Shortest Path still applies; you just need to change your thinking. Rather than include edges between every city on your route, translate Route 1 into Vertices at Edirne and Istanbul and a single edge between them (weighted to your route length). Ignore the fact that it goes through Kirklareli.
Do the same for your other routes and you'll have something like
Edirne--1--Istanbul--2--Zonguldak
|
3
|
Afyon--4--Anatlya
Then you can apply a shortest path and you'll find that Edirne to Anatlya is 1-3-4, which you then translate back into the full route (Edirne - Kırklareli - Istanbul - Isparta - Anatlya)