Tree-hugging, eucalyptus-chomping, sleep-loving: it is easy to see why the cuddly koala is an animal favourite for any tourist Down Under.

But visitors might not realise that tens of thousands of the cute marsupials now suffer from an exceptionally painful and often lethal condition. It is one caused by bacteria with a notorious reputation. Australia’s koalas are being killed by chlamydia.

“About half the koalas across Australia are infected,” says David Wilson, professor of infectious diseases at the Burnet Institute in Melbourne. “In closed populations, the majority can be infected – sometimes up to 80%.”

Koalas are struck by a different strain of the disease from that which affects humans – although it seems humans can catch the koala version through exposure to an infected animal’s urine. In koalas, the effects of chlamydia are devastating, including blindness, infertility and an infection known as ‘dirty tail’.

“Dirty tail is actually really awful," says Wilson. “The urinary tract gets inflamed and expands substantially; it’s incredibly painful. They get discharge and many koalas die.”

About half the koalas across Australia are infected

Clearly, the epidemic is doing nothing to help conserve a species that is already under severe pressure through habitat loss. In just 20 years, populations have dropped by 40% in Queensland and about 33% in New South Wales. In both regions the koala was added to the list of threatened species in 2012.

Koalas have been hit by hardship before. In the early 20th Century they were all but wiped out when some 8 million were hunted as part of the fur trade.

Nowadays koala threats include dog attacks, car accidents and deforestation – but Wilson says “disease is probably the largest reason there’s decline”. And it is not just chlamydia causing problems. Many koalas are also being infected by a retrovirus – similar to HIV – which most likely exacerbates the impact of the bacterial infection.

The chlamydia is non-discriminatory, striking males, females and even babies (known as joeys) who catch it from nursing on watery faeces in their mother’s pouch.

“Chlamydia is a very ancient pathogen,” says Wilson. “It’s been around tens of thousands of years and exists in many species.” Other victims include guinea pigs, sheep and crocodiles.

Wilson says it can be particularly problematic in birds, which can transfer the disease to humans via their faeces and nasal droppings.

Chlamydia strikes males, females and even babies

I wouldn’t breathe anywhere near the fountains in Europe, says Wilson, who thinks that bird dropping particles in the air can damage human lungs.

Back in Australia, though, there is not a lot that can be done for the iconic koala. While the pathogen can be treated by antibiotics, these have some pretty devastating side effects.

“Koalas have a gut full of bacteria that is essential to digest eucalyptus leaves,” says Peter Timms of the University of the Sunshine Coast in Queensland, Australia. “So if you’re giving them systematic antibiotics, it is actually killing this.”

What’s more, antibiotics are of little use once the disease is too far gone.

“You have got to get them early enough,” says Wilson. “We could do a huge, large-scale round up and bring them into hospital but it’s too resource intensive and not really feasible.”

Instead, he has come up with a controversial strategy. “My suggestion is this: the population is in decline. The way we can increase the population is, paradoxically, we should kill some of them.”

One hope is that clues to combating chlamydia will be found in the koala genome

“They’re transmitting chlamydia to each other and many of them can’t be healed. These koalas are in a lot of pain and if they’re out of the time-range of antibiotics being effective; the humane thing to do is probably to euthanize them.”

Wilson argues a strategic cull now would help the koala population begin to bounce back in the next 5 to 10 years.

It is not an unprecedented idea. Australia has plans to eradicate two million feral cats in the next five years, to protect native animals. And in the early 2000s there was a trial cull of native Tasmanian devils when the population began dwindling because of the rapid spread of a severe infectious facial cancer.

The Tasmanian devil cull was not successful, but Wilson says that was because the programme was badly implemented.

Scientists are also working on more palatable solutions to the koala problem.

One hope is that clues to combating chlamydia will be found in the koala genome. At last count, researchers had identified about 12,000 koala genes, and it is thought there might be about 20,000 genes in total.

The way we can increase the population is, paradoxically, we should kill some of them

One particular gene that has now been sequenced, IFN-g, has been described as the ‘holy grail’ for understanding how the koala immune system works, making it an important weapon in the fight against the disease.

Timms say they are on the cusp of something big. “I’d say in three months we’ll have the full genome sequence and that will tell us the full story. It should be pretty exciting.”

He says it will uncover countless things about the koalas, right down to how they can smell the difference between 400 types of eucalyptus leaves. He also hopes it will shed light on the koala retrovirus, as well as why some animals with the chlamydia infection go on to get severe clinical disease while others do not.

The end result will, with luck, help improve a vaccine already in development.

“End stage disease is hard to stop but if we get them early on, we might have a better chance,” says Timms. So far the team has completed eight trials including six in the lab, and two in the field. Timms says they are still testing but the results look promising.

The vaccine is something that works and it is something we can do now

Early trials have found the vaccines effective at stopping koalas picking up the infection. They have also found that despite strains of chlamydia varying across the country, it is possible to develop a vaccine that combats this. And they have managed to make the vaccine administrable in one dose rather than three.

“While the vaccine’s not perfect, we’re catching koalas all the time now. We should be vaccinating them now. Not waiting 10 or 20 years.”

Something quite remarkable they found is that the vaccine could almost turn back the clock, stopping the disease in its tracks. Testing a small sample of four koalas, the team has found it can function as a therapeutic vaccine, reducing the infection in animals that are already infected as well as preventing progression from infection to disease.

They are now testing it on a larger sample of 15 koalas at the Australia Zoo in Beerwah, Queensland.

Timms estimates a functional vaccine will be available in about three years. Still, he says, now is the time to act.

We are losing the fight when it comes to deforestation and other threats, he says. The vaccine is something that works and it is something we can do now. And it’s not only koalas that stand to benefit.

“The lessons that we learn can be applied to humans,” says Wilson. It is hoped studying koalas will provide an effective model to vaccinate against human chlamydia and to understand how infections affect human male infertility.