WASHINGTON – In a filing in federal court two weeks ago, the U.S. attorney in Sacramento named as the defendant 97 wedges of Gouda cheese. The co-defendant was 14 blocks of white cheddar, including the sage, white pepper and onion varieties.

It was an apt, if odd, quirk in an arcane legal process, as the government took steps to seize the cheese — 40 tons of it.

The Gouda and cheddar were made by Bravo Farms, a small artisanal cheesemaker whose award-winning morsels were linked to an outbreak of E. coli O157:H7 illness that sickened at least 38 people.

By invoking civil forfeiture law, the government could take immediate possession of the suspect cheese and prevent it from entering the food supply.

Cheese, it turns out, has been on the defensive over the past year, as federal regulators rachet up their scrutiny of a growing segment of the food business: artisanal cheesemakers.

Since April, the Food and Drug Administration has increased inspections of cheesemaking facilities, launched a review of its regulations and been reassessing the health risks posed by specialty cheeses.

Regulators say they are trying to prevent and reduce serious illnesses caused by contaminated cheese. Over the past five years, according to the FDA, more than 400 illnesses were caused by outbreaks involving raw milk cheese, leading to 87 hospitalizations, a stillbirth and two miscarriages.

But artisanal cheesemakers, and their boosters in the local food movement, say they are being unfairly targeted. They say the FDA does not understand their craft and is trying to impose standards better suited for industrial food companies.

The conflict is emerging particularly around cheese made from raw milk, especially soft cheeses — the kind that have inspired devotion from foodies and can garner $27 a pound in high-end markets.

As part of its new emphasis on cheese safety, the FDA is re-examining its rules on raw milk cheese and is likely to propose changes within the next several months.