Background. Diagnostics for tuberculosis (TB) and treatment monitoring remains a challenge, particularly in less-resourced laboratories. Further, the comprehensive sputum microbiota of TB patients during treatment are less described, particularly using long-read sequencers.
Methods. DNA from sputum samples collected from newly-diagnosed TB patients were sequenced with Oxford Nanopores MinION. MG-RAST and R packages (Phyloseq, Microbiome) were used to determine the OTUs abundances, alpha or beta diversities, functional components, OTUs networks and ordination plots. Statistical significance of the generated data were determined using GraphPad.
Results & conclusion. Antibiotics reduced the abundance and functional subsystems of each samples microbiota from baseline until day 7, when persistent, tolerant, and resistant microbiota, including fungi, grew back again. Variations in microbiota abundance and diversity were patient-specific. Closer microbiome network relationships observed in baseline samples reduced until day 7, when it became closer again. Bacterial microbiota networks and spatial ordination relationships were closer than that of other kingdoms. Actinobacteria phylum and Mycobacterium were more affected by antibiotics than other phyla and genera. Parasites, viruses, and fungi were less affected by antibiotics than bacteria in a descending order. Resistance genes/mechanisms to important antibiotics, plasmids, transposons, insertion sequences, integrative conjugative elements were identified in few samples.
MinION can be adopted clinically to monitor treatment and consequent dysbiosis, and identify both known and unknown pathogens and resistance genes to inform tailored treatment choices, specifically in TB.