“We are doing what we can to mitigate any risk to consumers through the shutdown,” Gottlieb said.

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The Center for Science in the Public Interest, a nonprofit advocacy group, described the inspection reductions as unacceptable.

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“That puts our food supply at risk,” said Sarah Sorscher, deputy director of regulatory affairs at the group. “Regular inspections, which help stop foodborne illness before people get sick, are vital.”

Foodborne illnesses are a major problem in the United States, sickening 48 million people each year and killing 3,000, the Centers for Disease Control and Prevention estimates.

Food inspections are just one of the public health and safety efforts that have been cut or curtailed during the shutdown, now deep into its third week. The federal government also keeps airplanes from colliding, inspects pharmaceutical drugs, pursues criminals and defends against possible terrorist and cyberattacks. It is a 24-7-365 effort to make Americans safer.

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But a shutdown upends the calculus of risk management as agencies including the FBI, Coast Guard, Secret Service, FDA, Federal Aviation Administration and Agriculture Department face drastically reduced resources.

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“You can’t shut down the United States government at this magnitude and expect that everything’s going to be hunky-dory,” said Bruce McIndoe, founder and president of WorldAware, a risk management firm with corporate clients around the globe. “You’re going to see a much higher risk of a failure in the system.”

Every federal agency has to make a judgment call about what to go without. Who is essential? Who is not? This is not simply about people, but also about functions. The government has operational mandates.

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Some of the results are clearly visible, as in the much-publicized cases of trash piling up in national parks. But there are subtler and more significant effects involving government functions that are unseen by most Americans but have far greater effects.

The FDA, for example, typically conducts about 160 routine food inspections a week in the United States, with about a third involving high-risk processing facilities, Gottlieb said.

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The agency’s inspectors look for problems such as unsanitary conditions, insect infestations, and salmonella and E. coli contamination — as it did, for instance, in the recent investigations of romaine lettuce.

Gottlieb said that legal guidance from the 2013 shutdownsaid the agency could not conduct regular food inspections during a funding shortfall. But after canceling more than 50 high-risk inspections, he said he has sought authority to call back about 150 furloughed inspectors to focus on high-risk facilities.

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The agency is continuing to inspect foreign manufacturers, imports and domestic producers involved in recalls or outbreaks, and places where inspectors suspect there may be a problem.

The U.S. Department of Agriculture operates in parallel with the FDA, inspecting meat, poultry and egg products, and those inspections have continued, according to a shutdown plan forwarded by a USDA representative.

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About 60 percent of the FDA’s activities are funded by user fees, which enable the agency to continue many operations, at least for now, including drug and device reviews. About 40 percent of the agency’s activities, including most of its food-related work, are paid for by appropriations, which have not been approved by Congress.

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Even by the standards of previous shutdowns, this event has been chaotic. It came on quickly, amid false expectations that a political deal over the budget was close. The Trump administration was not fully prepared for the cascading effects of closing major departments and halting the gears of the bureaucracy.

The Secret Service is mostly at work. But even there, according to the Department of Homeland Security’s shutdown plan approved last year, 1,242 of the 7,222 employees are deemed nonessential.

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In DHS’s Cybersecurity and Infrastructure Security Agency, 1,523 of the 3,531 employees are considered nonessential.

DHS’s Countering Weapons of Mass Destruction Office is two-thirds unstaffed. The DHS shutdown guide states that only 65 of the 204 employees of the Countering Weapons of Mass Destruction Office will remain on the job during a funding shortfall. The rest go home.

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McIndoe, the WorldAware president, listed multiple areas of concern for his clients who rely on commercial aviation, including stress on the Transportation Security Administration, where employees may quit if not paid and where there have been media reports of workers calling in sick in unusually large numbers — reports denied by TSA.

Another concern is air traffic control, a system that McIndoe said was chronically underfunded before the FAA ran out of money during the shutdown. He noted that the FAA’s functions are highly specialized and that if workers quit, they cannot quickly be replaced.

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As the shutdown continues, questions about safety and security issues are drawing more attention. On Tuesday, Rep. Bennie Thompson (D-Miss.), chairman of the House Committee on Homeland Security, issued 10 questions for DHS, all touching on security.

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He asked whether the office charged with countering weapons of mass destruction is still able to share bioterrorism and nuclear-threat information with state and local officials.

He also wanted to know whether the Cybersecurity and Infrastructure Security Agency is still inspecting high-risk chemical facilities.

DHS officials did not immediately respond to Thompson’s questions. The bulk of the department’s legislative affairs team has been furloughed.

But Tyler Q. Houlton, the department’s press secretary, said that most of the agency remains on duty and is “fully prepared to protect the homeland and keep Americans safe during this lapse in government funding.”

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Unions representing federal workers, and nonprofit organizations aligned with progressive causes, are less sanguine. The Air Line Pilots Association, International, the union representing pilots, sent a letter to President Trump saying the FAA has fewer inspectors on duty than are required “to ensure the air traffic control infrastructure is performing at its peak levels of performance.”

The letter, signed by Capt. Joe DePete, president of the union, urged Trump to “immediately end the shutdown of government agencies that is affecting the safety, security and efficiency of our national airspace system.”

New York University political scientist Paul Light noted that the federal government does a great deal of risk monitoring, ideally to anticipate major problems and be prepared to react to them. That work is compromised during a shutdown, he said.

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“Shutdowns are a perfect way to force a breakdown,” Light said. He has spent much of his career studying these breakdowns, which include the U.S. failure to anticipate the 9/11 terrorist attacks and the country’s slow response to the 2014 Ebola crisis.

“They have to be totally alert. This shutdown is producing enormous distraction even for agencies that are open,” Light said.

That thought was echoed by David Berteau, president and chief executive of the Professional Services Council, which represents about 400 companies that have contracts with the federal government.

“Under the shutdown, the government is forced to shift from detection and prevention to after-the-fact response — which more than likely is going to be too little, too late,” Berteau said.