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

Antibiotic resistance: how can genomics research solve this prressing 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.

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