Thousands of baby flying foxes are rescued across Australia each summer after heat stress events, habitat loss and other human impacts leave them orphaned. Volunteers often hand-feed them every few hours for months at a time.
But new research shows that human pollution in the environment may also be exposing these vulnerable animals to antibiotic-resistant bacteria.
A partnership between Macquarie University scientists and WIRES has uncovered worrying levels of resistance among rescued pups and developed practical solutions to protect both wildlife and carers from infection.
"The bacteria we're finding in these animals evolved in humans or domestic animals," says Dr Fiona McDougall, a Research Fellow at Macquarie's School of Natural Sciences.
"It's confronting to realise that we're effectively polluting the environment with microbes that then spill over into wildlife."
Tracking superbugs from people to flying foxes
The study focused on the grey-headed flying fox – critical native pollinators now listed as vulnerable. Over two and a half years, researchers collected more than 570 samples from orphaned flying fox pups in care.
Thirsty work: A grey-headed flying fox skims the water surface – a behaviour called 'belly-dipping that can expose pups to antibiotic-resistant bacteria from contaminated water sources.
They found almost one in three pups carried E. coli strains resistant to common antibiotics, and around one in 10 harboured bacteria that no longer respond to multiple drugs. Genomic sequencing showed that many of these strains closely match those found in human infections.
The infection pathway likely begins in water contaminated by human or animal waste. Adult flying foxes 'belly-dip' to drink – skimming the surface and licking water off their fur – while their babies cling to them, directly exposing pups to any bacteria in the water.
"For the first few weeks of life, these pups rely entirely on their mothers, so if the water is contaminated, they're infected early," Dr McDougall says. "Their gut bacteria are still developing, which makes them especially vulnerable."
In one tragic case, a pup in care died from sepsis linked to multidrug-resistant bacteria – a stark reminder of the real-world consequences of antimicrobial resistance.
Protecting wildlife – and their carers
The collaboration has led to new biosecurity guidelines for wildlife rehabilitation, including simple but powerful steps: wearing masks while cleaning cages, washing hands between handling animals, using separate equipment for each enclosure and keeping domestic pets away from wildlife.
"Wildlife carers give extraordinary amounts of their time, energy and even their homes to these animals," says Professor Michelle Power, who leads Macquarie's Wildlife Health and Disease team.
"Our goal is to make their work safer and more effective, using evidence-based strategies that can be applied globally."
Disease detective: Professor Michelle Power, pictured, works with flying fox carers to develop biosecurity guidelines that protect both animals and people from superbugs.
Professor Power says antibiotic overuse – in humans, pets and even wildlife care – is fuelling resistance, giving harmful bacteria an evolutionary advantage. Establishing antimicrobial stewardship in the wildlife sector, she says, is critical to protecting both animals and people.
A global model for 'One Health'
The findings reinforce the World Health Organisation's One Health principle – that human, animal and environmental health are deeply interconnected. By identifying how human-origin superbugs spread into wildlife populations, the Macquarie-WIRES partnership is helping to close the loop of infection.
"This is a global issue," Professor Power says. "Wildlife rehabilitation happens everywhere – and the lessons we're learning here in Australia can inform international best practice."
Training workshops for carers and veterinarians are now planned, focusing on biosecurity and responsible antibiotic use. The researchers hope their work will inspire similar collaborations worldwide, uniting scientists and volunteers in protecting the planet's most vulnerable species.
"Caring for wildlife is an act of compassion," Dr McDougall says. "Our research shows it's also part of safeguarding global health."
Dr Fiona McDonald and Professor Michelle Power are from the School of Natural Sciences in the Faculty of Science and Engineering.
