Bacteria that cause disease are increasingly resistant to antibiotics used to treat infections. This resistance is a major global public health challenge. Tracking the changes in genetics of bacteria is important for monitoring antimicrobial resistance along with providing insight into their bacterial biology.
The Langridge group here at the Quadram Institute work on a range of disease-causing bacteria including two of the leading causes of food poisoning Salmonella and Campylobacter.
“We’re trying to find out in more depth which antimicrobial resistance genes are there and if someone has Salmonella, are the bacteria all the same or is it a mixed group?
Answering these sorts of questions wouldn’t immediately change clinical outcomes, but it gives us more information to work with in a clinical setting”, explains group leader Dr Gemma Langridge.
Currently the group grow the bacteria from a sample on a petri dish, extract the DNA and then sequence this DNA to look at the genetics of the bacteria. However, previous methods to extract DNA resulted in small fragments that were difficult to piece together, so it was tricky to get a confident overall picture of the genome of a bacterium.
Quadram Institute partnered with UK-based genomics company RevoluGen to solve this issue. Its innovative technology is enabling the group to overcome these challenges and reveal the bacterial diversity behind clinical infections and increase the volume of microbes they can study.
“I first heard about RevoluGen’s Fire Monkey HMW-DNA spin column extraction kit about five years ago. This kit allows the DNA to be extracted in longer fragments, with a higher molecular weight in a relatively quick and easy process.”, says Gemma.
“Before, if we wanted to get high molecular weight DNA, we could use other kits, but it took a long time”.
Extracting the longer fragments of DNA involves a balance between breaking open cells and not destroying the DNA inside. The Fire Monkey kit’s ability to achieve this has enabled the team to generate long sequence reads and confidently piece together the fragments to study changes in bacterial genomes.
Steven Rudder, a PhD student in the Langridge group, explains, “Before, the fragments would be about 300 base pairs long. Now they’re 10,000s of bases, even up to over 100,000. It’s like having a jigsaw puzzle. Before we had lots of tiny pieces to put together, now we have big pieces that are easier to fit together”.
Steven’s PhD project is focused on the next step of scaling up and speeding up the process. Steven brings expertise from previously working in the sequencing team at Quadram Institute. The project is an iCASE studentship with RevoluGen focusing on using a robot to carry out the Fire Monkey DNA extraction process so the team can process samples more quickly.
“RevoluGen’s automated workflow is a real improvement. Previously, we’d extract DNA from each sample individually using tubes. The robot uses positive air pressure to push the sample through a filtration column in a multi-well plate format”, describes Gemma.
Steven continues, “We are pleased to be RevoluGen’s first installation of its benchtop automated process. There is always a learning curve with a new installation, so I’m troubleshooting using the robot. I’ve gone from 24 samples in one day being quite painful to now doing 96 in a morning and feeling like you’re flying through samples.
The robot has really helped us save lots of time and people’s minds from constantly pipetting into tubes. The results are a lot more uniform, as it removes some of the variability you get from human error in pipetting.”
Dr Georgios Patsos, Chief Scientific Officer of RevoluGen and inventor of the Fire Monkey technology adds, “It’s fantastic to see our technology transferred to a leading Institute such as the Quadram Institute and within months see the results they are achieving. Getting DNA out of cells is the first step in any DNA sequencing and it’s surprising that automation of such a critical step hasn’t seen more innovation. I am proud to have solved that problem and to be working with world-leading researchers to demonstrate its potential value to science and human health.”
All the samples processed by the robot have come from the Norfolk and Norwich University Hospital (NNUH) as Steven explains, “The first set were E. coli from Urinary Tract Infections and since then we’ve run Salmonella from stool samples. We’re planning to put Campylobacter through the process as well.”
Gemma highlights the potential of using the robot and extractions for other applications, in collaborations and beyond their group, “In our group we collaborate with the UK Health Security Agency. We’re keen to bring some of their sample collections through this high throughput processing. The idea of the robot being here is that it’s a piece of equipment the whole of the Quadram Institute can access so others can apply it to their research areas too.
We are one group among others working on this type of genome analysis at the Quadram Institute and there is expertise across the Norwich Research Park, such as at the Earlham Institute. We are in the right place to analyse the data and see in more detail the diversity of dangerous microbes”.