How a pathogen and genomics system is becoming a resource for the future
17 April 2023
A new genomics analysis system is allowing RISE to assess pathogens, and how they spread in the environment, in the quest to make informal settlements safer, healthier places to live.
Researchers at Micromon Genomics, Monash University’s specialist facility in advanced DNA and RNA technologies, have just generated DNA sequences from a range of different human and environmental samples from informal settlements. Gene sequencing is considered one of the most accurate tools to diagnose infections.
Scott Coutts who manages the facility in Melbourne, says it works by decoding a pathogen’s genetic material to read the identity of a cell. ‘We can use this information to work out which cells are microbes that might cause illness,’ he says.
‘We can also examine which microbes come and go with time or location – and that may, for example, correlate with other observations, such as flooding, or disease burden in the local area’.
Jacob Amy at Micromon operates the DNBSEQ-G400RS which supports DNA sequencing and data analysis for RISE.
Getting to this point of being able to analyse illness-causing microbes has taken time. Over the last few years RISE has steadily been building a robust genomics analysis system: this system relies on a chain of people with different skill sets, and collaboration from different locations around the world. And it starts in informal settlements.
Since the start of RISE back in 2018, community fieldworkers have been routinely collecting an array of samples from RISE’s participating informal settlements in Fiji and Indonesia – from soil and water samples, to human faeces, bloods and more. Much work has since gone into training Fijian and Indonesian laboratory technicians to analyse these samples using cutting-edge genomic methods.
Vinaina Waqa is one of these technicians who has been trained. Based at RISE Fiji’s lab at Fiji National University (FNU), Waqa is now skilled in DNA extraction (isolating DNA from the cells on an organism) and quantification (determining the average concentration of pathogens in an extracted sample).
‘This is the first time I’ve done it [extraction and quantification],’ she says. ‘It’s been very interesting to see the different types of organisms that are in the settlements: we are finding different kinds of helminth DNA, especially in child faeces. And we have also found leptospirosis, I’ve never seen that before.’
Hookworm (centre) in child faeces from an informal settlement, identified in Fiji.
Beyond seeing novel pathogens for the first time, the prospect of taking genomics beyond RISE to benefit Fiji more widely excites Waqa. ‘I’m excited to see where this could lead. It’s been great capacity building for me, and I would love to teach my friends at other hospitals in Fiji.
‘It would be much easier and quicker for my colleagues to diagnose patients with whatever bacterial viruses or pathogens that cause disease and illness, using the new analysis systems we have on RISE,’ she says.
Vinaina Waqa (right) performs DNA extraction at the RISE lab using a biohazard cabinet under strict sterile techniques.
There have been many Zoom sessions between the Fiji lab team and Dr Dieter Bulach. As a microbiology and bioinformatics specialist, Bulach’s work establishing protocols for storing and providing ongoing access to data has shaped RISE’s genomics analysis system.
In his many years of experience, Bulach believes the system RISE has created is unique in its ability to effectively deal with large, complex data sets.
‘The huge feat has been overcoming the barrier of bringing diverse data together in one secure place,’ Bulach explains. ‘In most cases, you have human health data collected, then separate water data, soil data, and so on. It can be very difficult to access such siloed information.
‘We have created an environment where we can bring all of our diverse data sets together into one secure place, where scientists from different disciplines can access and analyse it. It’s really a model environment for analysis of diverse data.’
At the heart of this genomics work is a belief held by all the different people who shape it, that this system has benefits far beyond RISE: for people living in informal settlements to lead healthier lives; for scientists studying these environments to have flexible access to data; and for policy makers to have the evidence that can underpin sustainable urban development strategies.
For Coutts, the learnings from such a large-scale research endeavour can be rolled directly back into the facility in Melbourne, ‘allowing us to distribute these benefits across more projects’ thanks to Micromon’s not-for-profit model.
Bulach sees RISE’s data as a powerful resource for the future. ‘This data is stored and organised in a way that it can be re-used by us and others researching informal settlements – the data is findable, accessible, interoperable and reusable – embodying the principles of ‘FAIR data’.
Waqa is the oldest of an extensive group of cousins. For her, the work is personal.
‘This work is special to me because of RISE’s focus on children under five. Children at that age don’t have the antibodies to fight off infection. So, through taking bloods and faeces, it’s a good way to help them and their families know about their health status and prevent future infection. I guess that’s where it comes from for me.’