Sweet Potato–Parsnip Soup with Bacon Croutons

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6 tablespoons extra-virgin olive oil

1 large onion, sliced

2 leeks, halved lengthwise and sliced crosswise into half-moons

4 teaspoons fresh thyme

Kosher salt and freshly ground pepper

1 pound sweet potatoes (about 2), peeled and chopped

1 pound parsnips (2 to 3), peeled and chopped

4 cups low-sodium chicken broth

Pinch of cayenne pepper, plus more to taste

3 slices bacon, finely chopped

4 ounces crusty bread, cut into 3/4-inch pieces (about 4 cups)

3/4 cup shredded gruyere cheese

Creme fraiche, for topping