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As kids in San Francisco this week head back to school from summer vacation, the public health department plans to fight the spread of whooping cough by ordering children who have not been immunized to stay home if their classmates get sick.

"We're going to potentially exclude kids from school who are not up-to-date on their vaccinations and who are in a setting where there is a high number of kids who aren't vaccinated and there are cases of whooping cough," said Dr. Susan Fernyak, director of communicable disease control and prevention for the San Francisco Department of Public Health. 

With a statwide epidemic of whooping cough underway, San Francisco had seen 50 cases of pertussis as of August 10, while last year the city only recorded 16 cases for the entire year. In 2008, 79.3 percent of kindergartners in San Francisco were up-to-date on their vaccinations, which means about 20 percent were not protected from vaccine-preventable diseases.

Last spring, as the pertussis epidemic began, some schools in San Francisco were hit harder than others. "There were a few schools that had a larger number of cases than you would normally expect," said Dr. Fernyak. "Some of those schools did have specific classrooms with low vaccination rates, where 40 percent of the kids weren't up to date with their immunizations."

Whooping cough is among the required vaccinations for entering kindergarten, but the school district will give a waiver to children whose parents request a "personal belief exemption" and opt out of immunizing their child. 

Exemption rates vary widely from school-to-school even within the same county. For instance, in 2009, 68 percent of kindergartners at the private San Francisco Walforf School were not up-to-date on their immunizations due to a personal belief exemption, while at the public Malcolm X Academy, 0 percent had such an exemption.

In the spring, public health officials tried to control the spread of the disease by instructing schools with confirmed cases to send home students who were coughing. But that policy wasn't well enforced, as more kids from the same classrooms kept turning up with whooping cough. "That strategy clearly did not work," said Dr. Fernyak. So, San Francisco decided to adopt the tougher policy this semester of actually ordering childern who are especially vulnerable to infection to stay away when cases break out.

Kids who are impacted by the new policy could potentially miss a lot of class. "The incubation period for pertussis is up to 21 days," said Dr. Fernayk. "If you’re an unvaccinated kid in a classroom with several cases of pertussis, and you were sent home, you could potentially be at home for 21 days, and maybe longer if there are on-going cases in your classroom." San Francisco last adopted a similiar policy for schools and daycare centers when there was an outbreak of measles about a year and a half ago.

Health officials are concerned not only about the health of unvaccinated children who might contract pertussis, but for their younger siblings or expectant mothers. The epidemic has killed seven children in California this year, all of them infants under three months of age.