Any biologist could have told us it was coming - and quite a few did - because it's evolution in action. Antibiotics work by pitting organism against organism: the active agent, commonly something secreted by a fungus, interferes with the working of the bacterium causing the infection.
In response, mutations in the genes of the "bad germ" can cause it to develop resistance; the members of its species that are resistant will prosper (or, as biologists put it, "be selected for") as it reproduces.
"It was utterly inevitable," says Ellis-Pegler. "It was only a matter of time. We could never have stopped it. The best we could have done is to delay it."
The extent of antibiotic resistance was forcefully brought home to him in 2004 when two women in a fortnight showed up at Auckland Hospital with urinary-tract infections caused by an extremely drug-resistant bacterium. Both had just come back from India.
"A urinary-tract infection is usually a trivial infection," says Ellis-Pegler. "GPs don't even do a test most of the time. They just [diagnose from symptoms and] give three days of cheap oral trimethoprim and the inflection is cured. These particular people were having to be admitted to hospital with these multi-resistant germs."
Further investigation revealed 27 similar cases across the health system; in 10, the patient had returned from the Indian subcontinent in the months beforehand. "It was the most dramatic event of my career: when you can't treat a urinary-tract infection with three days of pills, but you have got to bring them into hospital and give them the last antibiotic on the rack intravenously to make them better - that was terrifying."
In a paper published in the prestigious journal Lancet Infectious Diseases a year ago, scientists announced the discovery of a gene, which they named NDM-1, that gave bacteria a high level of resistance to all antibiotics.
The gene, related to the one seen in the New Zealand travellers, was also identified in India, but this is the age of cheap flights and mass tourism - not to mention "surgical tourists", who save money by getting procedures done on the cheap in countries where infection control is not as good as ours.
The reality that disease knows no borders came sharply into focus and the NDM-1 gene was found in bacteria in patients in Britain.
"In many ways, this is it," one of the authors of the paper, Professor Tim Walsh of Cardiff University, told the Guardian newspaper. "This is potentially the end. There are no antibiotics in the pipeline that have activity against NDM-1-producing [bacteria]."
The typical layman's response to such dire threats is to assume that science will find a solution, but such faith may be misplaced. All the antibiotics ever developed have been the product of private industry, not universities, and, to put it bluntly, there's no money in it: pharmaceutical companies make much more by developing medicines that a patient will take daily for life, not three times a day for five days.
But even if scientists started work immediately on discovering new antibiotics, the immediate threat would not be avoided. The consensus is that there is perhaps 10 years before medicine grapples with the reality that there is no pill available to treat some infections.
The implications are mind-boggling. Surgical patients are routinely given antibiotics before their operations to guard against potential infection: if antibiotics don't work, the risk of surgery will become unthinkable in all but emergency cases.
In the case of transplant surgery, it's even worse. Recipients of donor organs are given so-called immuno-suppressant drugs, which stop the body's natural rejection response to the new organ. That makes them extremely vulnerable to the most trivial of infections. Without effective antibiotics, they die.
The same goes for those receiving chemotherapy for cancer.
Half a century of medicine has taught us to take for granted that antibiotics will back up a whole raft of medical procedures that are not treating infection but are more or less impossible without effective infection control. Lose one, and you risk losing the lot. Welcome to the future.
Associate Professor Mark Thomas, a senior infectious diseases physician at Auckland Hospital and the University of Auckland's medical school, paints a grim picture of the view at the clinical coalface.
"There are very few cases in which evolution completely defeats us," he says, "where a patient has an infection that is completely untreatable that kills them or creates another catastrophic outcome. It probably happens fewer than 10 times a year in Auckland, and usually the patients concerned are people who have been in hospital and often have illnesses that make them more prone to have infections.
"But we are down to last-line antibiotics very frequently now. And the time will come when bacteria have resistance to those ones too. Too right it will."
The more we use any antibiotic, the more we select for germs that are resistant to that antibiotic, Thomas explains. But the antibiotic doesn't just target the germ that is causing your infection; it is also affecting a few hundred of the other species of germs that are living on us - on our skin, in our gut.
"They far outnumber the ones that are causing the infection. And the resistance can easily be passed to other germs. And when you shake hands with someone or touch a door handle in a public lavatory, you pass it on."
Quite what the future will look like is not plain, even to the experts. Certainly personal hygiene, such as hand-washing, and public health measures will become more important, but no amount of hand-washing is going to fight a serious infection.
Rod Ellis-Pegler rules out the possibility that the human race will be extinguished by infection.
"No, it won't die out. It will just get selected in a rather more vicious way. How did the human race get to here? We are the product of all those who died before us. The human genes that survived are the survival genes.
"We've only had antibiotics since 1941. Before that there were diseases like the plague that cleaned out every third person in the street. Those sort of numbers are unthinkable now."
The infectious apocalypse is not imminent, but it gets closer every day. And one of the things we can do to buy more time is to use antibiotics much more sparingly. There is good research evidence that when antibiotic use drops in a given population, the incidence of resistant bacteria drops too.
Ellis-Pegler encourages us to think, when we're feeling crook, of the words of the American physician Lewis Thomas: "The great secret of doctors, known only to their wives, but still hidden from the public, is that most things get better by themselves; most things, in fact, are better in the morning."
MEDICINE LACK MEANT ONE BUG AND YOU'RE OUT
When Len Lanigan got sick as a kid, the only medicine he was likely to see was aspirin.
The 95-year-old, who served as a Birkenhead Borough councillor - he was mayor of the borough for eight years - grew up in the age before antibiotics.
"When people got ill in those days they weren't sent to hospital. They were kept at home and the only thing they seemed to get was aspirin," he said.
Those were the days when as many as 20 per cent of women could die after giving birth because of a fever that could today be treated easily by antibiotics, and when a playtime scratch could turn septic - and things could turn ugly.
"I remember an incident when there were three chaps my age. They were big, strong fellows - rugby players. They were playing somewhere and they cut themselves and picked up a bug - I can't remember what they called it - but three able-bodied men just died. Nobody knew why.
"It was so easy to pick up a bug in those days. There was no antidote, you know. There were six of us - three girls and three boys - and fortunately we got through, but life was very tentative and uncertain.
"People were trying to be careful but mishaps happened, and no one knew what to do about it because the medical service was not very well founded.
"When the antibiotics came along, they thought it was the be all and end all."
