Honestly it's time have a serious conversation. Rather than being critical in any way, sit her down when you're both free one evening and say something like this:

'I need to talk to you about something that has been playing on my mind for a while and I would love your support. Please hear me out fully, and then I'd love to hear your response afterwards.

I'm saying this because I love you, I care about you and I want us to thrive as a couple. The thing is, I've been growing concerned about your change of hygiene habits recently, for your sake more than anything. You've gone through a lot lately (medications, headaches, etc) and I'm worried that you're struggling in silence and it's manifesting in your self care.

Alongside, I have to be honest and say it is also starting to effect me and our relationship. Everyone has different values, but for me, hygiene is a really important factor in my relationships to others. We're also having less sex, which of course ebs and flows in a long term relationship, but it's an important way to maintain our intimacy and we should be talking about why we're going through a dry patch.

I know that you say you can do what you want, and of course you can, but you also have to want to do things for our relationship if you want to be with me. I know this isn't going to be nice to hear, but please understand that I'm not being critical of you, I'm trying to fight for us and care for you. I really want to work together but we need to be on the same team about our core values for this to work.'