Antibiotic resistance: how can genomics research solve this pressing 21st Century problem?

Steven: Antibiotic resistance is a major threat to human health and also animal health. The research we do at i3 and with our collaborative partner New South Wales Department of Primary Industries takes a one-health approach to the study of antibiotic resistance.

The problems that we are working on here in Australia are global problems. They are problems, which affect animal production systems and food production systems globally.

So our research takes into the relationships through the food chain whereby food productions systems impact on human health but also in the way we produce animals for food production systems and the way that antibiotics get removed from their bodies and partially metabolise and in unmetabolised states and those antibiotics then get released into the environment and drive the antibiotic resistance in complex microbial and soil populations and aquatic environments.

AUSGEM is an acronym which stands for the Australian Centre for Genomic Epidemiological Microbiology and it's a collaboration between the NSW Department of Primary Industries and the i3 Institute.

So the partnership is really a very good one because it brings together the technological capabilities of i3 including access to cutting edge microscopy and in particularly super-resolution microscopy.

Our biothematics capabilities through the recruitment of key people from overseas has been able to build these pipelines which allows us to handle big data.

Our proteomics capabilities, which allows us to identify new vaxing targets. And the capabilities of the New South Wales Department of Primary Industries which is predominantly their vast collections of microbial populations which they have gathered over many years. It is these populations of bacteria which we want to mine using these technologies to help us to identify the types of bacteria that are so flounding in our food production systems and also our plant pathogens that affects plant health.

Over the last few years the cost of sequencing bacterial or microbial genome has come down enormously. So what we have been able to do now is to sequence a larger number of microbial genomes and we have been able to put these into databases. Now we are generating vast data sets, which require new ways to handle big data.

So the relationships that I have developed here at UTS and the i3 Institute involves experts that have the capacity to deal with big data sets with computational pipelines, to handle all that genomic sequence so that biologists such as myself can access the information we need to get a better handle on how antibiotic resistance is evolving and moving through microbial populations.

What we envisage is that in the next five to 10 years we will be able to sequence microbial genomes at the patient’s bedside. What that means is that a doctor can look at the information that is provided to them which indicates what antibiotic resistance genes are present in that pathogen that is causing this disease in this patient that is really ill and give the appropriate antibiotic regime to control that infectious disease.

The research environment that we have been fostering in the i3 Institute is really starting to pay a lot of dividends now because we have these excellent teams of people that are all working closely with one another.

Within i3 now, we are looking towards developing our international collaborations on a much greater scale. And already we have PhD students and collaborative interactions occurring. People spend considerable amounts of time in our laboratories to learn the developments that we have produced here within the i3 Institute.