The Research Group for Genomic Epidemiology holds Monday morning scientific presentations. The following was presented on 21 March 2022:
Testing protocols at sequencing sites and the feasibility of field sequencing at remote sites
Danida has recently funded a project in Tanzania, which will enable sequencing and surveillance of clinically relevant microbes found in Tanzania by six National Institute for Medical Research (NIMR) (https://www.nimr.or.tz/) sites scattered across the country.
Part of this project includes setting up the basic sequencing facilities, as these are non-existing in most parts of Tanzania. To test the feasibility of this setup we planned a field trip to Tanzania, where we would visit two of the NIMR sites, test the sequencing protocol at the sites and test the feasibility of field sequencing at remote sites.
To cover more ground, we decided to split up into two groups. Group 1 (see slide 10) successfully performed onsite sequencing and analysis of a water sample from Lake Victoria (see slides 22-28), from a spot located in a small Sukuma village without clean water supplies nor power lines (see slide 18). This meant that the lake water was used for various purposes, as this was the only reliable water source in the area (see slide 20).
After a successful field-sequencing test, we went to the NIMR center in Mwanza to engage them in the project and possibly test the protocols there. To our great pleasure, they had already collected samples of clinical interest, and performed DNA isolation of one culture negative vaginal swab from an expected Gonorrhea case. After DNA preparation, sequencing and bioinformatic analysis it was clarified that the infection was caused by Chlamydia trachomatis, with an otherwise normal vaginal microbiome. Additional analysis revealed no transferable antimicrobial resistance of the C. trachomatis strain, which meant that the treatment could be effectively changed to target C. trachomatis with a successful result.
With two successful tests, we continued to the NIMR center in Tabora, where we would meet up with the other group. Here the NIMR center had samples from a putative meningitis outbreak (16 samples, with one culture positive for Streptococcus pneumoniae), which became the subject for the final sequencing of the trip. Unfortunately, we were out of AMPure beads, which meant that we could not amplify or purify the DNA samples efficiently. As a result, we had to pool all 16 samples together in hope of identifying some meningitis causative microbes, with low chances of success. Generally, these kinds of samples contain mostly human DNA, which were even worse for these samples due to the lack of AMPure beads. However, we were able to identify S. pneumoniae as well as Neisseria sicca, which are both known agents causing meningitis in Tanzania.
Philip Thomas Lanken Conradsen Clausen's presentation