 84 (5), 1301-1311 (2016).</li><li>Martinez, V., Castilla-Lievre, M. A., Guillet-Caruba, C., Grenier, G., Fior, R., Desarnaud, S., Doucet-Populaire, F., Boue, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=(18)F-FDG+PET/CT+in+tuberculosis:+an+early+non-invasive+marker+of+therapeutic+response.">(18)F-FDG PET/CT in tuberculosis: an early non-invasive marker of therapeutic response.</a> Int J Tuberc Lung Dis. 16 (9), 1180-1185 (2012).</li><li>Malherbe, S. T., 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=Persisting+positron+emission+tomography+lesion+activity+and+Mycobacterium+tuberculosis+mRNA+after+tuberculosis+cure.">Persisting positron emission tomography lesion activity and Mycobacterium tuberculosis mRNA after tuberculosis cure.</a> Nat Med. 22 (10), 1094-1100 (2016).</li><li>Chen, R. Y., 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=PET/CT+imaging+correlates+with+treatment+outcome+in+patients+with+multidrug-resistant+tuberculosis.">PET/CT imaging correlates with treatment outcome in patients with multidrug-resistant tuberculosis.</a> Sci Transl Med. 6 (265), (2014).</li></ol>

The authors have nothing to disclose.

Data acquired from PET/CT can be used as surrogate measurements for many aspects of M. tuberculosis infection that would be unobservable without such technology. PET/CT is much more sensitive than X-ray technology, which is often used in macaques studies. PET/CT provides structural, spatial and functional information. The analyses described above have many practical applications such as monitoring disease progression, assessing effectiveness of drug treatment, and providing risk factors for reactivation6,10,11,13.
Tracking the spread of granulomas and FDG uptake of individual lesions can be compared between control and experimental groups to not only provide specific location of the infection, but also follow dissemination of disease25. For example, in work from Coleman et al. describing early infection in cynomolgus macaques, following the infection progression can determine whether the infection within an animal is going to remain active and worsen or be contained by the immune system (i.e. LTBI)11. This is just one example of the power that PET/CT imaging has in studying the progression of disease with respect to granulomas. The same method can be used to study a wide variety of experimental parameters over time. For example, enumeration of granulomas that establish by 4 weeks post-infection can provide a powerful outcome measure for a vaccine, since the best vaccines would prevent or limit granuloma establishment following challenge. Another outcome measure for vaccines could be in limiting dissemination. These quantifiable outcome measures provide important data without the need to perform early necropsies on the animals. A limitation of assessing individual granulomas is the sensitivity of the CT scanner; visualizing granulomas &#60;1 mm in size is often not possible.
Evaluation of mediastinal lymph nodes (MLNs) is important when studying M. tuberculosis infection as well. MLNs are important for T-cell priming and trafficking of immune cells during infection. However, in nearly all macaques, at least one, and sometimes several MLNs can become infected. Thus, MLNs are an additional site of bacterial persistence during active TB and LTBI, and can serve as a reservoir for bacteria, possibly contributing to reactivation26,27. In cases of severe MLN involvement, airways can be compressed. Large necrotic MLNs can erode into the airways, leading to dissemination of the infection. Analyzing PET/CT data on lymph nodes is more complex than granulomas because the structural components of the nodes are not readily visible on CT scans. Additionally, only the lymph nodes that are metabolically active can be analyzed due to FDG uptake. Because of this, when analyzing hot lymph nodes, it is important to ensure that the PET image is scaled to the same maximum and minimum intensity scale for each image analysis to ensure consistency. Since they can be large structures, the necrotic center can be negative for FDG avidity, and thus FDG avidity can appear to be reduced over time, even when disease is increasing in the MLNs.
Total lung FDG avidity represents the total inflammation within the lungs. The amount of lung inflammation is an indication of disease severity and is correlated with bacterial burden6,10,28 therefore this quantitative and objective assessment has numerous applications. To measure total FDG avidity, all voxels within a PET image that show an SUV of greater than 2.3 are combined in a single volume-of-interest (VOI) and the total SUV value of the entire VOI is the final avidity value. This value was selected from literature that compared SUV values of FDG uptake in lung tumors to various infectious pathologies in humans24. It is important to note that this total FDG avidity value is limited only to disease in the lung space and all FDG uptake non-disease related or located in close proximity to the lungs must not be considered. In addition, total lung FDG avidity does not include MLNs. While the avidity of individual granulomas and lymph nodes allows us to see the variability of TB outcomes within the host, FDG avidity of the total lung is integral to evaluating the host as a whole. These methods also function as analytical tools to measure drug response to TB disease. Previous work has shown that TB drug treatment can reduce the size and FDG avidity of individual granulomas over time12 and these changes were associated with reduced bacterial burden. Changes in inflammation over the full course of drug regimens can also be used to assess drug efficacy or failure.
Due to the highly detailed nature of these procedures, a fair amount of troubleshooting may be necessary in order to obtain the most consistent data during studies. It is the goal of this paper to outline the procedures to enable individuals throughout the world to use these techniques while keeping in mind that precise attention to detail is essential. Persons evaluating images should be very familiar with anatomy and physiology in order to recognize abnormality within particular scans. Image readers need to recognize non-normal probe uptake throughout the body because TB can spread beyond the thoracic cavity. Additionally, PET and CT registration in imaging is not a perfect process and occasional deviations on image registration can occur; recognizing this can be vitally important when evaluating very small disease features (i.e. 1 - 2 mm granulomas). A pre-infection scan can be particularly useful as a comparator to identify normal lung (and other organ) structures and PET patterns and recognize those that are new or changed post-infection. Another important component to this analysis is background measurement. All PET data are normalized to muscle uptake as a physiological baseline because FDG uptake is based on metabolism. A combination of rhomboid and serratus muscles in the back are used for background measurements because of proximity to the thoracic cavity and relative consistency in FDG uptake in fasted animals. In the case of M. tuberculosis-infected macaques, this is preferable to using another organ, such as the liver, for background measurements as M. tuberculosis can infect the liver and liver metabolism can be affected when treating animals with various anti-TB drugs. Taking the above factors into account as well as ensuring that all image regions-of-interest are saved at the end of analysis should yield highly reproducible results.
In summary, PET/CT offers a unique and powerful method for investigating M. tuberculosis infection in non-human primates, providing quantitative outcome measures that relate to initial infection, dissemination, and bacterial burden. This allows for tracking the variable outcomes of infection across individual animals without the need for necropsies at various time points, thus saving resources and reducing animal use. This technology is directly translatable to humans, as PET/CT has been used in several studies to assess drug treatment in TB, as well as LTBI in HIV- and HIV+ subjects10,29,30,31. Finally, this technology and quantitative tool set for analyzing PET/CT data are likely to be useful in the future for vaccine efficacy studies and can likely be used as a template for analysis of other infectious diseases in animal models and human subjects.

Mycobacterium tuberculosis has plagued humans for millennia and causes more mortality than any other single infectious agent in the world today. In 2015, there were 10.5 million reported new cases of tuberculosis (TB) globally1 with the majority of cases emanating from India, Indonesia, China, Nigeria, Pakistan, and South Africa. Estimates place the global death toll from TB at 1.4 million people during that same time period. This value is nearly 25% lower than the death rate 100 years ago. Although drug sensitive TB is treatable, the regimen is lengthy requiring multiple medications and compliance is a concern. The emergence of multi drug-resistant (MDR) strains accounted for ~580,000 of the new TB cases in 2015. The successful treatment rate of patients with MDR strains of M. tuberculosis is only estimated to be around 50%. Even more alarming is the emergence of extensively resistant (XDR) strains of M. tuberculosis, which are resistant to nearly every available drug. Thus, new techniques are needed within the TB research field that enhance the ability to diagnose TB, increase the immunological understanding of the disease process, and allow for the screening of novel treatments and prevention strategies including antibiotic regimens and vaccine efficacy studies.
M. tuberculosis is an aerobic acid-fast bacillus that is physically characterized by its very complex outer cell wall and slow growth kinetics. Infection generally occurs through inhalation of individual bacteria contained in aerosolized droplets that are expelled from a symptomatic, infected individual while coughing, sneezing, or singing. Of the exposed individuals that develop infection, only 5 - 10% of people develop active clinical TB. The remaining 90% have a varying spectrum of asymptomatic infections that ranges from subclinical infection to no disease at all, all of which is classified clinically as latent TB infection (LTBI)2,3. Of the population that has this asymptomatic infection, approximately 10% will develop active TB by reactivation of the contained infection in their lifetime. The risk of reactivation dramatically increases if a person with asymptomatic infection contracts HIV or undergoes treatment with an immunosuppressive drug, such as TNF inhibitors4,5,6. Active TB disease also presents as a spectrum, with most people having pulmonary TB, which affects the lungs and thoracic lymph nodes. However, M. tuberculosis can infect any organ, so that the infection can also present in extrapulmonary sites of involvement.
The pathologic hallmark of M. tuberculosis infection is an organized spherical structure of host cells, called the granuloma. Macrophages, T cells and B cells are major components of the granuloma, with variable numbers of neutrophils7. The center of the granuloma is often necrotic. Thus, granulomas function as an immune microenvironment to kill or contain the bacilli, preventing spread to other parts of the lungs. However, M. tuberculosis can subvert killing by the granuloma, and persist within these structures for decades. Consistent and regular monitoring for the development of active TB disease after new infection or reactivation of LTBI is impractical, scientifically challenging and time consuming. Techniques that study these processes longitudinally, in humans and human-like animal models, are extremely useful to the scientific community in furthering the understanding of the many complexities of M. tuberculosis infection and disease.
PET/CT is an extremely useful imaging technique that has been employed to study a vast range of disease states in humans and animal models8. PET is a functional technique that uses positron-emitting radioactive compounds as a reporter. These radioisotopes are typically functionalized to a metabolic compound, such as glucose, or to a targeting group that is designed to bind to a receptor of interest. Since the radiation emitted from PET isotopes is powerful enough to penetrate tissue, very low concentrations can be used which allows for study below saturation levels in receptor-targeting compounds and at a low enough concentration to have no impact on metabolic processes when using agents such as 2-deoxy-2-(18F)Fluoro-D-glucose (FDG). CT is a three-dimensional x-ray imaging technique that uses varying levels of x-ray attenuation to identify physical characteristics of organs within the body9. When paired with PET, CT is used as a map to determine specific locations and structures that show uptake of a PET radiotracer. PET/CT is a powerful tool for in vivo imaging of both humans and animal models infected with M. tuberculosis infection that has led to many important insights into pathogenesis, response to drug treatment, disease spectrum, etc6,10,11,12. This work describes specific PET/CT analytical methods to study TB in non-human primate models longitudinally using parameters such as granuloma size, FDG uptake in individual lesions, whole lung and lymph node FDG avidity, and detection of extrapulmonary disease6,10,11,12.
This manuscript describes methodologies of imaging analysis in non-human primates (NHPs), specifically cynomolgus macaques, which are used to longitudinally evaluate disease progression and drug treatment following infection with M. tuberculosis. NHPs are a valuable animal model because when inoculated with a low dose of M. tuberculosis Erdman strain, animals show a variety of disease outcomes with ~50% developing active TB and the remaining animals having asymptomatic infection (i.e. controlling the infection, LTBI), providing the closest model to the clinical disease spectrum seen in humans3,13,14,15,16. Reactivation of LTBI in macaques is triggered by the same agents that cause reactivation in humans, examples of which include human immunodeficiency virus (HIV, using simian immunodeficiency virus (SIV) as the macaque version of HIV), CD4 depletion or tumor necrosis factor (TNF) neutralization13,16. In addition, macaques present with pathology that is extremely similar to that seen in humans, including the organized granulomas that form in lungs or other organs17. Thus, this model has provided important insights into the basic host-pathogen interactions in M. tuberculosis infection, as well as valuable knowledge about drug regimens and vaccines for tuberculosis14,18,19,20,21.
PET/CT imaging provides the ability to follow the appearance, distribution, and progression of individual granulomas. This work has primarily used FDG as a probe, which, as a glucose analogue, incorporates into metabolically active host cells, such as macrophages, neutrophils, and lymphocytes8, all of which are in granulomas. Thus, FDG is a proxy for host inflammation. The analysis procedures detailed herein uses OsiriX, a widely used DICOM viewer available for purchase and use. The image analysis methods described track the shape, size, and metabolic activity (via FDG uptake) of individual granulomas over time and uses imaging as a map for identifying specific lesions upon animal necropsy. Additionally, a separate method has been developed that quantifies the summation of FDG uptake in the lung above a specific threshold (SUV &#8805; 2.3) and uses this value to evaluate differences between control and experimental groups across studies ranging from vaccine trials to co-infection models. These data support that this overall measure of FDG uptake in lungs is correlated with bacterial burden, thus providing information about the disease status. Similar analyses can be performed on the FDG uptake of thoracic lymph nodes to study progression of disease as well. The following protocol describes the experimental process from animal infection through image analysis.

<table>
	<tbody>
		<tr>
			<td>Ketamine</td>
			<td>Henry Schein</td>
			<td>23061</td>
			<td>Henry Schein</td>
		</tr>
		<tr>
			<td>Telazol</td>
			<td>Zoetis</td>
			<td>4866</td>
			<td>Henry Schein</td>
		</tr>
		<tr>
			<td>Cetacaine</td>
			<td>Patterson Vet Generics</td>
			<td>07-892-6862</td>
			<td>Patterson</td>
		</tr>
		<tr>
			<td>Sterile saline</td>
			<td>Hospira</td>
			<td>07-800-9721</td>
			<td>Patterson</td>
		</tr>
		<tr>
			<td>7H11 agar</td>
			<td>BD</td>
			<td>283810</td>
			<td>BD Biosciences</td>
		</tr>
		<tr>
			<td>IV catheter</td>
			<td>Surflash</td>
			<td>07-806-7659</td>
			<td>Patterson</td>
		</tr>
		<tr>
			<td>18F-FDG</td>
			<td>Zevacor</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Endotracheal tube</td>
			<td>Jorgensen Labs Inc</td>
			<td>07-887-0284</td>
			<td>Patterson</td>
		</tr>
		<tr>
			<td>Artificial tears</td>
			<td>Patterson Vet Generics</td>
			<td>07-888-1663</td>
			<td>Patterson</td>
		</tr>
		<tr>
			<td>Isoflurane</td>
			<td>Zoetis</td>
			<td>07-806-3204</td>
			<td>Patterson</td>
		</tr>
		<tr>
			<td>Neurologica Ceretom CT</td>
			<td>Samsung Neurologica</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Siemens Focus 220 microPET</td>
			<td>Siemens Molecular Imaging Systems</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Inveon Research Software</td>
			<td>Siemens Molecular Imaging Systems</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>OsiriX</td>
			<td>Pixmeo</td>
			<td>N/A</td>
			<td></td>
		</tr>
	</tbody>
</table>

analysis of 18fdg pet/ct imaging as a tool for studying mycobacterium tuberculosis infection and treatment in non-human primates

Mycobacterium tuberculosis remains the number one infectious agent in the world today. With the emergence of antibiotic resistant strains, new clinically relevant methods are needed that evaluate the disease process and screen for potential antibiotic and vaccine treatments. Positron Emission Tomography/Computed Tomography (PET/CT) has been established as a valuable tool for studying a number of afflictions such as cancer, Alzheimer&#39;s disease, and inflammation/infection. Outlined here are a number of strategies that have been employed to evaluate PET/CT images in cynomolgus macaques that are infected intrabronchially with low doses of M. tuberculosis. Through evaluation of lesion size on CT and uptake of 18F-fluorodeoxyglucose (FDG) in lesions and lymph nodes in PET images, these described methods show that PET/CT imaging can predict future development of active versus latent disease and the propensity for reactivation from a latent state of infection. Additionally, by analyzing the overall level of lung inflammation, these methods determine antibiotic efficacy of drugs against M. tuberculosis in the most clinically relevant existing animal model. These image analysis methods are some of the most powerful tools in the arsenal against this disease as not only can they evaluate a number of characteristics of infection and drug treatment, but they are also directly translatable to a clinical setting for use in human studies.

Identification and Analysis of Individual Lesions
Individual granulomas can be visualized for number, size, and FDG uptake qualitatively to understand the general scope of the infection process (Figure 1). Using these images, counting granulomas over time is a quantitative measure of disease spread. Figure 2 depicts individual granuloma counts over time in a group of 10 animals. Of the 10 animals, three developed active disease and six developed latent infection. One animal showed no signs of active disease but was occasionally culture positive (in gastric aspirate and/or bronchoalveolar lavage samples) for M. tuberculosis, placing it within the spectrum of disease between active and latent and was thus removed from the analysis for this particular experiment. Of the three animals with active disease, one animal developed miliary disease by 12 weeks post-infection and was euthanized (this is identified in Figure 2 as TNTC [Too Numerous To Count]). From 6 weeks after infection and thereafter, animals that would later develop active disease showed statistically higher numbers of granulomas than animals that would develop latent infection.
To better characterize and distinguish granulomas between active and latent animals, individual lesions on PET scans were analyzed to determine whether there was a difference in FDG uptake pattern between the two groups. In all of the active infection animals, there was an increase in FDG uptake in every granuloma from three to six weeks post infection (Figure 3A). Conversely, granulomas in animals that developed latent infection showed a variation in FDG uptake with some lesions increasing, decreasing, or showing the same uptake from three to six weeks (Figure 3B). These results are compared in groups showing the difference in change between latent and active animals at three weeks vs. six weeks (Figure 3C) and three weeks vs. 24 weeks (Figure 3D). In both cases, the granulomas of active animals showed a positive and significantly different change in SUV (within each individual animal (Figure 3A and 3B) and when compared by groups of animals (Figure 3C and 3D).
Analyzing FDG Uptake in &#34;Hot&#34; Lymph Nodes
As mediastinal lymph nodes are not readily visualized on CT scans unless greatly enlarged, PET images must be used to identify these diseased tissues. When analyzing lymph nodes, it is critical that the image is always scaled to the same maximum and minimum PET scale to maintain consistency throughout the process. When comparing the MLNs of animals that developed active or latent disease, Lin et al. showed through ROI analysis of MLNs that while FDG uptake in lymph nodes were similar between active and latent animals at 3 weeks, MLNs from active animals showed significantly higher uptake at 6 weeks11. Differences were seen to a greater degree at 8 and 12 weeks (Figure 4). Thus, PET/CT data can be utilized to assess significant differences in lymph nodes in addition to studying granulomas in infected animals.
Total Lung FDG Avidity
As an example of the power of evaluating total lung FDG avidity, Lin et al. showed that elevated lung inflammation in animals clinically classified as LTBI correlates with risk of reactivation6. In this study, LTBI cynomolgus macaques (infected with low-dose M. tuberculosis) were PET/CT imaged (6 months post-infection) prior to tumor necrosis factor (TNF) neutralization to assess the spectrum of lesions seen in clinically defined LTBI and determine risk of reactivation. Animals with higher total lung FDG avidity were more likely to reactivate (Figure 5). Over 90% of the animals with more than 103 lung FDG avidity or with visible (by scan) at least one extra-pulmonary site of infection reactivated after TNF neutralization. Only one animal that did not reactivate exceeded this total lung FDG avidity threshold. Thus, PET/CT parameters can be a powerful tool to predicting clinical outcome though the specific parameters must be scientifically identified.
As an example to show utility in drug treatment scenarios, Coleman et al. conducted a study testing oxazolidinones in humans and cynomolgus macaques where total lung FDG avidity was measured pre-drug treatment, and one and two months post-treatment10. Fold changes were calculated to show drug response one month (Figure 6A) and two months post-treatment (Figure 6B). At both time points, control animals showed significantly higher FDG avidity in the entire lung space than drug-treated animals. In all of the drug-treated animals, total lung inflammation decreased over the two-month treatment regimen, while in most of the control animals, total lung inflammation increased over time or was unchanged.

<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/56375/56375fig1.jpg" /> 
Figure 1. Serial FDG PET/CT Images Showing a Disseminating and Stable Pattern of Granuloma Evolution During the Course of Early Infection. 
(Top row) Primary granulomas (white arrows) were first established at 3 weeks post-infection, while new granulomas developed adjacent to existing lesions (green arrows) or in new sites (yellow arrows). Animals that would later develop active TB developed more lesions during the course of infection. (Bottom row) Primary granulomas (white arrows) of latent animals usually remained stable, with few new granulomas developing through the course of infection. wks PI, weeks post-infection. Figure taken from Coleman et al.11 <a href="https://cloudflare-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/56375/56375fig1large.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/56375/56375fig2v2.jpg" /> 
Figure 2. Representative Data of Depicting the Median and Range of Granuloma Counting from CT Scans Comparing Animals with Active Infection (Red Symbols) to Latent Infection (Green Symbols). 
Active infection animals had more granulomas than latently infected animals as early as six weeks post-infection. P &#60; 0.05 (*) by Mann-Whitney test. Weeks PI, weeks post-infection. TNTC, too numerous to count. Figure adapted from Coleman et al.11 <a href="https://cloudflare-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/56375/56375fig2v2large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 3" class="xfigimg" src="/files/ftp_upload/56375/56375fig3.jpg" /> 
Figure 3. Utilization of ROI Analysis on PET Images to Show that Metabolic Activity of Lung Granulomas Differs Between Active and Latently Infected Animals During Early Infection. 
Individual granulomas in active animals [A] have a significant increase in metabolic activity (measured as standard uptake value normalized to muscle uptake [SUVCMR]) between 3 and 6 weeks after infection while latently infected animals [B] do not. The change in metabolic activity in lesions between latent and active animals as groups were compared at 3 vs. 6 weeks [C] and 3 vs. 24 weeks [D] showing that actively infected animals (red squares) have a significantly larger change in uptake than latent animals (green circles) at both time points. Solid black lines represent the median. The Wilcoxon rank-sum test was used to analyze data in panels A and B. For panels C and D, values were analyzed by the Mann-Whitney test. P &#60; 0.0001 (****) for all panels. Figure adapted from Coleman et al.11 <a href="https://cloudflare-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/56375/56375fig3large.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/56375/56375fig4.jpg" /> 
Figure 4. ROI Analysis of PET Images to Show Differences in FDG Uptake in Mediastinal Lymph Nodes Between Animals with Active Disease (Red Squares) and Latent Disease (Green Circles). 
Uptake was higher in actively infected animals at 6, 8, and 12 weeks post infection. Each dot represents an individual lymph node. Solid black lines represent the median. P &#60; 0.05 (*), P &#60; 0.01 (**), and P &#60; 0.001 (***) by Mann-Whitney test. Figure adapted from Coleman et al.11 <a href="https://cloudflare-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/56375/56375fig4large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 5" class="xfigimg" src="/files/ftp_upload/56375/56375fig5.jpg" /> 
Figure 5. ROI Analysis of Total Lung FDG Avidity Measurements at Six Months Post Infection Highlighting Differences in FDG Uptake in Animals Which Reactivate from Latent Infection (Pink Squares) in Comparison to Animals Which Remain Latent (Green Circles). 
Three of the four &#34;reactivated&#34; animals that lie below the dotted line had extra-pulmonary disease prior to TNF (tumor necrosis factor) neutralization. Each dot represents one animal. Dotted line represents threshold value for likely reactivation risk. Solid black lines represent the median. P &#60; 0.01 (**) from Mann-Whitney Test. Data adapted from Lin et al.6 <a href="https://cloudflare-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/56375/56375fig5large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 6" class="xfigimg" src="/files/ftp_upload/56375/56375fig6.jpg" /> 
Figure 6. Representative Total Lung FDG Avidity ROI Measurements Highlighting Overall Change in Inflammation Measured in Lungs Comparing Untreated (Red Circles) and Linezolid Treated (Blue Circles) Monkeys. 
FDG avidity was measured before linezolid treatment (30 mg/kg daily) and the fold change in total FDG uptake was measured at 1 month [A] and 2 months [B] post treatment. Each monkey is represented by an individual circle. Solid black lines represent the median. P &#60; 0.01 (**) per Mann-Whitney Test. <a href="https://cloudflare-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/56375/56375fig6large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

Watch this Scientific Journal Video about Analysis of 18FDG PET/CT Imaging as a Tool for Studying Mycobacterium tuberculosis Infection and Treatment in Non-human Primates at JoVE.com

Analysis of 18FDG PET/CT Imaging as a Tool for Studying Mycobacterium tuberculosis Infection and Treatment in Non-human Primates

Here, we present a protocol to describe the analysis of 18F-FDG PET/CT imaging in non-human primates that have been infected with M. tuberculosis to study disease process, drug treatment, and disease reactivation.

Analysis of 18FDG PET/CT Imaging as a Tool for Studying Mycobacterium tuberculosis Infection and Treatment in Non-human Primates

Mycobacterium tuberculosis remains the number one infectious agent in the world today. With the emergence of antibiotic resistant strains, new clinically ...

analysis-18fdg-petct-imaging-as-tool-for-studying-mycobacterium

Nanyang Technological University

Research

JoVE Journal

Immunology and Infection

18.6K Views.  University of Pittsburgh School of Medicine. Here, we present a protocol to describe the analysis of 18F-FDG PET/CT imaging in non-human primates that have been infected with M. tuberculosis to study disease process, drug treatment, and disease reactivation.

Video: Analysis of 18FDG PET/CT Imaging as a Tool for Studying Mycobacterium tuberculosis Infection and Treatment in Non-human Primates

Introducing Shear Stress in the Study of Bacterial Adhesion

During bacterial infections a sequence of interactions occur between the pathogen and its host. Bacterial adhesion to the host cell surface is often the initial and determining step of the pathogenesis. Although experimentally adhesion is mostly studied in static conditions adhesion actually takes place in the presence of flowing liquid. First encounters between bacteria and their host often occur at the mucosal level, mouth, lung, gut, eye, etc. where mucus flows along the surface of epithelial cells. Later in infection, pathogens occasionally access the blood circulation causing life-threatening illnesses such as septicemia, sepsis and meningitis. A defining feature of these infections is the ability of these pathogens to interact with endothelial cells in presence of circulating blood. The presence of flowing liquid, mucus or blood for instance, determines adhesion because it generates a mechanical force on the pathogen. To characterize the effect of flowing liquid one usually refers to the notion of shear stress, which is the tangential force exerted per unit area by a fluid moving near a stationary wall, expressed in dynes/cm2. Intensities of shear stress vary widely according to the different vessels type, size, organ, location etc. (0-100 dynes/cm2). Circulation in capillaries can reach very low shear stress values and even temporarily stop during periods ranging between a few seconds to several minutes 1. On the other end of the spectrum shear stress in arterioles can reach 100 dynes/cm2 2. The impact of shear stress on different biological processes has been clearly demonstrated as for instance during the interaction of leukocytes with the endothelium 3. To take into account this mechanical parameter in the process of bacterial adhesion we took advantage of an experimental procedure based on the use of a disposable flow chamber 4. Host cells are grown in the flow chamber and fluorescent bacteria are introduced in the flow controlled by a syringe pump. We initially focused our investigations on the bacterial pathogen Neisseria meningitidis, a Gram-negative bacterium responsible for septicemia and meningitis. The procedure described here allowed us to study the impact of shear stress on the ability of the bacteria to: adhere to cells 1, to proliferate on the cell surface 5and to detach to colonize new sites 6 (Figure 1). Complementary technical information can be found in reference 7. Shear stress values presented here were chosen based on our previous experience1 and to represent values found in the literature. The protocol should be applicable to a wide range of pathogens with specific adjustments depending on the objectives of the study.

During the infection process, a key step is the adhesion of pathogens with host cells. In most instances this adhesion step occurs in the presence of mechanical stress generated by flowing liquid. We describe a technique that introduces shear stress as an important parameter in the study of bacterial adhesion.

During bacterial infections a sequence of interactions occur between the pathogen and its host. Bacterial adhesion to the host cell surface is often the ...

Sample Preparation of Mycobacterium tuberculosis Extracts for Nuclear Magnetic Resonance Metabolomic Studies

Mycobacterium tuberculosis is a major cause of mortality in human beings on a global scale. The emergence of both multi- (MDR) and extensively-(XDR) drug-resistant strains threatens to derail current disease control efforts. Thus, there is an urgent need to develop drugs and vaccines that are more effective than those currently available. The genome of M. tuberculosis has been known for more than 10 years, yet there are important gaps in our knowledge of gene function and essentiality. Many studies have since used gene expression analysis at both the transcriptomic and proteomic levels to determine the effects of drugs, oxidants, and growth conditions on the global patterns of gene expression. Ultimately, the final response of these changes is reflected in the metabolic composition of the bacterium including a few thousand small molecular weight chemicals. Comparing the metabolic profiles of wild type and mutant strains, either untreated or treated with a particular drug, can effectively allow target identification and may lead to the development of novel inhibitors with anti-tubercular activity. Likewise, the effects of two or more conditions on the metabolome can also be assessed. Nuclear magnetic resonance (NMR) is a powerful technology that is used to identify and quantify metabolic intermediates. In this protocol, procedures for the preparation of M. tuberculosis cell extracts for NMR metabolomic analysis are described. Cell cultures are grown under appropriate conditions and required Biosafety Level 3 containment,1 harvested, and subjected to mechanical lysis while maintaining cold temperatures to maximize preservation of metabolites. Cell lysates are recovered, filtered sterilized, and stored at ultra-low temperatures. Aliquots from these cell extracts are plated on Middlebrook 7H9 agar for colony-forming units to verify absence of viable cells. Upon two months of incubation at 37 &deg;C, if no viable colonies are observed, samples are removed from the containment facility for downstream processing. Extracts are lyophilized, resuspended in deuterated buffer and injected in the NMR instrument, capturing spectroscopic data that is then subjected to statistical analysis. The procedures described can be applied for both one-dimensional (1D) 1H NMR and two-dimensional (2D) 1H-13C NMR analyses. This methodology provides more reliable small molecular weight metabolite identification and more reliable and sensitive quantitative analyses of cell extract metabolic compositions than chromatographic methods. Variations of the procedure described following the cell lysis step can also be adapted for parallel proteomic analysis.

Sample Preparation of Mycobacterium tuberculosis Extracts for Nuclear Magnetic Resonance Metabolomic Studies

The metabolomic profile of Mycobacterium tuberculosis is determined after growth in broth cultures. Conditions can be varied to test the effects of nutritional supplements, oxidants, and anti-tuberculosis agents on the metabolic profile of this microorganism. Procedure for extract preparation is applicable for both 1D 1H and 2D 1H-13C NMR analyses.

Mycobacterium tuberculosis is a major cause of mortality in human beings on a global scale. The emergence of both multi- (MDR) and extensively-(XDR) ...

Growth of Mycobacterium tuberculosis Biofilms

Mycobacterium tuberculosis, the etiologic agent of human tuberculosis, has an extraordinary ability to survive against environmental stresses including antibiotics. Although stress tolerance of M. tuberculosis is one of the likely contributors to the 6-month long chemotherapy of tuberculosis 1, the molecular mechanisms underlying this characteristic phenotype of the pathogen remain unclear. Many microbial species have evolved to survive in stressful environments by self-assembling in highly organized, surface attached, and matrix encapsulated structures called biofilms 2-4. Growth in communities appears to be a preferred survival strategy of microbes, and is achieved through genetic components that regulate surface attachment, intercellular communications, and synthesis of extracellular polymeric substances (EPS) 5,6. The tolerance to environmental stress is likely facilitated by EPS, and perhaps by the physiological adaptation of individual bacilli to heterogeneous microenvironments within the complex architecture of biofilms 7.
In a series of recent papers we established that M. tuberculosis and Mycobacterium smegmatis have a strong propensity to grow in organized multicellular structures, called biofilms, which can tolerate more than 50 times the minimal inhibitory concentrations of the anti-tuberculosis drugs isoniazid and rifampicin 8-10. M. tuberculosis, however, intriguingly requires specific conditions to form mature biofilms, in particular 9:1 ratio of headspace: media as well as limited exchange of air with the atmosphere 9. Requirements of specialized environmental conditions could possibly be linked to the fact that M. tuberculosis is an obligate human pathogen and thus has adapted to tissue environments. In this publication we demonstrate methods for culturing M. tuberculosis biofilms in a bottle and a 12-well plate format, which is convenient for bacteriological as well as genetic studies. We have described the protocol for an attenuated strain of M. tuberculosis, mc27000, with deletion in the two loci, panCD and RD1, that are critical for in vivo growth of the pathogen 9. This strain can be safely used in a BSL-2 containment for understanding the basic biology of the tuberculosis pathogen thus avoiding the requirement of an expensive BSL-3 facility. The method can be extended, with appropriate modification in media, to grow biofilm of other culturable mycobacterial species.
Overall, a uniform protocol of culturing mycobacterial biofilms will help the investigators interested in studying the basic resilient characteristics of mycobacteria. In addition, a clear and concise method of growing mycobacterial biofilms will also help the clinical and pharmaceutical investigators to test the efficacy of a potential drug.

Growth of Mycobacterium tuberculosis Biofilms

Mycobacterium tuberculosis forms drug tolerant biofilms when cultured in certain conditions. Here we describe methods for culturing M. tuberculosis biofilms and determining the frequency of drug tolerant persisters. These protocols will be useful for further studies into the mechanisms of drug tolerance in M. tuberculosis.

Mycobacterium tuberculosis, the etiologic agent of human tuberculosis, has an extraordinary ability to survive against environmental stresses including ...

Demonstrating a Multi-drug Resistant Mycobacterium tuberculosis Amplification Microarray

Simplifying microarray workflow is a necessary first step for creating MDR-TB microarray-based diagnostics that can be routinely used in lower-resource environments. An amplification microarray combines asymmetric PCR amplification, target size selection, target labeling, and microarray hybridization within a single solution and into a single microfluidic chamber. A batch processing method is demonstrated with a 9-plex asymmetric master mix and low-density gel element microarray for genotyping multi-drug resistant Mycobacterium tuberculosis (MDR-TB). The protocol described here can be completed in 6 hr and provide correct genotyping with at least 1,000 cell equivalents of genomic DNA. Incorporating on-chip wash steps is feasible, which will result in an entirely closed amplicon method and system. The extent of multiplexing with an amplification microarray is ultimately constrained by the number of primer pairs that can be combined into a single master mix and still achieve desired sensitivity and specificity performance metrics, rather than the number of probes that are immobilized on the array. Likewise, the total analysis time can be shortened or lengthened depending on the specific intended use, research question, and desired limits of detection. Nevertheless, the general approach significantly streamlines microarray workflow for the end user by reducing the number of manually intensive and time-consuming processing steps, and provides a simplified biochemical and microfluidic path for translating microarray-based diagnostics into routine clinical practice.

Demonstrating a Multi-drug Resistant Mycobacterium tuberculosis Amplification Microarray

An amplification microarray combines asymmetric PCR amplification and microarray hybridization into a single chamber, which significantly streamlines microarray workflow for the end user. Simplifying microarray workflow is a necessary first step for creating microarray-based diagnostics that can be routinely used in lower-resource environments.

Simplifying microarray workflow is a necessary first step for creating MDR-TB microarray-based diagnostics that can be routinely used in lower-resource ...

A 3D Human Lung Tissue Model for Functional Studies on Mycobacterium tuberculosis Infection

Tuberculosis (TB) still holds a major threat to the health of people worldwide, and there is a need for cost-efficient but reliable models to help us understand the disease mechanisms and advance the discoveries of new treatment options. In vitro cell cultures of monolayers or co-cultures lack the three-dimensional (3D) environment and tissue responses. Herein, we describe an innovative in vitro model of a human lung tissue, which holds promise to be an effective tool for studying the complex events that occur during infection with Mycobacterium tuberculosis (M. tuberculosis). The 3D tissue model consists of tissue-specific epithelial cells and fibroblasts, which are cultured in a matrix of collagen on top of a porous membrane. Upon air exposure, the epithelial cells stratify and secrete mucus at the apical side. By introducing human primary macrophages infected with M. tuberculosis to the tissue model, we have shown that immune cells migrate into the infected-tissue and form early stages of TB granuloma. These structures recapitulate the distinct feature of human TB, the granuloma, which is fundamentally different or not commonly observed in widely used experimental animal models. This organotypic culture method enables the 3D visualization and robust quantitative analysis that provides pivotal information on spatial and temporal features of host cell-pathogen interactions. Taken together, the lung tissue model provides a physiologically relevant tissue micro-environment for studies on TB. Thus, the lung tissue model has potential implications for both basic mechanistic and applied studies. Importantly, the model allows addition or manipulation of individual cell types, which thereby widens its use for modelling a variety of infectious diseases that affect the lungs.

A 3D Human Lung Tissue Model for Functional Studies on Mycobacterium tuberculosis Infection

Human tuberculosis infection is a complex process, which is difficult to model in vitro. Here we describe a novel 3D human lung tissue model that recapitulates the dynamics that occur during infection, including the migration of immune cells and early granuloma formation in a physiological environment.

Tuberculosis (TB) still holds a major threat to the health of people worldwide, and there is a need for cost-efficient but reliable models to help us ...

Murine Lymphocyte Labeling by 64Cu-Antibody Receptor Targeting for In Vivo Cell Trafficking by PET/CT

This protocol illustrates the production of 64Cu and the chelator conjugation/radiolabeling of a monoclonal antibody (mAb) followed by murine lymphocyte cell culture and 64Cu-antibody receptor targeting of the cells. In vitro evaluation of the radiolabel and non-invasive in vivo cell tracking in an animal model of an airway delayed-type hypersensitivity reaction (DTHR) by PET/CT are described.
In detail, the conjugation of a mAb with the chelator 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) is shown. Following the production of radioactive 64Cu, radiolabeling of the DOTA-conjugated mAb is described. Next, the expansion of chicken ovalbumin (cOVA)-specific CD4+ interferon (IFN)-&#947;-producing T helper cells (cOVA-TH1) and the subsequent radiolabeling of the cOVA-TH1 cells are depicted. Various in vitro techniques are presented to evaluate the effects of 64Cu-radiolabeling on the cells, such as the determination of cell viability by trypan blue exclusion, the staining for apoptosis with Annexin V for flow cytometry, and the assessment of functionality by IFN-&#947; enzyme-linked immunosorbent assay (ELISA). Furthermore, the determination of the radioactive uptake into the cells and the labeling stability are described in detail. This protocol further describes how to perform cell tracking studies in an animal model for an airway DTHR and, therefore, the induction of cOVA-induced acute airway DHTR in BALB/c mice is included. Finally, a robust PET/CT workflow including image acquisition, reconstruction, and analysis is presented.
The 64Cu-antibody receptor targeting approach with subsequent receptor internalization provides high specificity and stability, reduced cellular toxicity, and low efflux rates compared to common PET-tracers for cell labeling, e.g.64Cu-pyruvaldehyde bis(N4-methylthiosemicarbazone) (64Cu-PTSM). Finally, our approach enables non-invasive in vivo cell tracking by PET/CT with an optimal signal-to-background ratio for 48 h. This experimental approach can be transferred to different animal models and cell types with membrane-bound receptors that are internalized.

Murine Lymphocyte Labeling by 64Cu-Antibody Receptor Targeting for In Vivo  Cell Trafficking by PET/CT

Following the preparation of a 64Cu-modified monoclonal antibody binding to a transgenic murine T cell receptor, T cells are radiolabeled in vivo, analyzed for viability, functionality, labeling stability and apoptosis, and adoptively transferred into mice with an airway delayed-type hypersensitivity reaction for non-invasive imaging by positron emission tomography/computed tomography (PET/CT).

This protocol illustrates the production of 64Cu and the chelator conjugation/radiolabeling of a monoclonal antibody (mAb) followed by murine lymphocyte ...

System for Efficacy and Cytotoxicity Screening of Inhibitors Targeting Intracellular Mycobacterium tuberculosis

Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), is a leading cause of morbidity and mortality worldwide. With the increased spread of multi drug-resistant TB (MDR-TB), there is a real urgency to develop new therapeutic strategies against M. tuberculosis infections. Traditionally, compounds are evaluated based on their antibacterial activity under in vitro growth conditions in broth; however, results are often misleading for intracellular pathogens like M. tuberculosis since in-broth phenotypic screening conditions are significantly different from the actual disease conditions within the human body. Screening for inhibitors that work inside macrophages has been traditionally difficult due to the complexity, variability in infection, and slow replication rate of M. tuberculosis. In this study, we report a new approach to rapidly assess the effectiveness of compounds on the viability of M. tuberculosis in a macrophage infection model. Using a combination of a cytotoxicity assay and an in-broth M. tuberculosis viability assay, we were able to create a screening system that generates a comprehensive analysis of compounds of interest. This system is capable of producing quantitative data at a low cost that is within reach of most labs and yet is highly scalable to fit large industrial settings.

System for Efficacy and Cytotoxicity Screening of Inhibitors Targeting Intracellular Mycobacterium tuberculosis

We have developed a modular high-throughput screening system for discovering novel compounds against Mycobacterium tuberculosis, targeting intracellular and in-broth growing bacteria as well as cytotoxicity against the mammalian host cell.

Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), is a leading cause of morbidity and mortality worldwide. With the increased spread ...

Imaging Mycobacterium tuberculosis in Mice with Reporter Enzyme Fluorescence

Reporter enzyme fluorescence (REF) utilizes substrates that are specific for enzymes present in target organisms of interest for imaging or detection by fluorescence or bioluminescence. We utilize BlaC, an enzyme expressed constitutively by all M. tuberculosis strains. REF allows rapid quantification of bacteria in lungs of infected mice. The same group of mice can be imaged at many time points, greatly reducing costs, enumerating bacteria more quickly, allowing novel observations in host-pathogen interactions, and increasing statistical power, since more animals per group are readily maintained. REF is extremely sensitive due to the catalytic nature of the BlaC enzymatic reporter and specific due to the custom flourescence resonance energy transfer (FRET) or fluorogenic substrates used. REF does not require recombinant strains, ensuring normal host-pathogen interactions. We describe the imaging of M. tuberculosis infection using a FRET substrate with maximal emission at 800 nm. The wavelength of the substrate allows sensitive deep tissue imaging in mammals. We will outline aerosol infection of mice with M. tuberculosis, anesthesia of mice, administration of the REF substrate, and optical imaging. This method has been successfully applied to evaluating host-pathogen interactions and efficacy of antibiotics targeting M. tuberculosis.

Imaging Mycobacterium tuberculosis in Mice with Reporter Enzyme Fluorescence

We describe the optical imaging of mice infected with Mycobacterium tuberculosis (M. tuberculosis) using reporter enzyme fluorescence (REF). This protocol facilitates the sensitive and specific detection of M. tuberculosis in pre-clinical animal models for pathogenesis, therapeutics and vaccine research.

Reporter enzyme fluorescence (REF) utilizes substrates that are specific for enzymes present in target organisms of interest for imaging or detection by ...

Modeling Tuberculosis in Mycobacterium marinum Infected Adult Zebrafish

Mycobacterium tuberculosis is currently the deadliest human pathogen causing 1.7 million deaths and 10.4 million infections every year. Exposure to this bacterium causes a wide disease spectrum in humans ranging from a sterilized infection to an actively progressing deadly disease. The most common form is the latent tuberculosis, which is asymptomatic, but has the potential to reactivate into a fulminant disease. Adult zebrafish and its natural pathogen Mycobacterium marinum have recently proven to be an applicable model to study the wide disease spectrum of tuberculosis. Importantly, spontaneous latency and reactivation as well as adaptive immune responses in the context of mycobacterial infection can be studied in this model. In this article, we describe methods for the experimental infection of adult zebrafish, the collection of internal organs for the extraction of nucleic acids for the measurement of mycobacterial loads and host immune responses by quantitative PCR. The in-house-developed, M. marinum-specific qPCR assay is more sensitive than the traditional plating methods as it also detects DNA from non-dividing, dormant or recently dead mycobacteria. As both DNA and RNA are extracted from the same individual, it is possible to study the relationships between the diseased state, and the host and pathogen gene-expression. The adult zebrafish model for tuberculosis thus presents itself as a highly applicable, non-mammalian in vivo system to study host-pathogen interactions.

Modeling Tuberculosis in Mycobacterium marinum Infected Adult Zebrafish

Here, we present a protocol to model human tuberculosis in an adult zebrafish using its natural pathogen Mycobacterium marinum. Extracted DNA and RNA from the internal organs of infected zebrafish can be used to reveal the total mycobacterial loads in the fish and the host&#39;s immune responses with qPCR.

Mycobacterium tuberculosis is currently the deadliest human pathogen causing 1.7 million deaths and 10.4 million infections every year. Exposure to this ...

Use of the Invertebrate Galleria mellonella as an Infection Model to Study the Mycobacterium tuberculosis Complex

Tuberculosis is the leading global cause of infectious disease mortality and roughly a quarter of the world&#8217;s population is believed to be infected with Mycobacterium tuberculosis. Despite decades of research, many of the mechanisms behind the success of M. tuberculosis as a pathogenic organism remain to be investigated, and the development of safer, more effective antimycobacterial drugs are urgently needed to tackle the rise and spread of drug resistant tuberculosis. However, the progression of tuberculosis research is bottlenecked by traditional mammalian infection models that are expensive, time consuming, and ethically challenging. Previously we established the larvae of the insect Galleria mellonella (greater wax moth) as a novel, reproducible, low cost, high-throughput and ethically acceptable infection model for members of the M. tuberculosis complex. Here we describe the maintenance, preparation, and infection of G. mellonella with bioluminescent Mycobacterium bovis BCG lux. Using this infection model, mycobacterial dose dependent virulence can be observed, and a rapid readout of in vivo mycobacterial burden using bioluminescence measurements is easily achievable and reproducible. Although limitations exist, such as the lack of a fully annotated genome for transcriptomic analysis, ontological analysis against genetically similar insects can be carried out. As a low cost, rapid, and ethically acceptable model for tuberculosis, G. mellonella can be used as a pre-screen to determine drug efficacy and toxicity, and to determine comparative mycobacterial virulence prior to the use of conventional mammalian models. The use of the G. mellonella-mycobacteria model will lead to a reduction in the substantial number of animals currently used in tuberculosis research.

Use of the Invertebrate Galleria mellonella as an Infection Model to Study the Mycobacterium tuberculosis Complex

Galleria mellonella was recently established as a reproducible, cheap, and ethically acceptable infection model for the Mycobacterium tuberculosis complex. Here we describe and demonstrate the steps taken to establish successful infection of G. mellonella with bioluminescent Mycobacterium bovis BCG lux.

Tuberculosis is the leading global cause of infectious disease mortality and roughly a quarter of the world&#8217;s population is believed to be infected ...