Experts say it is more important than ever that babies are immunised as early as possible against whooping cough.

Experts say it is more important than ever that babies are immunised as early as possible against whooping cough. Photo: Greg Newington

The bacteria that causes deadly whooping cough has mutated to more easily evade its vaccine, potentially putting hundreds of thousands of children at risk.

Experts fear a new booster shot may be needed for 18-month-olds, and say it is more important than ever that babies are immunised as early as possible to prevent exposure from people whose vaccines have worn off.

A study by NSW researchers has found almost 80 per cent of whooping cough cases analysed were caused by a mutated bacteria that had stopped producing pertactin – one of the three key proteins targeted by the vaccine.

"Clearly it is a red light in terms of how well the vaccination works," said Peter McIntyre, study author and director of the National Centre for Immunisation Research and Surveillance of Vaccine Preventable Diseases. "Immunisation is still the best and only way to protect against the most extreme cases of the disease ... but the effectiveness is waning and the bug mutation could be contributing to the vaccine wearing off faster."

The number of whooping cough cases in Australia has more than doubled since 1994, reaching a peak of 38,000 people diagnosed at the height of the epidemic in 2011.

Professor McIntyre said while overall cases were down this year, there was a substantial increase in two- to four-year-olds diagnosed in the past five years.

"We are seeing a lot more cases in older immunised kids which is very concerning if those children have younger siblings ... It could be because we are better at finding it but there seem to be issues in children after [they] turn two."

The study, published in Emerging Infectious Disease, analysed 320 samples of Bordetella pertussis bacteria from patients with whooping cough from 2008 to 2012, with the proportion of pertactin-free bacteria jumping from 5 per cent in 2008 to 78 per cent in 2012.

Lead author Connie Lam said the "huge increase" in mutated bacteria, which has also been found in the US and France, was unexpected.

“The fact that they have arisen independently in different countries suggests it's a response to the vaccine,” said Ms Lam, of the University of NSW school of biotechnology and biomolecular sciences.

"It could also mean that these pertactin-free strains have gained a selective advantage over other bacteria, making it less obvious for the body to find and destroy."

Professor McIntyre said more research was needed to determine if the "phenomenon" of the bug without pertactin was weaker or more virulent than other bacteria, with the reintroduction of the 18-month booster being "seriously considered". "There are other vaccines being trialled, including one where patients receive a weakened pertussis bug that is still alive. The vaccine would cause a mild infection but would not cause any of the other symptoms."

The major problem with the current "acellular" vaccine – which has less side-effects than the former whole cell version – is there are only three components, he said, "so if one of them is waning then you haven't got a lot to fall back on".

At present, about 95 per cent of children aged two in NSW are immunised against whooping cough.