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Pedro can be defeated by Claire and Moira during their part of the campaign, in which case Barry and Natalia will not encounter him, and instead will find the drill earlier, giving them access to a secret room.
Access to this room is necessary in order to collect all of the insect larvae during Chapter 2. There is also some Magnum ammo that the player cannot get otherwise from this area.
It is also notable that if not defeated by Claire, Pedro is the only Afflicted encountered by Barry since his mutation is the most recent comparing to the other Afflicted which were already transformed to Rotten.