What is an egg?

That's the question Panera wants the Food and Drug Administration to answer.

The restaurant company is known for its focus on healthy and fresh food and for challenging its competitors to step up their food game. This time, it's targeting the eggs in their breakfast sandwiches.

"Panera and our competitors use the FDA definitions to guide our product descriptions and names," said Sara Burnett, director of wellness and food policy at Panera. "But in the case of 'eggs,' we have no guidance. Brands can say they offer an egg sandwich, but sell an egg product that contains multiple additives."

Burnett said a number of competitors — such as Burger King, Taco Bell and Dunkin — sell egg patties that contain more than five ingredients.

Over the last four months, Panera has slowly swapped out the eggs that it uses in its breakfast sandwiches. Previously, the company hard-fried its eggs in a circular template on the grill to firmly cook the egg and shape it to better fit within the sandwich. Now, it's cracking extra large pasteurized eggs right on the flattop, cooking them over-easy and serving them on a brioche bun nice and runny.

It took the team at Panera about 18 months to perfect a cooking technique that created a delicious egg and could be replicated by cooks at all of its restaurants.

Panera has long been shedding artificial ingredients and preservatives from its menu. In early 2017, the company completed its review of more than 450 ingredients and announced that its menu was "100 percent clean."

This new egg is no exception.

Panera is petitioning the FDA to define the term "egg" to better inform consumers about what they are getting when they order "egg" from a restaurant. Currently, there is no clear definition, Burnett said.

The restaurant has challenged its competitors on a number of fronts in recent years, adopting new welfare programs for livestock, cleaning up its bacon and calling out McDonald's sugary kid's meals. Panera even ruffled the feathers of Chipotle, leading the pair to quibble over what constitutes a truly additive-free menu.

"The mission is not to call people out or claim that we are holier than thou," CEO Blaine Hurst told CNBC. "We want to start a conversation about transparency."

Hurst took the post of CEO from Ron Shaich late last year and is continuing the company's commitment to creating food that tastes good and is good for you. He said that Panera will focus a bit more on the breakfast category in the future, having spent much of the last few years honing in on the lunch menu, ramping up delivery and integrating technology into all facets of the restaurant.

The breakfast space has become popular with restaurants, particularly for fast-food chains, in the last few years. Taco Bell dabbled with waffle tacos and A.M. Crunch Wraps in 2014, and McDonald's launched its all-day breakfast menu in 2015. Since then, a number of chains have sought to beef up their morning offers in hopes of seeing a sales boost.

As of 2016, breakfast is about 12 to 15 percent of total food-service sales, according to Technomic data.