I have a previously rooted Nexus 5 on 4.4 and updated it recently with the Lollipop OTA. I am trying to re-root it again but it is not recognized using my Windows 7, Windows 8 or Ubuntu 14.04 machines. I have tried the WUG toolkit on windows by installing and reinstalling the drivers and adb on linux, turning on/off the Developer-usb-debugging mode, turning on-off the MTP mode. I was previously using TWRP. Now when I go to recovery mode, the phone shows "No command" with the green droid.
Perhaps it is issue of USB connector. Most of the times due to dust it does not get proper contacts on USB pins and its not recognized over USB. Try to check that.