Preheat oven to 375°.
Place bread cubes in a 1 1/2-quart baking dish coated with cooking spray.
Heat a large nonstick skillet over medium-high heat. Coat pan with cooking spray. Add onion to pan; sauté 3 minutes or until tender. Add spinach and garlic; sauté 2 minutes or until spinach wilts. Remove from heat.
Combine thyme, salt, black pepper, egg whites, and egg in a medium bowl; stir with a whisk. Stir in the spinach mixture and tomato. Pour egg mixture over bread cubes in baking dish; sprinkle with cheese.
Bake at 375° for 20 minutes or until set; let stand 5 minutes.