Essentia Health has fired roughly 50 employees who refused to get flu vaccinations under a new policy that pits personal choice against public health interests.

Hundreds of workers got their shots last week after being warned that they would otherwise lose their jobs, the Duluth-based health system said Tuesday.

But a fraction of workers still refused and did not meet Essentia’s medical or religious criteria for exemptions, according to Dr. Rajesh Prabhu, an infectious disease specialist and Essentia’s chief patient safety officer.

Severely ill patients are at greater risk of complications and death if they catch the flu, Prabhu said, so there is a greater need to vaccinate hospital workers who interact with them. And even though flu vaccines are not 100 percent effective, federal health officials say they greatly reduce the likelihood of infection. “We are working in a different environment,” Prabhu said. “We’re taking care of patients. We have a different sort of ethical obligation.”

Three unions objected to Essentia’s policy, which was imposed to reduce the spread of influenza in the health system’s 15 hospitals and 75 clinics in northern Minnesota and three other states.

The United Steelworkers, which represents some of the workers, unsuccessfully sought a federal court injunction to block the company from firing workers who refused vaccine.

The Minnesota Nurses Association (MNA) and the American Federation of State County and Municipal Employees, Council 65, also lodged complaints about the practice with the National Labor Relations Board. The nursing union announced Monday that it would file grievances on behalf of any nurse who lost a job over the flu shot policy.

“We tried to sit down with management, but Essentia executives told us they intend to follow through with terminations and mandatory flu shots regardless,” said Steve Strand, co-chair of the MNA’s bargaining unit in Duluth.

As many as 400 doctors, nurses or other workers hadn’t been vaccinated as of Nov. 15, when Essentia reported 97 percent compliance among its 15,000 employees. But many of those holdouts got shots or filed exemptions before the company’s Nov. 20 deadline.

Prabhu said 99 percent of Essentia’s workers have now complied — though the company is still reviewing some exemption requests.

Flu shot mandates aren’t as common in Minnesota as they are in other states, including Wisconsin and Colorado. Sanford Health has required its workers to receive vaccinations each year or file exemptions since 2013.

Hennepin County Medical Center in Minneapolis requires workers to get vaccinated or opt out in writing.

Prabhu said the requirement is an important step in broader efforts to reduce hospital-acquired infections. Minnesota ranks 44th out of 50 states in the rate of health care personnel vaccinated against influenza, he added.

Jen Hutzell, a cleaner and care aide at Essentia’s Oak Crossing long-term care facility in Detroit Lakes, said she sought a formal exemption unsuccessfully. She argued she is a seasonal worker who travels to the South during the winter and doesn’t present a risk of infection to residents. Hutzell said she is being allowed to take a leave — although much earlier than planned — and to return to work in the spring.

She said her objection is based on personal experience. Hutzell said the only year she suffered flu-like illnesses was 1995 — the one year she received a flu shot in order to be around her newborn son, who was born prematurely and needed intensive care.

“That was the sickest year of my life,” she said.

Scot Harvey received a letter at his home near Chisholm, Minn., Tuesday confirming he was fired from his job as an administrator on nights and weekends at Essentia’s hospitals in Duluth.

He refused vaccination based on the fatigue and symptoms he suffered after receiving vaccinations as a soldier in preparation for the first Gulf War.

Harvey said his request for an exemption was denied. He said the form limited exemptions to medically documented vaccine allergies or histories of Guillain-Barre Syndrome following vaccinations. Even egg allergies didn’t qualify, he said, because vaccines made without eggs are available.

A registered nurse, Harvey said his stance might make it harder to find work.

But he felt it was an issue of free choice.“If nobody stands up and says, ‘Hey, this isn’t right,’ ” he said, “then next year everybody in health care is going to have to have a flu shot, and then everybody in every job is going to have to have a flu shot.”

Prabhu said he has heard all the concerns, including the belief that the vaccine’s inactive virus causes flu and the objection that the shot provides only weak protection. He noted that multiple studies have found the vaccine reduces the threat of illness by 40 to 60 percent.

“If you catch influenza while hospitalized for some other purpose,” he said, “you have a higher likelihood of a bad outcome, including death.”