I experience exactly the same problem with 2 sites that I updated recently to WP 4.6 ! It is worst when I log in on back-end. Physical Memory Usage and I/O Usage goes crazy! I really do not know what to do! I’m quite sure it is about the 4.6 update, otherwise it is a really strage coincidence. I hope there will be a bug-fix from wordpress very soon.
My sites are https://tutoriale-video.ro/
and https://www.exe.org.ro/