Food inspections, assessing health effects of toxic chemicals and cash assistance for groceries – all are services performed by the federal government, and all are now frayed by the partial government shutdown.

The US Food and Drug Administration, responsible for inspecting more than 80,000 food facilities, has curtailed inspections. The Agency for Toxic Substances and Disease Registry has suspended health exposure assessments. Cash assistance to buy groceries, commonly called food stamps, are funded through February – but beyond that is a question mark.

As the partial US government shutdown appears to be heading into its fourth week over a row of border wall funding, funds for programs like these increasingly look like reservoirs in a drought, with bureaucrats shuffling money to keep taps flowing but little more than uncertainty on the horizon.

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Advocates say that puts public health at risk, delays long-term risk planning, and harms vulnerable communities which depend on government programs.

“The federal government should not be held hostage to a political negotiation,” said Sarah Sorscher, the deputy director of regulatory affairs at Center for Science in the Public Interest. “And our food safety shouldn’t be held hostage.”

The FDA is responsible for ensuring the safety of about 80% of the US food system. Inspectors looking for “rodents, feces, unsanitary practices” at even high-risk facilities have been furloughed. A small number are expected to resume work mid-January, but it still leaves a huge chunk of the food system at risk, Sorscher said.

“The longer the shutdown goes on, the greater the chances this disruption is going to lead to consequences for consumers,” said Sorscher. “It could mean having more filth in our food, and it could mean foodborne illness.”

She went on: “You shouldn’t have to think about whether your food is safe or not, it should be safe.”

Meanwhile, advocates said the shutdown has already damaged communities who rely on subsidies and other food assistance, to say nothing of the federal employees working without pay to administer them.

“Families may not fully understand that Wic is open for business. Retail grocers may not understand Wic is open for business,” said Douglas A Greenway, the CEO of the National Wic Association, about the Women, Infants, Children (Wic) food subsidies program. WIC programs feed more than half the infants born in the United States.

“There are two examples of Wic retailers who posted signs that said, because of the government shutdown they are not accepting Wic instruments,” said Greenway. The retailers were corrected, Greenway said, but they show the shutdown “does real damage to the program and does real damage to the families served by the program”.

Roughly one-quarter of US government workers are furloughed, and an estimated 800,000 work without pay. Most contractors will not receive back pay. Reassurance that programs such as food stamps would remain funded came only in week three of the shutdown. Schools that provide free and reduced-price meals to children in poverty are operating on grants likely to run out before the school year is over.

Trump precipitated a government shutdown on 21 December 2018, after Congress – then controlled by Republicans – failed to pass a government spending bill. The stalemate has dragged on since, as congressional Democrats offered to pass a spending bill, but refused to provide the $5.7bn necessary to construct the wall. Recent attempts to negotiate have offered little hope to an end to the shutdown.

Although most public health services remain open – including those which monitor the flu, operate public health insurance programs such as Medicare and Medicaid, and inspect food at the border – those considered “non-essential” have come to a halt.

Preventive health clinics and food pantries run by the Indian Health Service are shut down, and only services that meet the “immediate needs of the patients, medical staff, and medical facilities”, continue.

The Agency for Toxic Substances and Disease Registry is operating with a bare-bones staff, and can’t provide exposure assessments or technical assistance to local and state partners. Their capacity to ensure safe drinking water is limited.

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Many of those furloughed at the Agency for Toxic Substances and Disease Registry, “are doing long-term research that is important to public health”, said Sorscher. “It could impact our ability to plan for the future.”

The National Science Foundation, which has typically already given out nearly $100m in grants by mid-January, has completely stopped payments and review of applications.

“Federally funded science supports the economy, it’s a job creator,” said Benjamin Corb, a spokesperson for the American Society for Biochemistry and Molecular Biology. “If you want to talk about American competitiveness, it’s not a great idea to add unnecessary pressures to the system that makes America a global leader in scientific innovation.”