The National Alert System for Critical Antimicrobial Resistance (CARAlert) identified 1,064 bacteria highly resistant to last-line antibiotics between 17 March 2016 and 31 March 2017 across 73 laboratories.

"These are super-superbugs," said Professor John Turnidge senior medical advisor at the Australian Commission on Safety and Quality in Health Care, which oversees CARAlert. 

"They're the bugs we can't afford to let get out of hand," he said.

The early warning system for the potentially dangerous spread of the critically antimicrobial resistant bugs (CARs) found a strain of a gonorrhoeae-causing bacterium - Neisseria gonorrhoeae - was the most frequently reported and most stubborn superbug between December and March, according to program's first publicly available report, to be released on Wednesday.

The rise of the resilient bacterium, combined with a rise in gonorrhoea cases nationally, leaves patients with no effective treatment options and aids the spread of the sexually transmitted infection, Professor Turnidge said.

The antibiotic azithromycin had become close to useless against the strain, which accounted for almost two thirds of all superbugs detected in February and March and the number of reports had increased threefold in NSW and Western Australia, the Commission found.

Azithromycin-resistant N. gonorrhoeae was the most common CAR reports among 15 to 49 year olds. 

The number of super-superbug detections overall was still relatively low, Professor Turnidge said of the eight high priority CARS monitored by the surveillance system, including Staphylococcus aureaus, Streptococcus pyogenes, Salmonella species, and Enterobactriaceae. 

But their emergence meant  "we are getting close to untreatable infection with these super bugs," he warned.

"Not having antibiotics to treat these infections would be a nightmare. It means people will die that don't need to die. 

"At the sharp end, you have patients who develop blood poisoning and septicaemia … these patients get desperately ill and end up in intensive care units," he said.

Patients who were infected with the "super-superbugs" were left scrambling for access to unregistered drugs, most commonly old antimicrobials that had not been used for decades. 

Overprescribing antibiotics was "certainly" fuelling the rise of the highly multi-drug resistant infections, as well as poor hygiene and lax infection control in hospitals and nursing homes, Professor Turnidge said.

The report also found more than one third of all CAR bugs were from patients in the community, rather than hospitals or nursing homes.

Seventy per cent of all CAR reports were from the three most populous states – New South Wales (34 per cent), Victoria (21 per cent) and Queensland (15 per cent). 

"What's happening here is happening around the world. Superbugs are endemic in the community and in hospitals. We are no different to other countries alarmed by by the risks of the spread of gonorrhea," Professor Turnidge said

The CARAlert system, funded by the federal department of health, was "an extraordinarily valuable extra tool that helps health authorities around Australia pinpoint the emergence of dangerous strains of bacteria with minimal delay," Professor Turnidge said.

Health authorities and clinicians get weekly notifications from CARALert.

But after only a year in operation, it was not yet possible to draw specific conclusions from the data. 

Sweden was the only other country that used a similar system, Professor Turnidge said.