While symptomatic children have been encouraged to stay home, Rupp said unvaccinated students are no longer being "excluded" or quarantined because classes are scheduled to end June 2.
"Now it's more or less everywhere," Rupp said. "We've elected to not pursue those exclusions and just let the school year play out."
Pertussis is a highly contagious, but vaccine-preventable, bacterial disease that for most people carries symptoms similar to a severe cold with a lingering and sometimes violent cough. It poses the greatest risk to infants and individuals with chronic respiratory conditions or compromised immune systems.
Rupp said whooping cough is relatively common, with roughly 50 cases reported in Salt Lake County during 2016. The disease ebbs and flows on a multiyear cycle, he said, with the county reporting more than 60 confirmed or suspected cases so far this year.
"We're on the upswing," Rupp said. "AISU is certainly contributing to that increase."
Utah law requires that public school students be vaccinated, but allows parents to declare an exemption and opt out for any reason.
The Salt Lake County Health Department recommends schools have an opt-out rate no higher than 5 percent to achieve "herd immunity," or the rate at which vaccination is so prevalent the spread of a disease is effectively halted.
At the American International School of Utah in Murray, the vaccination opt-out rate is 11 percent. Rupp said there is "no doubt" the high number of unvaccinated children contributed to the spread of pertussis.
"We are struggling to control the outbreak because of that exemption rate," he said. "The lack of vaccination is a problem."
The health department sent a letter to AISU staff and parents Tuesday, encouraging sick children be treated by medical providers and kept home. The letter also encouraged families to complete immunizations if they had not already done so.
"The most important message is that if your child is not vaccinated, not adequately immunized, please consider getting it done," Rupp said.
Kelly Casaday, AISU's director of operations, said the school's attendance rates have returned to normal since last month's school closure, but the outbreak disrupted end-of-year events like testing, and a choir concert other schools were invited to participate in has been rescheduled.
"We're going to postpone that two weeks," Casaday said. "We don't want to put anybody else at risk."
He said students and staff have been told to assume any health issues are the result of whooping cough and to stay home from school.
He also said several parents have indicated they will reconsider their vaccine exemptions as a result of the outbreak.
"We're going to obey state law," Casaday said. "But as we can see right now, it's a whole lot better to get people vaccinated and that's what we would encourage people to do."