This seems a bit extreme and not quite like a messy person. Leaving clothes on the floor for instance is something you can certainly be annoyed with, but typically of messy people, busy people, or people who don't care I guess. Having puke on the floor uncleaned and dishes so bad you have to throw them out, especially when she knows someone else is living there now strikes me more as something tied to a potential mental illness of some sort. Has she tried getting help for this at all? 

You do have choices. It is possible this could cause a break up. That is your choice. I have other ideas, but that's one that is there. You want compatible lifestyles in certain areas and to be able to work together. If it is a deal breaker, then it is. You could also set really firm boundaries around this. Maybe make a list of chores that need to be done and when. This should all be things she agrees to and not things you force of course, but it is fair to really expect her to follow through and have some sort of reasonable consequence if not. I'm not sure what that could be in this situation. It shouldn't be a punishment, but just a way of saying you won't tolerate it and it seems the only way you can do that would be leaving. This might take a little thinking through. If you are committed to making this work and understand where she is coming from (you didn't say what the excuses are) and you communicate and set boundaries and all else fails, I guess you could get more creative with getting a cleaning company or something. Or you could let it go and decide you clean if she helps out more in some other area of the relationship. I'm not recommending what is best here, just laying out all the options I can think of. 

This is a tough situation. You have every right to be mad and unhappy with what happened. I think getting to the root of what is going on with her and working on improvement through there may help best. I wish you the best of luck with it. Hopefully things improve or you are able to move out. If you plan a future together, this is good to know now. It might impact any decisions for moving into a house together or getting married or children or whatever.