New York City's health commissioner, Dr. Oxiris Barbot, submitted her resignation on Tuesday morning, marking a shakeup in one of the most critical city agencies during the pandemic.

"It has been an honor and privilege to serve at the helm of an agency with its long and distinguished history in promoting and protecting New Yorkers’ health through ordinary times and during some of the most challenging moments in our city’s history," she wrote in the email provided by the Health Department.

The note did not provide a reason, but in a copy of her resignation letter obtained by the Times, Barbot told de Blasio, "I leave my post today with deep disappointment that during the most critical public health crisis in our lifetime, that the Health Department’s incomparable disease control expertise was not used to the degree it could have been."

Listen to Elizabeth Kim discuss Dr. Barbot's resignation with WNYC's Jami Floyd on All Things Considered:

De Blasio quickly called a press conference after a report of Barbot's resignation broke on NY1. He announced the appointment of Dr. Dave Chokshi as the city's new health commissioner. Chokshi, a primary care internist at Bellevue Hospital, comes to the job after holding several senior leadership roles over the last six years in the city's public hospital system known as Health + Hospitals.

During questions from reporters, the mayor's remarks suggested that Barbot was asked to resign.

He referred to her resignation as "timed to create a new approach to where we have to go."

"You have to keep refining, you have to keep learning from experience," he said. "You have to learn how to put together the best team."

Although asked directly several times, however, de Blasio did not say whether he had in fact fired Barbot.

Barbot's relationship with Mayor Bill de Blasio was reportedly tense, especially after the city Health Department was largely stripped of its contact tracing duties. The decision to allow the city's hospital system to run contact tracing was controversial, with many public health experts, including former health commissioners Dr. Thomas Frieden and Dr. Mary Bassett, criticizing the move.

“It makes absolutely no sense to move a function that has been done well by a great health department for decades to an organization that does not have the legal, epidemiologic, administrative or technical experience to manage it,” said Dr. Tom Frieden, a former city health commissioner and former director of the Centers for Disease Control and Prevention, in a New York Times editorial.

On Tuesday, City Councilmember Mark Levine, who chairs the health committee, issued a statement calling Barbot's departure "a grave blow to the fight for public health here."

He added: "Dr. Barbot has stood up fearlessly and consistently on behalf of science, no matter how strong the opposition.  Her loss is a major setback in our fight against this pandemic."

In May, Barbot issued an apology to a police department officer after a remark she made during the height of the coronavirus crisis was leaked to the press. The New York Post reported an anonymous source as saying that during a heated argument about mask supplies for the NYPD, Barbot had said to Chief of Department Terence Monahan, “I don’t give two rats’ asses about your cops."

In response to the Post story, a police union leader leveled a misogynistic attack on Barbot, calling her a "bitch."

De Blasio said he would investigate the incident.

"If what is being reported is accurate, the commissioner needs to apologize to the men and women of the NYPD, unquestionably," he said at the time.

The mayor's handling of the situation was criticized by some City Councilmembers who said it showed a lack of support for a woman of color in a leadership position. A significant number of female City Hall staffers have quit over the course of de Blasio's tenure. Some complained of the mayor's management style, saying he can be condescending or belittling, and in some cases, openly hostile to women.

In a statement, City Councilmember Carlina Rivera, who chairs the hospital committee, alleged that the mayor had a double-standard for managing his staffers and that Barbot had been forced out for disagreeing with him.

"I am disappointed that women in leadership like Dr. Barbot are pushed out after speaking their mind, while people like NYPD Commissioner Dermot Shea, who has publicly clashed with the Mayor, disagreed with him, and has completely failed in handling the City’s response to this summer’s protests, remains in his position without even the slightest bit of critique from his boss," she said.

Barbot has notably not appeared at the mayor's press conferences for weeks. Instead, the mayor has allowed Dr. Jay Varma, his senior adviser for public health, to field questions at his press briefings.

Barbot was promoted to the role of health commissioner in 2018 after serving as a deputy. She was the first Latina to head the department.