In a food processor or blender, pulse the bread and sage leaves into fine crumbs. Add to a small bowl and toss with olive oil. Set aside.
Heat a large pot over medium heat with olive oil. Saute the onions with salt and pepper until golden, about 10 minutes.
Add the butter to the pot and melt. Stir in the flour and cook for about 2 minutes.
Slowly whisk in the milk until smooth. Then add the pumpkin puree and thyme sprigs. Gently simmer for about 8 minutes, until thickened. Make sure to stir often.
Remove the thyme sprigs and add in the cheddar, gruyere, and 2 ounces of fontina. Stir until the cheese is melted.
Add in the prosciutto and mix until all ingredients are thoroughly combined. Season with nutmeg, salt, and pepper. Turn the heat to low.
Preheat the oven to 400°F. Cook the pasta in salted boiling water until several minutes shy of packaged instructions.
Add the cooked pasta to the sauce pot and stir until fully coated. Transfer the mac and cheese to a greased baking dish. Sprinkle with the remaining fontina cheese and top with desired amount of sage breadcrumbs.
Bake for 15 minutes, until the cheese is melted and the breadcrumbs are golden brown.
Serve warm and enjoy!