MTI-plus project develops Microbial Variance Tracker

Dr David Kateete, a molecular biologist and EDCTP Career Development fellow from Uganda, has developed clinical metagenomic tools with Dr Adrian Muwonge, a collaborator in the United Kingdom. These tools will be used to analyse the bioinformatics data generated by the MTI-plus project: Microbial variance tracker which allows rapid examination and comparison of samples by their structural variability as well as a tool that would allow quick viewing of shotgun sequencing data.

To test the analytical pipelines, the team conducted a pilot study in which they sequenced sputum samples from 120 treatment-naïve TB patients in Uganda, and investigated changes in microbiota of 30 patients with treatment-response follow-up samples on months 2 and 5. Using these tools, they found that HIV-status and anti-TB treatment were associated with microbial structural and abundance changes. The microbiota core comprised of 44 genera that were stable during treatment. Hierarchical clustering of this core’s abundance distinctly separated baseline (month 0) samples from treatment follow-up samples (months 2/5). Overall, contrary to findings from Asia and/or the developed countries where similar studies have been conducted, this pilot study shows that in a TB-endemic setting with prevalent HIV infection, sputum microbiota parameters of treatment-naïve TB patients map to patient characteristics regarding clinic visits, HIV and nutritional status. Results of the pilot study were published and the developed tools are being used in the analysis of sequence data generated by the project.