Preheat oven to 350 degrees F. Spray a 9x13- inch baking dish with nonstick cooking spray; set aside. Cook pasta according to package directions; drain and set aside.
Add ground beef, onion, pepper and mushroom to a large skillet over medium-high heat. Cook, breaking up meat, until cooked through and vegetables are tender. Add garlic and cook for an additional minute.
Add ketchup, Worcestershire sauce, salt and pepper to the skillet and stir to combine. Mix cooked pasta and meat sauce together until combined. Spread shell mixture into prepared pan and set aside.
Melt butter in a saucepan over medium-high heat. Add flour and whisk for 1-2 minutes or until golden brown. Whisk in milk and salt until smooth and let simmer for a few minutes, until thickened.
Remove from heat and stir in cheese until smooth. Pour cheese sauce over shells and bake, uncovered, for 15 minutes.