For jungle look for people that he can't get a lead from early but can scale hard later on. In the ekko mains discord the most common counters in the jungle would be kindred and nidalee, mostly because of how they can beat him (keyword can, since you need to know those champs) at all stages of the game. For midlane you literally just lock kassadin galio or irelia and it's basically one of the easiest matchups of all time, unless you first time the champs and don't know what to do
Personally I'd play Rek'Sai or Warwick into him as they both have stronger early games. You might have to find a pick that works for you, depending on your champion pool. Maybe check out win rates and see if there are any champions you play that tend to win against Ekko.
As for items, obviously magic resist is a good option. Honestly in a lot of cases you don't need to worry about itemizing against him if you can beat him early. Ekko only necessitates MR once he gets a few AP items or if he's way ahead of everyone. If you're playing a tank jungler, getting magic resist is obviously going to give you a better shot of dealing with him in fights.
Gameplay-wise, he has a lot of mobility, so whatever you pick needs to be able to fight him or he'll just force you out of your jungle. You don't really need to chase him, just blowing his cooldowns and getting him low can be good enough. Once he has ult, he'll try to bait your major cooldowns and then reset his health bar to win fights. Especially in team fights, make sure you and your team don't blow everything at the start before he uses ult.
As for items, obviously magic resist is a good option. Honestly in a lot of cases you don't need to worry about itemizing against him if you can beat him early. Ekko only necessitates MR once he gets a few AP items or if he's way ahead of everyone. If you're playing a tank jungler, getting magic resist is obviously going to give you a better shot of dealing with him in fights.
Gameplay-wise, he has a lot of mobility, so whatever you pick needs to be able to fight him or he'll just force you out of your jungle. You don't really need to chase him, just blowing his cooldowns and getting him low can be good enough. Once he has ult, he'll try to bait your major cooldowns and then reset his health bar to win fights. Especially in team fights, make sure you and your team don't blow everything at the start before he uses ult.
If you want to play against him in jg sust use a tank with magic resist or cc (Amumu or Maokai).