Members of the Chicago Teachers Union narrowly approved the COVID-19 safety agreement reached this week with the school district, bringing to a formal end the standoff between the union and the school district and the mayor that closed schools for five days.

Nearly 56% of 18,600 CTU members who voted said yes to the agreement, the CTU announced Wednesday evening. The slim margin reflects a strong sentiment by school staff that the deal did not include enough protections to make a difference for student and staff safety.

Teachers and parents also continue to worry about staff shortages, and that was borne out Wednesday as some schools struggled to staff their classrooms and offer instruction. The school district said nearly 89% of teachers reported to work overall.

CTU President Jesse Sharkey issue a scathing statement showing the depth of the bitter feelings that remain after negotiations with Mayor Lori Lightfoot. 

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“Put bluntly, we have a boss who does not know how to negotiate, does not know how to hear real concerns and is not willing to respect our rank and file enough to listen to us when we tell her we need more protection,” Sharkey said in the statement. “Our members’ vote today represents a union’s, and a city’s, frustration with a mayor that has simmered since the beginning of this pandemic.”

Sharkey said “this agreement covers only a portion of the safety guarantees that every one of our school communities deserve.” On Tuesday, he said the CTU leadership accepted it because it was as good as they thought they could get. Sharkey said the mayor was simply unwilling to budge on some issues. On Wednesday night he vowed to keep fighting.

CTU Vice President Stacy Davis Gates emphasized that getting a safety agreement was significant. The last COVID-19 agreement expired in August. While the two sides talked on a weekly basis, the school district did not feel pressure to reach a deal.

Striking a conciliatory tone after the agreement was announced on Monday, CPS CEO Pedro Martinez said it included many good parts. He pointed to provisions to increase testing and ensure students and teachers get N95 masks.

In a statement issued before Sharkey’s, Lightfoot said “We are pleased we have come to an agreement that guarantees predictability and stability for the rest of the school year …  The science tells us that the safest place for our students is to be in the classroom,” she said, reiterating the strong stance she took during the five-day shutdown. She encouraged families to get their children vaccinated and to sign up for in-school COVID-19 testing.

One key part of the agreement could soon make a difference: The school district set a trigger for when a high number of teacher absences could move a school to remote learning. This fall, there were examples of schools with high cases and quarantines, but remained open with skeleton crews and staff and no way to pause to slow the spread.

The school district said no schools moved to all remote learning on Wednesday, though at least one had the vast majority of classes learning remotely. The school district has so far refused to put out school level information on how many classes are flipped to remote. Some schools had multiple classrooms that were flipped to remote temporarily. CPS says that’s a short-term measure while it investigates a COVID-19 case.

Still, the teachers union could not get the mayor and school district to compromise on some key issues.

Top among them was when to restart in-person learning. The union wanted to wait until Jan. 18, with students remote until then. The mayor was dead set against any plan that had the whole district remote learning.

The mayor refused to consider any sort of metric to move the school district to shift to all remote learning, even during an extreme surge in COVID-19 cases. The union pushed hard for this.

The other area where the mayor would not relent is on who would get COVID-19 testing. The union wanted all students automatically eligible for testing unless a parent opted them out. They wanted 10% of randomly selected students to be tested each week. The mayor would not give in, saying parents had to affirmatively opt their children in.

The mayor and school district agreed to the 10% testing of students at each school. But this depends on teachers and staff getting enough students to opt into the testing. The school district will provide a $1,000 stipend for school staff to sign up students for testing and vaccinations.

The district also is allowing for verbal consent to testing, rather than waiting for parents to sign up online, which some parents have found cumbersome.

Still up in the air is whether the five canceled days will be made up and teachers paid for wages lost during the shut down. The union maintains they should be if the school district is worried about children missing instruction.

But the mayor punted the question to Martinez. He hasn’t said what he intends to do.

Meanwhile, at some schools on Monday, students and parents said little instruction was taking place because of staff absences. At Taft High School on the far Northwest Side, junior Emma Pakieser asked her mother to pick her up after spending much of the morning in the auditorium after class after class had no teacher or substitute.

Emma said she didn’t feel safe in an auditorium with dozens of other students, many of whom didn’t have quality masks and pulled down their masks to talk to friends. She said the school handed out N95-type masks at the beginning of the day, but many kids were still wearing lower quality ones.

Her mother, Sean Pakieser, said it’s better to keep students home if there is no learning happening and safety protocols aren’t followed. Her daughter was able to log into some classes from home. She says the debate has gone beyond school safety.

“It’s not even a fight about ‘is it safe or not’ ” Pakieser said. “It is: Are the schools actually able to function? This is not a functional school if students are locked together into a crowded auditorium.”

Chicago Public Schools said 82% of teachers reported to Taft on Wednesday. Student attendance was still being calculated. It was low on Jan. 3 and 4, the first days after winter break, at 66% and 72% respectively. CPS’ COVID tracker shows that 9,200 students and 2,200 adults were in quarantine as of Tuesday.

CPS said in some cases in high schools when there isn’t a substitute, students can be moved to an auditorium and the majority are supposed to be logged into remote classes. CPS says it’s facing a national substitute shortage and is offering incentives to hire more. The school district says it’s added 455 since the start of the school year.

Sarah Karp covers education for WBEZ. Follow her on Twitter @WBEZeducation and @sskedreporter.