Strictly speaking, the every is still optional, but for some reason, when you invert the order, as you have done, it sounds better to have it.
I was thinking about this after I posted. "One in a thousand" can be almost an idiom for "very, very few" but if you say "one in every thousand" is sounds more scientific. It's as though the first ("a thousand") is an estimate, but the second is an actual measurement. So for scientific writing, I'd recommend that you keep the every, but in conversation, you don't need it.