The abrupt resignation Wednesday of the director of the Centers for Disease Control and Prevention (CDC) comes at a difficult time for the agency, with officials fighting a deadly flu outbreak even as they seek to beat back proposed budget cuts from the White House.

The CDC is always on the front lines dealing with public health threats, and it has been working overtime this year to address drug shortages and an unusually active flu season.

Just last week, Brenda Fitzgerald told reporters 37 children had died from the flu this year. But Fitzgerald is now out as CDC director, following reports that she bought tobacco stocks while in office — something that runs counter to the CDC’s public health mission.

Her departure arrives at an inopportune moment, public health experts say, but they’re confident career staff and the acting director will be able to run the agency smoothly until a replacement is named.

“CDC has a skilled and professional staff, but sound leadership can always make a public health response better,” said Georges Benjamin, executive director of the American Public Health Association.

“The agency’s remaining leadership can handle this until a new director is named. We need to ensure the next director is science-based and knows public health well so they can hit the ground running,” he said.

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Anne Schuchat, principal deputy director of the CDC, will serve as acting director until a replacement is named.

She was the agency’s acting director for the first half of 2017, until Fitzgerald was appointed.

Officials said last week this year’s flu season is more intense than any since the 2009 swine flu pandemic and likely to get worse. Forty-nine states have reported widespread activity for three consecutive weeks.

But the agency already has leadership in place and public health advocates anticipate minimal disruptions in the agency’s response to the flu.

The CDC didn’t respond to a request for comment.

The CDC has an Influenza Division dedicated to outbreaks, headed by Daniel Jernigan, who has been with the agency since 1994.

“The employees of the CDC are dedicated professionals. They will do everything possible to keep the work on track,” said John Auerbach, a former CDC official who is now president and CEO of the Trust for America’s Health, a public health nonprofit.

Of greater concern, Auerbach said, is the fact that the Trump administration will be releasing its budget proposal next month, and the CDC likely won’t yet have a permanent leader to defend itself from cuts.

Public health advocates widely expect proposed cuts similar to the ones laid out in last year’s proposal — about $1.2 billion. Those cuts never came to pass, as Congress refused to consider them.

“This comes at an unfortunate time because the budget will soon be released by the administration, and we’re concerned that, as was the case last year, the CDC’s budget may be significantly reduced in the proposed administrative budget,” Auerbach said.

The departure of the CDC director so close to the budget discussions is significant because agencies rely on political appointees to communicate and negotiate with the administration that appointed them, said Boris Lushniak, a former deputy surgeon general and acting surgeon general who is dean of the University of Maryland School of Public Health.

“What I think that most major government organizations lose when there is a resignation is a political connection — the connection with the administration at the White House falls on the shoulders of career-track people, who are capable of that, but are not tuned to the political forces that exist out there,” he said.

“This is an important time period in terms of the budget cycle. An appointed leader running the charge, both on discussions about the budget and discussions at the executive and legislative level, that is a stronger approach for budget negotiations than you would see in the hands of a career-track person,” Lushniak said.