From 5th to 30th September 2022, Martha Chipinduro (medical laboratory scientist, ERASE-TB laboratory intern and Stellenbosch PhD student) visited the Research Centre Borstel, Germany, the result of her being awarded the one month short-term Monteillet- MusioIik (Musiolik) Fellowship to train in conventional and sequencing methods for diagnosis and surveillance of Mycobacterium tuberculosis.
Below, Martha describes in her own words what she learnt as well as some of the highlights of her stay:
"At the beginning of September 2022, three flights from home (Zimbabwe), I was standing at the entrance of the famous Research Centre Borstel, a mixture of excitement, eagerness and nervousness. I was going to be learning from some outstanding tuberculosis (TB) researchers, including Prof Stefan Niemann and Prof Christoph Lange. These are researchers I had only “met” on published manuscripts! I was one of two Musiolik fellows, the other awardee was from Pakistan. We begun with a tour of the facilities. The institute is set in a picturesque landscape boasting of a park and lake. It is a hub of diverse TB research activities by a diverse group of researchers including Masters, PhD and Doctoral students. The TB research activities vary from diagnostic research, clinical research to molecular epidemiology surveillance. Some research is based on biophysics and some used animal models.
Our fellowship was divided into four blocks, each week focusing on different activities. We spent the first week in the Mycobacteria reference laboratory. The laboratory receives specimens from all over the country for diagnosis and drug resistance profiling. We were shown how the samples are received, decontaminated and cultured. Of particular interest was the use of the Hain’s line probe assay and targeted sequencing using the Deeplex assay for the detection of drug resistant mutations. Soenke and Doris were very knowledgeable and patient tutors as they taught us how to interpret the mutations in line with the new World Health Organization drug resistance mutations catalogue released this year. I really enjoyed these interpretative sessions. Also it was great to see that these results had impact on patient management.
Our second week was spent in the sequencing laboratory, joined by another colleague from South Africa. We learnt about the different sequencing platforms, their advantages, limitations and considerations for setting up in a molecular laboratory. The sequencing laboratory is host to the Illumina sequencing platforms, from the Miseq to the Nextseq sequencers. We were provided with samples to process for targeted sequencing. As each one of us had brought samples from our respective countries, we also processed a few of these for whole genome sequencing. This was a week of firsts for me. First time processing samples for sequencing, from checking quality using the Qubit to making the polymerase chain reaction mix, to library preparation and finally pooling of the libraries for a multiplex run. Oh, you really needed a grip on the pipette! The historic first moment was pressing the start button on the Nextseq sequencer! It was a pleasurable learning time in the lab and with the help of Tanja and Vanessa, we looked and felt like experts.
Just thinking about the third week was daunting. It was a week of analysing our sequences – Bioinformatics! Again we were joined by two colleagues from Kyrgyzstan. Bringing some comfort in numbers. I need not have worried so much. Christian, Viola and Ivan took us through the concepts in such an amazing way that definitely a lot of skills were imparted to us. The quality indicators for our sequences were quite good, all thanks to Tanja and Vanessa overseeing our library preparations. We managed to identify mycobacteria lineages and drug resistance profiles for our targeted sequences. We were also able to construct phylogenetic trees using different tree building online soft wares. I was thrilled to see my tree. All my training and learning culminated in this tree.
Interspersed within our laboratory trainings, were personal lectures from Prof Christoph Lange. These were focused on TB history and TB implementation research. It was a privilege to receive these lectures and I am grateful for the time given to us. We were also invited to clinical case presentation which helped us relate laboratory findings to different clinical presentations.
Recognising that all work and no play is not ideal, the Research Centre Borstel team kindly organised outings for us on Saturdays. We went to see the harbour city of Hamburg and rode on the ferry. We visited Lübeck, an old city which served as the trading gateway into Europe. Here, I had my first marzipan cake. We visited Kiel, a port city on the Baltic sea coast. In Kiel, we had dinner with the funders for the Musiolik fellowship.
It was a great and humbling opportunity. Many thanks to the people who took us to Hamburg, Lübeck and Kiel; Inna and Martin, Prof Stefan Niemann and Tanja, and Prof Christoph Lange, respectively.
The first two days of our last week was spent overviewing of our training. On the last Wednesday, we departed for Romania. Christoph Lange’s team were gracious to invite us, the Musiolik fellows, to a conference in Romania which they had organised on TB and migration in Europe. It was the icing on the cake! It was really interesting to see from the evidence presented that TB is a disease that does not respect boundaries, affecting anyone, anywhere and so calls for collective efforts.
It was indeed a great opportunity to be part of the Musiolik fellowship. I learnt the best from the best in the field. I hope to be able to apply what I have learnt and impart the skills to others."