TORONTO - Ontario's universal flu shot program isn't making much progress with the under-two crowd, a new study suggests.

Vaccination rates among children aged six to 23 months is very low and has been since Ontario started offering free flu shots for all, said the study, published Monday in the journal Pediatrics. Ontario's universal flu shot program began in 2000.

The rate of toddlers who were fully immunized for flu from 2002 to 2009 never topped 10 per cent, the research showed. From a high of seven to nine per cent in the three seasons following the province's SARS outbreak in 2003, the rate slipped downward to four to six per cent in the latter part of the study period.

The 2003-04 winter was a harsh flu season with an unusually high pediatric death rate in the United States. In fact as a result of that season, the U.S. Centers for Disease Control began to collect data on pediatric flu deaths. And 2003 was also the year when the Canadian and U.S. bodies that advise on vaccine policy first recommended flu shots for children in this age group.

This study captures how little progress has been made towards enacting that recommendation. In addition to estimating percentages of kids who got flu shots, it analyzes which children were more likely or less likely to have a flu shot in any given year.

So which children in this age group were at greatest risk of not getting a flu shot? "The majority of children in Ontario," senior author Dr. Astrid Guttmann said with a rueful chuckle.

Guttmann put the failure to reach these children down to a couple of related factors -- "vaccine fatigue" among parents and concern on the part of doctors that flu vaccinations might be a shot too far for their young patients or their parents.

"There's a pretty good body of evidence around vaccine fatigue in parents," said Guttmann, a pediatrician at the Hospital for Sick Children and a senior scientist at Toronto's Institute for Clinical Evaluative Sciences.

"I think the prioritization that goes on, again, at physicians's offices really is: If parents are going to say yes to two and not three, which ones are you going to give?"

If doctors are making those mental calculations, flu shots are likely going to fall out of the lineup, suggested Dr. Allison McGeer, an infectious diseases expert at Toronto's Mount Sinai hospital.

"In Canada, pediatricians really have trouble wrapping their heads around influenza being a significant pathogen," said McGeer, who was not involved in this study.

"And that's having a big impact on pediatric vaccination rates, no question."

The study looked at records for over 760,000 Ontario children born from April 2002 to March 2008. It focused on the six-to-23-month group because toddler-aged children can become severely ill when they contract influenza.

"If infants and young children at that age get influenza, many of them need to be hospitalized. They get much sicker than their older siblings. And some of their hospitalization rates are comparable to the elderly," Guttmann said.

Injectable flu vaccine is licensed for children six months and older. (It isn't effective in children younger than six months.) Children need two shots -- a primer and a booster -- the first time they receive flu vaccine. From then on, only one shot per season is needed.

An earlier attempt to estimate flu shot coverage in Ontario toddlers by this same group of researchers suggested the rate was higher than seen in this study. The team conducted a telephone survey during the 2006-07 season and found that under 15 per cent of children aged six to 23 months got a flu shot.

McGeer questioned whether the method for this new study presents a more accurate picture of what is happening, noting that reliance on doctors' billing records to see which children had a shot is problematic.

In Ontario there is a generic billing code for giving a shot, and a specific billing code for giving a flu shot. Both represent the same amount of income to a doctor, and there's no requirement or incentive for them to use the specific billing code. Many don't, McGeer said.

If the researchers missed flu shots that were coded as a generic vaccination, it would have the effect of lowering the numbers and making it seem like fewer children got flu shots than was actually the case.

Guttmann said her team is pretty confident they are capturing most of the flu shots given to this age group. But even if they didn't, she said, their major interest was in trying to figure out which kids are not being vaccinated, so that flu shot promotion efforts could be better targeted.

Rates of coverage were somewhat higher in children who had chronic health conditions and who had been born at a low birth weight. If a baby's mother got a flu shot, the child was more likely to get one as well.

Babies who had been in neonatal intensive care units and who were discharged during the winter were also more likely to get flu shots. Guttmann said the team can't say for sure, but suspects those parents may be prompted to have their child immunized around the time of the discharge.

Several other provinces -- Nova Scotia, Saskatchewan and Alberta among them -- are doing a better job vaccinating toddlers for flu, Guttmann said.

But making progress in Ontario may not be easy, McGeer suggested.

"Pediatricians will give needles to kids because they know kids need needles. But it doesn't mean they like it. Nobody likes causing pain to children."

She suggested the new nasal spray flu vaccine, which may become part of free flu shot programs next season, may make it easier to make progress in children. It is puffed up a child's nostril, eliminating the dreaded needle.

But the nasal spray vaccine won't help with the youngest of the children in this group, Guttmann said. That vaccine is only licensed for children aged two and older.