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Cross your fingers that the U.S. doesn’t see any big outbreaks of food poisoning or measles and that flu season doesn’t kick into gear early, at least during the government shutdown that has idled most work at the nation’s public health agencies.

More than half of staff at agencies overseen by the Department of Health and Human Services – some 40,000 employees — were slated for furlough under contingency staffing plans outlined by HHS.

That includes about 8,700 of the nearly 13,000 workers at the Centers for Disease Control and Prevention and about 6,600 of the nearly 15,000 employees at the Food and Drug Administration.

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It means the government’s daily work of tracking salmonella outbreaks, monitoring measles epidemics and inspecting worksites to ensure that food and drugs are safe has ground to a halt, the few officials still on the job told NBC News.

“The vast majority of CDC’s activities will shut down completely,” said Barbara Reynolds, a CDC spokeswoman. “Our public health response will be slowed.”

For instance, CDC will not be conducting multi-state foodborne illness outbreak investigations, although local health departments will stay on the job.

Bare-bones emergency operations will continue, but at a reduced level. At the FDA, high-risk recalls for food and drugs will continue, and the U.S. Department of Agriculture will continue meat inspections despite the shutdown.

But surveillance for the start of flu season and for emerging infectious diseases such as H7N9 and MERS will be “weakened,” Reynolds said.

At the same time, other agencies will be cutting back significantly as well. The National Institutes of Health, for instance, where nearly 14,000 of nearly 19,000 employees were set for furlough, will continue care for current patients, but will not admit new patients during the shutdown. Research will be halted temporarily, including clinical trials.

Of course, all of this delayed work will have to be made up when the government reopens. Staffers at the National Center for Health Statistics asked reporters to withhold embargoed reports on the nation’s health until business as usual resumes.

“We’re obviously sorry for this inconvenience,” said Jeff Lancashire, an agency spokesman.