The drugs Vancomycin, Aciclovir and metronidazole are the latest in a long list of antibiotic shortages over the past few years which are the most effective, least expensive, least toxic and least likely to cause resistance, infectious diseases doctors say.

When hospitals are out of stock or have to ration these antibiotics, doctors are driven to use back-up treatments including giving patients broader spectrum antibiotics which can cause potentially catastrophic complications such as bowel inflammation, and potentially put the community at greater risk of superbugs. .

"These are decisions that will lead to the deaths of people if they can't get an effective antibiotic," said Professor of infectious diseases at Australian National University, Peter Collignon.

Vancomycin supply – used to treat one of the most common superbugs in Australian hospitals methicillin resistant staphylococcus aureus (MRSA) – is not expected to be replenished for two months, according to manufacturer Pfizer's out-of-stock report.

"That's a serious problem. Vancomycin is critically important for patients with MRSA," Professor Collignon said. ,

"Not having the drug is almost the same as having a bug so resistant the drug doesn't work; patients do very badly.

"This is, in my view, is absolutely unacceptable," Dr Collignon said.

"Yes, doctors will find work-arounds; there are alternatives, but they're a lot more toxic, and expensive," he said.

Aciclovir stock will potentially be replenished this week, and intravenous metronidazole supplies should start flowing on December 20, Pfizer advises.

"If someone has herpes encephalitis and a brain infection, Aciclovir is the drug that patient needs," Dr Collignon said.

"These are infections that kill. To not have these drugs I just find it unbelievable," he said.

Hospitals were often not notified of an impending shortage of antimicrobials until the pharmaceutical company was out of stock, said infectious diseases doctor and spokesman for the Australasian Society for Infectious Diseases Associate Professor Allen Cheng.

"We don't have the opportunity to plan. If we knew a shortage was coming we could preserve our stocks but we are finding out at the last minute, which is making managing shortages difficult," Associate Professor Cheng said.

Infectious diseases experts told Fairfax Media the core problem was pharmaceutical companies effectively had a monopoly over the supply of antibiotics to Australia where only one manufacturer was approved by the Therapeutic Goods Administration (TGA) to import a specific drug.

Australia does not manufacture any of the key active pharmaceutical ingredients in antimicrobials.

"We're entirely reliant on sourcing from around the world," said Professor John Turnidge, head of the Australian Commission of Safety and Quality in Health Care's national surveillance program of antimicrobial and antibiotic resistance.

If a major manufacturer found a quality problem with a batch of drugs, or if regulators discovered quality issues with a plant's operations, manufacturing can completely shut down, cutting off national, even multinational supply, Professor Turnidge said.

"We work with hospitals and health departments to provide advice of the best alternatives during these shortages, but for Vancomycin in particular the alternatives are quite limited, Professor Turnidge said.

"We can use what we call the 'last-line' box of antimicrobials, which we reserve for cases of resistance with Vancomycin, but if we use them widely they'll be useless as well," he said.

About 500 superbug cases are detected in Australia every year.

A spokesperson for Pfizer said the interruption of supply of metronidazole and Vancomycin was due to "increased demand as a result of other manufacturers and distributors exiting the market or experiencing their own supply disruptions on their medicines".

"There is no concern with the quality, safety or efficacy of any of the three medicines," the spokesperson said in a statement, apologising for the disruption.

A spokeswoman for the TGA said the administration had approved the use of an alternative product during the shortage of the Australian registered Aciclovir, and was communicating with companies to find out when the shortage of Vancomycin and metronidazole would end, and whether alternative products might be able to be imported from overseas to cover the shortage.

Commenting on the appropriateness of using broader spectrum or last-resort antimicrobials amid the current concerns over superbugs, the spokeswoman said "the TGA is confident that clinicians will use the most appropriate alternative antibiotics that are available".

NSW and Victorian Health departments said they were aware of the shortages and were monitoring the situation closely.

"At this stage there had been no impact to patients," the spokesperson for NSW Health said.

The department was liaising with the TGA, and the National Centre for Antimicrobial Stewardship had provided advice on appropriate alternate pharmaceuticals available.

The Pfizer spokesperson said the company had a "dedicated team of professionals who review supply forecasts, however it should be noted that Quality Sterile Injectable manufacturing is complex and it takes time to respond to rapid market forces such as competitor supply disruptions and market withdrawals," the spokesperson said.

With Julia Medew and Rania Spooner