Preheat the oven to 375°.

Bring a large pot of salted water to a boil. Cook pasta until al dente. Drain, toss with a splash of oil to prevent sticking and place in large bowl.

While the pasta is boiling, starting cooking the bacon. Heat a 8- or 9-inch cast iron skillet over low heat, and add the bacon.

Cook, stirring occasionally, until crispy. Using a slotted spoon, remove the bacon from the pan and set aside.

Whisk the flour into the bacon fat to create a roux. Cook, stirring, for 1 to 2 minutes. Add the nutmeg and cook for an additional 30 seconds.

Gradually whisk in the milk. Bring to a boil and reduce the heat to a simmer. Cook on low heat for about 5 minutes. Season with salt and pepper to taste.

Remove from the heat and whisk in the cheeses until melted.

Stir the cooked pasta into the sauce followed by the crispy bacon and jalapeños.

Top with the breadcrumbs, and bake until golden brown and bubbly, about 35 minutes.