Dissecting the effect of single- and co- infection of TB and COVID-19 pathogens on the sputum microbiome

Tuberculosis (TB) and COVID-19 are both respiratory diseases and understanding their interaction is important for effective co-infection management. Although some studies have investigated TB and COVID-19 co-infection in terms of immune responses, microbial dysbiosis in such cases remains unexplored. In this study, we understand the interface between TB and COVID-19 by systematically inspecting the microbial composition of sputum samples collected from four groups of individuals: TB only, COVID-19 only, and both TB and COVID-19 (TBCOVID) infected patients, and uninfected group (Controls). Besides metagenomic analysis of the microbiome of these sputum samples, we also performed whole genome sequencing analysis of a subset of TB-positive samples. Different bioinformatic analyses ensured data quality and revealed significant differences in the microbial composition between Control vs. disease groups. To understand the effect of COVID-19 on TB, we compared TBCOVID vs. TB samples and observed (i) higher read counts of TB-causing bacteria in the TBCOVID group, and (ii) differential abundance of several taxa such as Capnocytophaga gingivalis, Escherichia coli, Prevotella melaninogenica and Veillonella parvula. Functional profiling with PICRUSt2 revealed significantly elevated pathways in the TBCOVID group relative to TB group, some of which are related to metabolism of pulmonary surfactant lipids (e.g., Cytidine diphosphate diacylglycerol (CDP-DAG) biosynthesis pathway with fold change of 7.46). Further clustering of these significantly elevated pathways revealed a sub-cluster of individuals with adverse treatment outcomes. Two individuals in this sub-cluster showed prevalence of respiratory pathogens like Stenotrophomonas maltophilia - knowing such information can help personalize the antibiotic treatment to match the pathogen profile of the individual. Overall, our study reveals the effect of COVID-19 in the airway microbiome of TB patients, and encourages the use of co-microbial/co-pathogen profiling to personalize TB treatment. Author summaryThe community of microbes in an individuals airway tract can play a complex role in respiratory diseases like TB and COVID-19. Although changes in microbial composition in TB and COVID-19 patients have been studied separately, we present a first-of-its-kind investigation of the airway tract microbiome of individuals simultaneously infected with TB and COVID-19 pathogens. Our results highlight that co-infection with COVID-19 in TB patients alters the abundance of certain bacterial species and their related pathways. For instance, Capnocytophaga gingivalis is abundant in co-infected patients, but not present in the TB-only patient group. This species and other differentially abundant species that we identified in the co-morbid condition, if replicated in independent cohorts, can help explain how COVID-19 could exacerbate the severity of lung infection in TB patients. Our study also stimulates future longitudinal studies using expanded datasets to understand the role of concomitant pathogens, and assess whether adjusting the antibiotic regimen accordingly can improve TB treatment outcomes.