Illuminae by Amie Kaufman and Jay Kristoff.
Illuminae brings the science fiction thriller to a YA audience. I'm not aware of a lot of real science fiction being written for young readers. Note that all the other Speculative Fiction nominees were fantasy. Illuminae also has an interesting format. Like World War Z (the book, not the abysmal movie), it's an account of a disaster that is already over. The basic premise is that a tech group has collected information about the aftermath of an attack on an illegal mining colony and the ordeal the survivors suffered after they are evacuated . We don't know who is doing the collecting or who the information was collected for. So the story is told with documents--various types of reports, communications, transcripts of videos, etc., and a little commentary from the mystery technician. This can be risky, in my opinion. There's always the possibility that all the shifts will slow down narrative drive. And thrillers are all about narrative drive. No problem here. Drive, drive, drive.
Oh, and there's a plague. That's always good. And some neat plot twists at the end. And I haven't even started on the clever main characters and the little role reversal thing they've got going on, with Kady being the heroic nerd going all out to save Ezra, her guy in distress. Plus there's a sequel, Gemina, which offers a different setting and some new characters. I would read that.
Check out the YA Speculative Fiction Committee's write-up on Illuminae, as all as all the other Cybils winners.