Mix cream cheese, confectioners’ sugar, 2 tablespoon milk, and 1 teaspoon vanilla extract in a bowl until smooth and creamy; fold in 1 cup blueberries.
Cover the bottom of a 10×14-inch baking dish with 1 layer bread cubes. Spread cream cheese mixture over bread layer; top with remaining bread cubes.
Whisk 2 cups milk, eggs, 2 teaspoons vanilla extract, cinnamon, and nutmeg together in a large bowl; pour over bread mixture. Sprinkle 1 cup blueberries over bread-egg mixture. Cover dish tightly with aluminum foil and refrigerate, 8 hours to overnight. Remove from refrigerator 30 to 60 minutes before baking.
Preheat oven to 375 degrees F (190 degrees C).
Bake in the preheated oven for 45 minutes. Remove foil and continue baking until center is set, about 30 minutes.
If cream cheese mixture is too thick, add more milk.
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