The Argentine striker was limping as he was withdrawn with 13 minutes remaining at the Etihad Stadium and while Guardiola says it is too early to know how serious the muscular problem will be, he admitted he has some initial concerns.
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There was better news regarding Rodrigo and David Silva, who also appeared to be carrying knocks when they came off in the second half, but the boss is not expecting the midfield duo to be out for any length of time.
“It doesn’t look good for Aguero,” he said. “It’s muscular.
“The doctor said we will see tomorrow. I’ve no idea how long he will be out.
“For Rodri and Silva it is more tiredness and cramps.
“Rodri was out for a month and games like today are so demanding, but with determination and suffering in certain moments, we did it.”
Both City and Chelsea played their part in an entertaining game which had plenty of attacking intent.
The visitors started better at the Etihad, where Guardiola‘s side had less possession than the opponents for the first time in his managerial career, but he was pleased with how his players responded to the early dominance of a team he was left hugely impressed by.
“We scored a goal when they were better,” he added.
“Normally we believe to score you have to be better, but they were in that moment.
“Before the goal from Kante it was tight and after we suffered. We created chances after that to score more goals.
“With the problems we have with injuries, we beat an incredible, top side. I judge managers on courage to play and Chelsea are [courageous].
“They have a fantastic team. [It is a] great victory for us and we will see.”