Background: The microbiome likely plays a role in tuberculosis (TB) pathogenesis. We evaluated the site-of-disease microbiome and predicted metagenome in people with presumptive tuberculous pericarditis, a major cause of mortality, and explored for the first time, the interaction between its association with C-reactive protein (CRP), a potential diagnostic biomarker and the site-of-disease microbiome in extrapulmonary TB. Methods: People with effusions requiring diagnostic pericardiocentesis (n=139) provided background sampling controls and pericardial fluid (PF) for 16S rRNA gene sequencing analysed using QIIME2 and PICRUSt2. Blood was collected to measure CRP. Results: PF from people with definite (dTB, n=91), probable (pTB, n=25), and non- (nTB, n=23) tuberculous pericarditis differed in β-diversity. dTBs were, vs. nTBs, Mycobacterium-, Lacticigenium-, and Kocuria-enriched. Within dTBs, HIV-positives were Mycobacterium-, Bifidobacterium-, Methylobacterium-, and Leptothrix-enriched vs. HIV-negatives and HIV-positive dTBs on ART were Mycobacterium- and Bifidobacterium-depleted vs. those not on ART. Compared to nTBs, dTBs exhibited short-chain fatty acid (SCFA) and mycobacterial metabolism microbial pathway enrichment. People with additional non-pericardial involvement had differentially PF taxa (e.g., Mycobacterium-enrichment and Streptococcus-depletion associated with pulmonary infiltrates). Mycobacterium reads were in 34% (31/91), 8% (2/25) and 17% (4/23) of dTBs, pTBs, and nTBs, respectively. β-diversity differed between patients with CRP above vs. below the median value (Pseudomonas-depleted). There was no correlation between enriched taxa in dTBs and CRP. Conclusions: PF is compositionally distinct based on TB status, HIV (and ART) status and dTBs are enriched in SCFA-associated taxa. The clinical significance of these findings, including mycobacterial reads in nTBs and pTBs, requires evaluation.

The authors have declared no competing interest.

This work and authors were supported by the European & Developing Countries Clinical Trials Partnership (EDCTP; project numbers SF1041, TMA2019CDF-2738-ESKAPE-TB), National Research Foundation, South African Medical Research Council (SAMRC), Harry Crossley Foundation and Stellenbosch University Faculty of Health Sciences. We also acknowledge funding from Veterans Affairs (IK2BX005309-01A2) and the National Institutes of Health under award number KL2TR001446, and CHEST Foundation Research Grant in Chronic Obstructive Pulmonary Disease. CCN and GT acknowledge funding from the National Institutes of Health under award numbers K43TW012302 and R01AI136894. GRN acknowledges funding from L'Oreal-UNESCO For Women in Science Sub-Saharan Africa Young Talents Award, and the International Rising Talents Award. The content is the solely the responsibility of the authors and does not necessarily represent the official views of the funders.

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