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SAN JOSE — Katie Denise Oxley Thomas was fun-loving, athletic — a marathon runner — and looking forward to starting a new job as an executive assistant at Applied Materials after the new year.

But 48 hours after coming down with the flu on Jan. 2, the 40-year-old San Jose mother of three was dead.

Thomas was one of 42 Californians under 65 who have died since the flu season began Oct. 1, according to California public health officials. The vicious outbreaks kicked in aggressively by early November, they say, and are now on track to being the worst in a decade.

“I can tell you that she seemed absolutely fine on New Year’s Eve and called a friend Tuesday morning saying she had a sore throat, and by Wednesday she was in the ICU,’’ said Thomas’ sister Amber.

The latest tally of flu deaths, reported by the state on Friday, represents a dramatic jump from the 27 fatalities that officials had announced on Tuesday.

Thomas was also among 19 flu deaths reported so far in the greater Bay Area, including six in Contra Costa County; five in Santa Clara County; two each in San Benito, Monterey and Solano counties; and one each in Santa Cruz and Marin counties.

Thomas’ anguished relatives attended her funeral Saturday. The tragedy of her rapid physical deterioration has left them devastated, said her brother Anthony Oxley. And it stunned physicians at Good Samaritan Hospital who worked desperately to save her life, he said.

“They brought in specialists — they were baffled,’’ said the commercial contractor, who lives in Gilroy and had rushed to the hospital’s Intensive Care Unit early Thursday morning to be with his sister.

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“The doctor was saying that he had never seen anything like this, and it was not supposed to happen,’’ Oxley recalled.

The results of an autopsy are expected to be released this weekend, he said.

His sister had gone into septic shock before she died, possibly linked to a broken hand she had suffered in a recent car accident.

The impact from the car’s airbag left “her fingers in places they shouldn’t have been,’’ he said.

Surgery to repair the damage “didn’t go well,’’ and another was required. It led to an infection that was still evident on her hand while she lay in her hospital bed, Oxley said.

Medical experts, however, say sepsis and septic shock can result from an infection anywhere in the body, including flu and pneumonia.

The series of events leading up to her death have puzzled Thomas’ family. Oxley said his sister’s boyfriend said she had complained of feeling achy, feverish and had a sore throat on Tuesday, so she rested. But as her symptoms worsened that day, she made an appointment to see her doctor, who examined her and confirmed she had the flu. The doctor advised her to go home and rest.

The next day, Oxley said, Thomas felt even worse, so she headed to Good Samaritan’s emergency room, where the staff also told her she had the flu — and should return home.

But late Wednesday night, after she was having trouble breathing, her boyfriend drove her back to the hospital ER, where X-rays revealed that she had developed pneumonia, Oxley said. Thomas was immediately placed on a ventilator to help her breathe.

About 6 a.m. Thursday, Oxley said, her boyfriend called to meet him at the hospital. Not long after he arrived, they were told she had gone into septic shock.

“She had a high fever, but I could still talk to her and she could still respond by nodding,’’ Oxley said.

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Still, a worried Oxley asked the doctor overseeing her if her three children — ages 7, 15 and 17 — who had just visited their mother over the holidays should fly back from San Diego, where they live with their father. The doctor said yes.

Oxley said a handful of other doctors were called in from their homes or offices. Arriving in business suits, they quickly reviewed her case, and she was given more oxygen.

About 15 minutes later, she began fading, and Oxley watched as the doctors — who by then had ditched their jackets — tried everything they could to save her life.

“She was not conscious anymore. The fever had consumed her body,” Oxley said. “She was a mess — there were tubes everywhere.”

By about 5 p.m Thursday, he said, his sister was pronounced dead.

“We were all together at Christmas, and she was healthy,’’ Oxley said sadly, adding that he believes his sister had gotten her flu shot — but he wasn’t sure.

“I would definitely tell people to get the flu shot,” he said. “I know it might not keep you from getting the flu, but it might keep you from dying from it.”

Indeed, as hospital emergency rooms continue to be overwhelmed with flu patients, public health officials everywhere are urging anyone who has not yet received a flu vaccine to get one as soon as possible.

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Next up: Californians brace for the ‘twindemic’ State public health officials said on Tuesday that most of the victims were adults — and 70 percent were not vaccinated.

Experts say vaccines are especially important for people at high risk for serious flu-related complications that can lead to hospitalization and even death. That includes pregnant women; children younger than 5, but especially children younger than 2 years old; people 65 and older and people who have certain medical conditions, including asthma, diabetes and heart disease.