Anthony Fox was a young father of two with a career in the public service ahead of him when a stroke knocked him down.

Key points: Father-of-two Anthony Fox struggled to recover from a stroke after contracting a superbug during surgery

Father-of-two Anthony Fox struggled to recover from a stroke after contracting a superbug during surgery Researchers have identified four key infections and fungi that pose a threat to Australia

Researchers have identified four key infections and fungi that pose a threat to Australia Experts worried Australia doesn't have real-time monitoring of superbugs and have called for a focus on agriculture and waterways

But it was an antibiotic-resistant superbug that meant he would never again properly get back up.

"I was found lying on the floor at 5:00am in the morning," he said.

Mr Fox had developed a clot on his brain following a neck manipulation by a physiotherapist, officially known as a carotid artery dissection.

He was rushed to hospital and needed his skull opened to relieve the pressure on his brain.

But the worst was still to come.

"I was lying in the recovery bed and my mum came into visit and she noticed my head had swelled up to twice the size and my eyes were bulging," Mr Fox said.

"I was rushed into an operating theatre."

During his first surgery, Mr Fox had contracted methicillin-resistant Staphylococcus aureus (MRSA), commonly known as resistant golden staph.

The Adelaide man needed further surgery to get rid of the infection, and to remove part of his brain to reduce the swelling.

He spent the next month in hospital on drip antibiotics as his body fought both MRSA and tried to recover from the stroke.

But, he says the MRSA severely hampered his road back.

"It was absolute hell," he said.

"The staph infection stopped me doing a lot of the rehab activities, particularly not being able to go into the swimming pool to learn how to walk to again."

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'Black hole' in superbug surveillance

Researchers are worried about the rise of antibiotic-resistant superbugs. ( ABC News )

Health authorities would like to avoid experiences like Mr Fox's through better detecting and preventing antibiotic-resistant infections.

Writing in the Medical Journal of Australia, clinical microbiologist Deborah Williamson, from the Doherty Institute, and fellow infectious disease experts have argued there is a "black hole in surveillance" in antibiotic resistance in Australia.

The researchers named four key infections and fungi that pose the biggest threat to the health of Australians in the future.

In hospitals, the researchers have said a top concern is a group of bacteria that are resistant to carbapenems, a type of strong antibiotic.

The number of cases of these infections resistant to carbapenems in Australia has risen more than 14 per cent in one year, from 527 cases in 2017 to 603 in 2018.

Without treatment, about 40 per cent of patients die and many more suffer life-altering side effects.

The experts are also concerned by a yeast called candida auris that is resistant to several antifungals and has previously been brought into Australia from overseas.

In the community, microbiologists are worried about strains of gonorrhoea that are showing resistance to treatments and appear to have been transmitted via South-East Asia.

Travellers to and from places like Pakistan are also being warned about a drug-resistant type of typhoid thought to be acquired through E. coli bacteria.

"We know these are emerging overseas and they are really pathogens that are on our doorstep," Associate Professor Williamson said.

"If there are no options available … it's looking at a Darwinian struggle of survival of the fittest."

Deborah Williamson said authorities needed to be smart in how they tackled the bugs. ( Supplied )

Associate Professor Williamson said while there were some good patient surveillance systems in Australia, the country needed to take a more sophisticated approach.

"The bugs are pretty smart and we need to be equally smart in the way we respond to them."

Her suggestions included creating real-time monitoring systems that could identify the genetic make-up of certain strains and track their movement to prevent further spread.

The University of Melbourne academic was particularly concerned that some labs now tested for infections like gonorrhoea using techniques that resulted in only a positive or negative result.

As a result, patients could potentially be prescribed ineffective antibiotics and continue to spread the illness without knowing.

This was instead of generating a bacteria for culture that could indicate whether it was a strain that was resistant to antibiotics or not.

"That does create a black hole in resistance surveillance. That's a very real threat," she said.

For example, in Australia less than 30 per cent of all gonorrhoea tests were cultured.

"That's a huge amount we're missing in resistance," she said.

Resistance in waterways and animals

Peter Collignon, an infectious diseases physician at the Australian National University, has echoed calls for better monitoring, particularly in waterways and agriculture.

Professor Collignon said he felt federal authorities adequately tracked cases of antibiotic resistance in humans, but said other sectors needed to follow suit.

"What goes around in one sector eventually is likely to come to another sector," he said.

"It's a big soup which feeds on itself.

"But the trouble is we don't have a real-time ongoing surveillance similar to what we've got in people."

Professor Collignon said antibiotic resistance in agriculture had not been monitored for many years and meant there was little understanding of antibiotic resistance in meats like cattle, chicken and pigs.

Peter Collignon has called for improved monitoring in waterways and agriculture. ( ABC News: Sonya Gee )

"We also need to see what is coming into this country — there's huge amounts of aquaculture coming in and other products and they come often from areas with very poor water supplies."

The Australian Commission on Safety and Quality in Health Care has effectively clamped down on hygiene practices in hospitals and halved the spread of infections like MRSA in the past 15 years.

Similar public programs in the veterinary and water sectors could do the same, Professor Collignon said.

"The vast majority of people who come in contact with these bugs are not sick at all," he said.

"What it means is that you then carry the superbug in your bowel — that eventually disappears if you're in a good country.

"But there is basically a tsunami of many of these superbugs right at our doorstep."

Associate Professor Williamson described the current system for monitoring animals and the environment as "patchy and pretty ad hoc".

"We could respond in real-time to some of these emerging threats rather than just counting numbers retrospectively."

Patient urges consideration of prescription decisions

Anthony Fox has urged medical professionals to consider the impact of their prescriptions. ( Supplied. )

It has been nearly seven years since Mr Fox lost most of his ability to walk and since then he has also lost his marriage and sees his children only once a month.

He spends most of his time in a wheelchair and can no longer work.

Mr Fox urged doctors, regulators and other health authorities to consider the impact of their prescribing decisions on people like him.

"Unfortunately because of this infection I believe my capacity of being able to walk was affected," he said.

"My life is very limited, I am stuck in my house most of the day until I get a support worker.

"Everything flowed on from the infection."

But he also said he now sees the world through a different lens.

"For me, I was able to fight off the bug," he said.

"Every day is a blessing, but I'm also not really wanting to live because life's so difficult."