In 2024, JIDCuk supported the establishment of an Oxford Nanopore Technologies MinION sequencing facility at the National Animal Health Research Center (NAHRC) in Lalitpur, Nepal. As part of this project, I had the privilege of receiving funding to travel out to the region, alongside 2 colleagues, to conduct comprehensive in person training on both the theoretical foundations of sequencing and to deliver practical hands-on sessions for the techniques involved. This once in a lifetime opportunity equipped local scientists to develop their understanding and undertake their own DNA sequencing endeavours independently – facilitating the investigation of pathogens effecting their local animal populations and the study of antimicrobial resistance profiles associated with their region.
At NAHRC, we were welcomed by a great number of enthusiastic scientists and had the opportunity to tour their vibrant working environment, including the laboratory facilities that were so different from our own. In total, 5 talented scientists joined us for the entire 5-day course, with a further 4 dropping in for a number of the sessions. Our training commenced with in-depth discussions regarding what local scientists hoped to gain from the course, allowing us to shape its contents to be as useful for them as possible. Knowledge exchange began with emphasising the importance of sample preparation prior to sequencing, to ensure optimal efficiency. We explored the capacity of MinION flow cells, and how to calculate the number of samples and amount of DNA which could be utilised per run across a variety of different scenarios. Furthermore, DNA extracted by the local scientists from >50 samples was quantified using a Qubit, paving the way for subsequent stages of the course.
The following day, local scientists conducted high-molecular weight DNA extraction using the Revolugen Firemonkey kit, and were taught the tips and tricks used by myself and colleagues in our lab to ensure optimal yield was achieved. These samples were quantified, and used to supplement those already obtained prior to our arrival, to ensure sufficient DNA was available for a sequencing run. Post-quantification, we worked on calculating the volumes needed from each sample to obtain the precise volumes needed for concentration in our next step, and also shared how issues at this stage could be overcome utilising the scientists understanding and informed logical thinking.
Using those calculations, we then worked on purifying and concentrating the local samples into more suitable volumes for downstream use, using AMPure beads. The principals behind this process and rationale for its use were explained before moving into the lab and getting hands-on. Unfortunately, we encountered an unexpected challenge at this point in the course. Due to shipping and customs issues, a number of essential reagents we not going to arrive before the end of the course. While unfortunate, we worked around this set back and adapted- re-designing the parts of the course to deepen the local scientists theoretical understanding while thoroughly overviewing the techniques that could not be carried out hands-on to ensure they were fully prepared to carry out the processes once the materials arrived.
We delved deeper into the core mechanics and underlying theory of Nanopore technology and indeed sequencing itself, and discussed in detail for purpose of each reagent used at every step of the protocol. Although the local library could not be fully prepared, participants on the course had the opportunity to practice loading MinION flow cells that we had bought over with us, with no consequences if anything was to go wrong. I believe this part of the training was invaluable, as I consider the loading of flow cells to be the most tricky and nerve wracking part of the entire sequencing process, thus the scientists feeling confident with this crucial step was highly important. I believe that throughout the course, the fact that I am a student allowed me to relate and better understand some of the issues encountered by the local scientists who were earlier in their careers. I was able to understand the problems they regularly encountered in the laboratory on a day-to-day basis thanks to being at similar points in our scientific progression and believe this opened the doors to many in depth discussions that enhanced both their and my own understanding of the science and the scientific industry as a whole.
Our final day focussed on how to check the viability of flow cells upon their arrival, and how to perform pre-sequence checks. Participants were then guided on how to initiate a run once the DNA library was loaded, what to expect over the course of the experiment and how to troubleshoot any issues they may encounter. Finally, using data from experiments previously run in our lab, we delved into the kinds of bioinformatic analyses available on user-friendly platforms such as Epi2Me and Galaxy. The local scientists were able to attempt downstream data analysis themselves using our data, and we explored the types of programmes and tools they may want to use based on the specific goals of their work. The culmination of this course therefore equipped the Nepalese scientists to carry out sequencing and bioinformatic analyses on both bacterial and viral samples from a range of hosts – and most importantly ensured that they also understood all the concepts and theory behind the actual work being carried out.
This training course could not have been carried out without the generous funding from JIDCuk. In addition to enabling me to provide face-to-face training at NAHRC, they also provided all the essential equipment for the local scientists, including a MinION starter kit and laptop appropriate for the computational strain of sequencing.
JIDCuk funding has significantly advanced the sequencing technologies accessible to scientists in Nepal, who can now prioritise their work to directly address local challenges and continue to build local sequencing infrastructure.
This support has empowered local scientists to empower the research and has greatly bolstered in-country expertise in a critical area of microbiology- ensuring modern, cutting-edge science can flourish where it is needed most.
Looking to the future, the local scientists at NAHRC are now fully equipped to carry out their own sequencing projects and can continue to rely on us for any support they may require. I cannot express my gratitude to JIDCuk for granting me this incredible opportunity. Not only has this experience opened my eyes to the true breadth of science being undertaken around the world, but is has allowed me to improve my teaching and knowledge mobilisation/exchange skills and has even enhanced my own understanding of DNA sequencing.
This experience has without doubt helped shape me into a better scientist, and I truly believe it has made a substantial difference in closing the gap between science in lower-middle income and higher income countries, thus shaping the entirety of modern science for the better.
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