Supporting the first nanopore sequencing in Fiji

In August 2023, Professor John Wain and I gave four days of training in Fiji on DNA sequencing, which enabled Fijian scientists and staff to identify the microbe responsible for an outbreak in a neonatal unit of a hospital. This was part of a collaboration between JIDCuk, the Quadram Insitute and Fiji National University (FNU). 

Scientists from Fiji and the JIDCuk charitable trust standing outside a containment laboratory at Fiji National University for a group photo.

Our trip developed a previous collaboration between Dr Gemma Langridge’s lab group at the Quadram Institute, project manager Timoci Naivalulevu and FNU. Previous interactions included work we have done giving training remotely through online videos and sharing methods of how we sequence DNA. 

The week before we arrived in Fiji, FNU had opened a new containment lab built for virology. The lab is made of two shipping containers and has a collection window for people to hand in samples. Inside the containment lab, there is state of the art equipment including Oxford Nanopore’s MinION which allows rapid sequencing of samples. 

John and I went to the lab in Suva, Fiji to share our knowledge of sequencing the DNA of viruses and microbes using MinION. Our training course covered all steps including preparation of extracted DNA for library prep, laptop and MinION set up, sequencing, basecalling and standard data analysis. 

Dr Emma Waters leading discussions with Fijian scientists on a covered area outside the containment laboratory.

The people we were training came from a variety of backgrounds. There was a masters student, a nurse, a lecturer from the university and staff running the new containment lab. There was also an ecologist interested in soil microbiomes and viruses. Some people were interested in bacteria, some people were looking more at metagenomics, while some were planning to sequence viruses - it was a real mix! The good thing about sequencing using nanopore sequencing is that you can use it for sequencing different organisms. But for each organism, there are slightly different methods that are used. 

Our expertise in the Langridge group is on sequencing bacteria, so we initially developed the training using protocols for bacteria. We were flexible with our training, and we highlighted other protocols that could be used on other types of samples at each step. Towards the end of the training, we covered data analysis. Depending on what your sample is, your data analysis could be very different. We suggested ideas of the different ways you could use the data whether putting it into a pathogen identification tool or looking for antimicrobial resistance genes. 

One of the aspects of the training that I enjoyed most was adapting the course as it progressed, to each of the people taking part and their different areas of interest. I enjoyed visiting Fiji as a country too. It’s the first time I’ve ever been to the southern hemisphere and to the other side of the world. It took us three days of travelling to get there. The scenery of tropical forest and endless ocean was stunning - though negative impacts of the colonial period on Fijian communities were apparent in places. 

Rural view from the laboratory buildings depicting palm trees and single story buildings.

While we were in Fiji, there was an outbreak in the neonatal department of the local hospital. The scientists and staff we trained used their new skills to perform the first outbreak sequencing in Fiji. They found that the outbreak was caused by the bacteria Acinetobacter baumannii and that it was resistant to the antibiotic carbapenem. Often short-read sequencing is used which is very good at showing you small changes in DNA called single nucleotide polymorphisms (SNPs), which can be important for monitoring resistance or changes in pathogenicity. In this case, the Fijian researchers used long-read sequencing which gives even more information and allows you to see genome rearrangements. 

Fijian scientists getting hands on training with nanopore sequencing.

Understanding genome rearrangements is something we study in the Langridge lab group at the Quadram Institute. We know that these rearrangements can make a microbe go into a kind of dormant stage, so it won’t necessarily show up as an active infection, but it could be lying dormant and still be infecting others. 

The week after we left, our Fijian colleagues adapted one of the protocols we used on the training course to do long-read sequencing of these outbreak isolates. They sequenced the two outbreak samples from the hospital, and a couple of Salmonella Typhi and Escherichia coli samples so they could compare them. They got complete genome assemblies, which was amazing for a first sequencing run.  

Gaining experience loading flowcells was a key part of the training delivered.

Within two weeks those we trained went from having the equipment, to using it, to responding to a public health situation independently. 

The trip was only possible thanks to funding from the JIDCuk Charitable Trust which supports scientific research and scientists in developing countries through funding training courses and postgraduate projects for students registered at institutions in developing countries. 

https://quadram.ac.uk/blogs/supporting-the-first-nanopore-sequencing-in-fiji/