Children getting flu vaccines in New Hampshire will find it very hard to avoid the needle this year, following the CDC’s surprising recommendation that doctors and clinics use only injections and stop using a nasal spray version of the vaccine, which has not worked well.

As a result of the change, the New Hampshire Department of Health and Human Services has canceled its order for some 52,000 doses of FluMist, the commercial variant of the nasal flu spray, ordered in preparation for the 2016-2017 flu season. The doses will be replaced with vaccines given by a shot.

“The big difference is that kids are going to be: ‘What do you mean I can’t get the stuff up the nose?’ ” said Peter Lozier, who owns Crossroads Family Medicine in Concord.

New Hampshire offers free flu vaccinations for everybody under age 19, and provides most of the pediatric flu vaccines in the state.

For the upcoming flu season, which usually hits New Hampshire in September, the state ordered has 151,000 doses of influenza vaccine for children. Of those, 35 percent or 52,000 doses had been the spray version until the recent change.

“We’re concerned that we have been putting out a product that has not been efficacious,” said Marcella Bobinsky, acting director of Public Health Services for the DHHS.

The decision will mostly affect pediatric and school-based vaccination programs. Virtually all adult patients get a flu shot.

Nasal spray vaccine has been around for over a decade and was projected to make up about 8 percent of 176 million doses of this year’s flu vaccine. It was thought to be especially effective for children under age 8, which is part of the reason that last week’s announcement from an CDC committee known as ACIP against FluMist was such a surprise.

In New Hampshire, spray vaccine is chosen by between one-third and half of children getting vaccines in school clinics, Bobinsky said. All those kids will now have to face a shot for flu season.

“I’m a little concerned that parents won’t be able to tell their kids that they don’t have to get a shot, and might not show up at the flu clinic if they have to convince them to get a shot,” said Barry Barns, a pharmacy doctor who helps oversees Dartmouth-Hitchcock’s flu vaccine program.

Barns said his main concern is whether enough doses can be made and shipped to New Hampshire in time.

“I don’t know if the manufacturers will be able to fill the vacancy — that’s millions of doses,” Barns said. “If the state is trying to replace the vaccine they had ordered, there might not be a whole lot to go around.”

Dartmouth-Hitchcock ordered about 51,000 doses of flu vaccine for its hospitals, clinics and other facilities, Barns said. All of it is the injected vaccine, because the state covers virtually all pediatric vaccines.

The recommendation about FluMist was a surprise because in 2014, CDC’s Advisory Committee on Immunization Practices supported FluMist for most children aged 2 to 8 after studies indicated that it seemed to work better for them — plus, kids don’t like shots, so a spray produced wider coverage.

Since then, according to CDC, analysis of patients over the last two winters indicated that the mist vaccine was not working well in the real world. In 2015-2016, in fact, it hardly worked at all: FluMist’s efficacy among children 2 to 17 years old was only 3 percent, essentially providing no protection, says the CDC. (FluMist’s manufacturer, AstraZeneca, disputes that finding.)

The injectable vaccine had a efficacy of about 60 percent, which is better than it sounds, said Lozier.

“Even when it doesn’t protect completely it almost always gives partial immunity, protects you to some extent — a shortened course of disease, shortened (time for) passing on to others,” he said.

It’s not clear why such a promising technology as FluMist suddenly failed.

Vaccines work by using safe levels of diseases to activate a response from our immune system, so that when we encounter the disease in the wild our bodies are ready to fight it.

One different with variants of the nasal spay is that they use a live but attenuated version of flu-causing viruses to trigger the immune response, whereas injectable vaccines use an inactivated, or dead, form of the virus.

(Scientists don’t like the term “dead” for viruses because it’s not entirely clear these microscopic entities are actually alive in the first place.)

However, live viruses have often been used successfully in vaccines, so that alone can’t explain the problem.

Another possible cause for the shortcoming is that the FluMist tested well when it involved three different strains of flu, but recently the CDC has increased the number of strains in vaccines to four, to better anticipate what variant of flu will sweep through the country. Vaccines take months to create in large numbers, so officials must guess what strains will be prevalent long before the annual move of flu strains east from Asia.

Or it might be that that it failed against a strain of flu, called H1N1, that has been prevalent recently.

“Flu is a real problem. It’s a difficult vaccine to make, a difficult vaccine to stay on top of, because flu changes every year,” said Bobinsky.

The ACIP committee meets in April to decide what strains of flu to target in this year’s vaccine, based on what has been seen in Asia and the southern hemisphere, where the disease starts each year and then moves to us.

It takes many months to create and manufacture tens of millions of doses of flu vaccine, so officials have to guess what will be happening half a year later.

Sometimes the guess is off and the vaccine doesn’t work very well, as happened in 2014.

Whatever the cause, many doctors are concerned that the switch will make it harder to convince people to get an annual flu vaccine.

“We will continue to work with parents to make sure they understand the importance of the vaccine, no matter how it’s delivered; and work with medical providers to encourage parents to get that vaccine. … It’s still the very best way to protect against influenza,” said Bobinsky.

And although it may not seem like it, Bobinsky said the about-face speaks well for the vaccination program.

“This is a great example of we always watch our vaccines; we don’t just put them out there and let them go. Vaccines are constantly monitored, to make sure they’re safe, that they work — that’s how we understand how something needs to be pulled,” she said.