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Inequality is rife throughout South Africa. The first wave of COVID-19 may have affected people in lower socioeconomic groups worse than the affluent. The SARS-CoV-2 seroprevalence and the specificity of anti-SARS-CoV-2 antibody tests in South Africa is not known. We tested 405 volunteers representing all socioeconomic strata from the workforce of a popular shopping and tourist complex in central Cape Town with the Abbott SARS-CoV-2 IgG assay. We assessed the association between antibody positivity and COVID-19 symptom status, medical history, and sociodemographic variables. We tested 137 serum samples from healthy controls collected in Cape Town prior to the COVID-19 pandemic, to confirm the specificity of the assay in the local population. Of the 405 volunteers tested one month after the first peak of the epidemic in Cape Town, 96(23.7%) were SARS-CoV-2 IgG positive. Of those who tested positive, 46(47.9%) reported no symptoms of COVID-19 in the previous 6 months. Seropositivity was significantly associated with living in informal housing, residing in a subdistrict with low income-per household, and having a low-earning occupation. The specificity of the assay was 98.54%(95%CI 94.82%-99.82%) in the pre-COVID controls. There is a high background seroprevalence in Cape Town, particularly in people of lower socioeconomic status. Almost half of cases are asymptomatic, and therefore undiagnosed by local testing strategies. These results cannot be explained by low assay specificity.

Oxidized cholesterols have emerged as important signaling molecules of immune function, but little is known about the role of these oxysterols during mycobacterial infections. We found that expression of the oxysterol-receptor GPR183 was reduced in blood from patients with tuberculosis (TB) and type 2 diabetes (T2D) compared to TB patients without T2D and was associated with TB disease severity on chest x-ray. GPR183 activation by 7 ,25-dihydroxycholesterol (7 ,25-OHC) reduced growth of (Mtb) and BCG in primary human monocytes, an effect abrogated by the GPR183 antagonist GSK682753. Growth inhibition was associated with reduced IFN-β and IL-10 expression and enhanced autophagy. Mice lacking GPR183 had significantly increased lung Mtb burden and dysregulated IFNs during early infection. Together, our data demonstrate that GPR183 is an important regulator of intracellular mycobacterial growth and interferons during mycobacterial infection.

The development of a rapid and affordable assay to screen participants for Q12 additional testing could streamline TB screening in resource-limited settings and for community-wide health screens. Sputum remains the primary testing sample, making it potentially ideal for a screening testing. Neutrophils are highly expanded in sputum from individuals with pulmonary TB with high specificity and have potential as a biomarker for TB. Three neutrophil associated proteins, neutrophil gelatinase associated-lipocalin (NGAL), the protein heterodimer S100A8/A9 and the protein death ligand-1 (PDL-1), were measured in presumptive TB cases from participants attending a primary healthcare clinic in Durban, South Africa, using commercially available ELISAs on a total of 79 participants from a 109-participant cohort. Participants with microbiologically confirmed TB were sampled after 1 month of treatment. Proteins were also measured in tongue swab samples in participants from this cohort at baseline. Baseline results were confirmed in a second TB cohort which recruited a total of 51 participants with presumptive TB from the Western Cape. Finally, we investigate sputum neutrophil protein levels in individuals with community diagnosed asymptomatic TB. Significant increases in all proteins were detectable in sputum from clinic-diagnosed TB participants relative to symptomatic controls. Performance approached the WHO target product profile for a TB triage test, with ROC AUCs reaching 0.866 (with a 95% confidence interval of 0.7683 - 0.9633) in the case of S100A8/A9. Sputum protein levels did not correlate with bacterial burden and did not consistently decrease following one month of drug therapy. Only PDL-1 was detectable in mouth swab samples. Sputum neutrophil proteins tended to be elevated in participants with asymptomatic community diagnosed TB, as compared to asymptomatic community controls within the Vukuzazi cohort using a sample size of 42 participants, although this was not significant. This study provides a proof of principle that neutrophil proteins can be easily measured in standard sputum samples and have potential as a screening test for TB. However, more work is needed to explore whether this approach, using these three neutrophil proteins, can meet the WHO target product profile for a triage test worth developing further.

Successful TB treatment is hampered by increasing resistance to the two most effective first-line anti-TB drugs, namely isoniazid and rifampicin, thus innovative therapies focused on host processes, termed host-directed therapies (HDTs), are promising novel approaches for increasing treatment efficacy without inducing drug resistance. We assessed the ability of Sildenafil, a type-5 phosphodiesterase inhibitor, as a repurposed compound, to serve as HDT target, by counteracting the suppressive effects of myeloid-derived suppressor cells (MDSC) obtained from active TB cases on T-cell responsiveness. We confirm that MDSC suppress non-specific T-cell activation. We also show that Sildenafil treatment fails to reverse the MDSC-mediated suppression of T-cell functions measured here, namely activation and proliferation. The impact of Sildenafil treatment on improved immunity, using the concentration tested here, is likely to be minimal, but further identification and development of MDSC-targeting TB host-directed therapies are warranted.

TB is a highly infectious disease, with granulomas as its hallmark. Granulomas play an important role in the control of M. tuberculosis infection and as such are crucial indicators for our understanding of host resistance to TB. Tuberculous granulomas that develop in response to Mycobacterium tuberculosis ( M. tuberculosis ) infection are highly dynamic entities shaped by the host immune response and disease kinetics. Within this microenvironment, immune cell recruitment, polarization, and activation are driven not only by coexisting cell types and multicellular interactions but also by M. tuberculosis -mediated changes involving metabolic heterogeneity, epigenetic reprogramming, and rewiring of the transcriptional landscape of host cells. There is an increased appreciation of the in vivo complexity, versatility, and heterogeneity of the cellular compartment that constitutes the tuberculosis (TB) granuloma and the difficulty in translating findings from animal models to human disease. Here, we describe a novel biomimetic in vitro three-dimensional (3D) human lung spheroid granuloma model, resembling early “innate” and “adaptive” stages of the TB granuloma spectrum, and present results of histological architecture, host transcriptional characterization, mycobacteriological features, cytokine profiles, and spatial distribution of key immune cells. A range of manipulations of immune cell populations in these spheroid granulomas will allow the study of host/pathogen pathways involved in the outcome of infection, as well as pharmacological interventions. IMPORTANCE TB is a highly infectious disease, with granulomas as its hallmark. Granulomas play an important role in the control of M. tuberculosis infection and as such are crucial indicators for our understanding of host resistance to TB. Correlates of risk and protection to M. tuberculosis are still elusive, and the granuloma provides the perfect environment in which to study the immune response to infection and broaden our understanding thereof; however, human granulomas are difficult to obtain, and animal models are costly and do not always faithfully mimic human immunity. In fact, most TB research is conducted in vitro on immortalized or primary immune cells and cultured in two dimensions on flat, rigid plastic, which does not reflect in vivo characteristics. We have therefore conceived a 3D, human in vitro spheroid granuloma model which allows researchers to study features of granuloma-forming diseases in a 3D structural environment resembling in vivo granuloma architecture and cellular orientation.

Background There is a concern that SARS-CoV-2 infection may drive poor outcomes after Mycobacterium tuberculosis Mtb exposure and infection. We performed an ex vivo Mtb killing assay using peripheral blood mononuclear cells (PBMC) from three groups: healthy household contacts of people with active TB with and without serologic evidence of previous SARS-CoV-2 infection (COV+HHC and COV-HHC), and participants with active TB and previous SARS-CoV-2 (COV+TB+). Methods Twenty participants per group from Cape Town, South Africa were classified according to SARS-CoV-2 anti-S and anti-N antibody tests. We infected PBMC from each participant at a MOI of 0.001 with Mtb strain H37Rv in a 4-day growth inhibition assay. Mycobacteria were quantified through inoculation into Bactec Mycobacteria Growth Indicator Tube (MGIT) liquid culture. PBMC from a subset of participants were infected in the presence of autologous time-matched serum and Mtb-uninfected control PBMCs were included. Results There was no difference in the time to detection of Mtb or the normalised Mtb growth ratio (log10CFUsample – log10CFUcontrol) between groups in the standard protocol, or when infected cells from the COV+HHC and COV+TB+ (n=10 each) groups were cultured with autologous time-matched serum. The group with active TB demonstrated the best Mtb growth control. Extracellular Mtb measured by culturing the supernatants of the infected cell cultures also did not show any difference between groups. Five (14.3%) uninfected controls were culture positive. Conclusion Our results show that previous SARS-CoV-2 does not affect the Mtb killing ability of circulating mononuclear immune cells in vitro. Previous SARS-CoV-2 is unlikely to affect the outcome of Mtb infection through this mechanism.

We explored the underlying mechanisms that may drive post-tuberculosis (TB) lung disease, a multifactorial, heterogenous, and prevalent disease. Extensive clinical phenotyping through fluorine-18 Fluorodeoxyglucose (FDG) positron emission tomography (PET)-computed tomography (CT) scans, pulmonary function testing, and symptom and quality of life questionnaires, was performed on a cohort of 48 adults who completed TB treatment within 6 months prior. Immunological characteristics of paired blood- and bronchoalveolar lavage fluid (BALF)-derived immune cells were assessed by multiplex bead-based immunoassay, ELISA and flow cytometry. There was agreement between measures of inflammation on PET, the severity of anatomical abnormalities on CT, and pulmonary function testing. However, of these, only PET was associated with exercise tolerance and symptom scores. Measures of radiologic extent (total glycolytic activity and SUVmax on PET, and segments involved on CT) also correlated with proteins detected in blood that implicate type 1 (IFN-γ, TNFα, IL-12) and type 2 (IL-4, IL-33) responses, ongoing remodelling of lung tissue (MMPs), airways and vasculature (VEGF), as well as subsets of activated CD8 + and CD4 + T-cells. The radiologic extent of structural post-TB lung involvement is associated with a range of impaired lung function measures and immunological dysregulation. Our findings suggest that obstructive and restrictive lung pathology due to pulmonary TB do not occur in opposition but rather point towards a mixed pathology in most TB survivors.

Background Tuberculosis (TB) remains a debilitating, deadly disease that warrants innovative research tools to fully understand the pathogenesis and host immune responses, particularly at the site of infection and disease. In this regard, bronchoscopies with bronchoalveolar lavage (BAL) serve as a valuable technique for site of disease sample retrieval for further clinical- and basic research. Here we investigate the feasibility of research bronchoscopies in a low/middle-income area, where TB remains rife, and assess the value of retrieved BAL cells (BALC) for downstream fluorescent-based cellular evaluations. Methods Using quantitative and qualitative methods, we evaluate the outcomes, safety, tolerability, participant -perception and -experience, while also providing insight into participant recruitment and screening processes of our study. Using light microscopy differential counting for BALC analysis, we evaluate the cellular composition of BAL fluid (BALF) from TB patients, healthy community controls and patients with other lung diseases. We also use flow cytometry to describe the challenges associated with fluorescence-based phenotypic analysis of autofluorescent BALC. Results Our findings suggest that research bronchoscopies are safe, acceptable procedures for research participants and are indeed a feasible technique for future study design. We also suggest that the majority of participants are receptive to the proposition of a second research bronchoscopy. This poses an important avenue for research entailing follow-up investigations of the same study participant. Furthermore, our results show that smoking is characterized by retrieval of BALC containing particulate matter, that interferes with fluorescence-based flow cytometry data analysis. Based on light microscopy differential cell counting, our findings suggest that there are differences in the cell yields and cellular composition of the BALF between TB patients, healthy community controls and patients with other lung diseases. We also report on subject characteristics and demographic factors, namely gender and age, that have the potential to affect cell yields and cellular data of BALF. Conclusions These findings will serve as a valuable reference for appropriate planning and design of studies involving clinical bronchoscopies for TB and lung disease research.

Background Natural immunity against Mycobacterium tuberculosis exists, and > 90% of those infected remain disease-free. Innate and adaptive immune responses required to mediate such protection against tuberculosis (TB) are, however, poorly understood. Methods This is an analytical study exploring protective and non-protective pathways of immunity against Mycobacterium tuberculosis . Adults without HIV infection are recruited at community healthcare clinics in high TB incidence areas of the Western Cape Province, South Africa. Data regarding participants’ medical, social and medication usage will be collected, and clinical examinations and point-of-care tests documented. Reference tests for TB (chest radiographs and sputum tests for GeneXpert MTB/RIF Ultra®, Auramine smear and liquid cultures) and investigations to classify infection states [interferon-gamma release assay (IGRA) and SARS-CoV-2 polymerase chain reaction (PCR) nasopharyngeal swab and IgG], are done on all participants who meet the inclusion criteria. 18F-Fluorodeoxyglucose positron emission tomography combined with computerized tomography will be done on all close contacts (contacts) and healthy control (controls) participants. Participants are divided into 12 study groups representing a spectrum of TB clinical phenotypes and prior SARS-CoV-2 infection based on their TB status, exposure history, results of IGRA test at baseline and 3 months, SARS-CoV-2 serology, and PCR results, and for contacts and controls, PET-CT imaging findings indicative of sub-clinical TB lesions. Samples for experimental assays include whole blood for isolation of peripheral blood mononuclear cells and blood in PAXgene® tubes for RNA isolation. All SARS-CoV-2 PCR negative study participants undergo bronchoscopy for collecting bronchoalveolar lavage samples. Discussion The paired blood and BAL samples will be used for comprehensive analyses of the tissue-specific and systemic immunity that will include e.g., cytometry by time-of-flight analyses, RNA-sequencing, multiplex immunoassays, epigenetic analysis, and mechanistic studies of control of infection by Mycobacterium tuberculosis . Results will be integrated with those from mice and non-human primate studies to provide a comprehensive analysis of protective pathways in natural and vaccine-induced immunity against Mycobacterium tuberculosis .