The previous epidemic was the most serious recorded in her specialist unit's 25-year history and resulted in the deaths of three infants.
Of particular concern, she said, was malignant or critical pertussis which created complications that could be fatal.
"Those most at risk of malignant pertussis are those newborns and infants who are unimmunised, they are the four-to-six week old babies who have never had, or might have had one dose of the vaccine, but are certainly mostly unimmunised."
It was infants who were most likely to develop pneumonia, had a very high white blood cell count and had high blood pressure in their lungs.
"Caring for very sick babies with severe pertussis can be extremely difficult on our staff and parents often express feelings of guilt knowing that their baby has a preventable illness."
This month, a Gold Coast mother spoke out about the importance of vaccination after watching her daughter suffer with the illness.
The woman said she had not wanted the vaccine because she was an "organic" type who had a healthy pregancy until she contracted whooping cough two weeks before the birth of her daughter, Eva.
Shortly after, Eva was diagnosed with the illness - a situation her mother, who did not want to be named, described as a "nightmare".
"She ended up in intensive care... they go red, they go blue and sometimes they go black and then for a moment you think they are dead in your hands, they flop. A lot of suffering for a tiny little thing you love so much."
An analysic showed that over 10 years, around half of the 62 admitted to the unit with pertussis came during the most recent epidemic.
Nearly all were less than six months of age and 84 per cent were less than three months of age.
"Of these children, 63 per cent were too young to be immunised," Dr Ganeshalingham said.
"There were 11 children with malignant pertussis and six of these children died."
Another Starship paediatric intensivist, Dr Fiona Miles, said the death of an infant from whooping cough had a "huge impact" on doctors as well as families.
"It's really distressing for the whole team to be unable to save these babies, and to see the raw grief of parents losing a baby."
Ensuring vaccinations were carried out on time -- and that all family members who came into contact with infants were immunised, a term known as "cocooning" -- would help to stem outbreaks.
"The main group we need to worry about are the very small babies, newborn babies who are too young to be immunised, and have no protection and have the highest risk of dying from whooping cough," Dr Miles said.
"What that means is we need to be very vigilant about immunising everyone around them. While there has been some success with the immunisation of mothers and grandparents I think fathers need to realise that they pose a risk to their babies and need to be immunised.
"The pertussis vaccine we know doesn't last forever, so people who haven't been immunised since they were children have low immunity and if there's an outbreak then it's very easy for it to be transmitted on."
On-time immunisation with whooping cough vaccine at six weeks, three months and five months of age was one of the most effective way to protect infants against whooping cough.
Whooping cough vaccination is funded for all children as part of the National Immunisation Schedule and is also free for pregnant women between 28 and 38 weeks.
What you need to know
• Whooping cough (pertussis) is a highly infectious disease that is spread by coughing and sneezing and caused by bacteria which damage the breathing tubes.
• It can be very serious for babies and children - especially those under 1 year old. If babies catch whooping cough, they may not be able to feed or breathe properly, may become so ill they need to go to hospital and could end up with serious complications such as pneumonia and brain damage.
• The symptoms of whooping cough usually appear around a week after infection. Early symptoms include a runny nose, sneezing, slight fever a mild irritating cough and feeling generally unwell. Later symptoms include intense bouts of coughing, which bring up thick phlegm, a 'whoop' sound with each sharp intake of breath after coughing, vomiting after coughing, especially in infants and young children and tiredness and a redness in the face from the effort of coughing.
• On-time immunisation with whooping cough vaccine at six weeks, three months and five months of age was one of the most effective way to protect infants against whooping cough.
• Whooping cough vaccination is funded for all children as part of the National Immunisation Schedule and is also free for pregnant women between 28 and 38 weeks.
