The forward has failed to recover from an ankle injury he suffered in the club's north London derby defeat to Spurs on March 3 and will miss the return leg against his former club
The 27-year-old forward sustained an ankle injury during Arsenal's 2-1 defeat to Tottenham on March 3 and has failed to recover in time to face his former club.
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Jack Wilshere has already been confirmed as an absentee for the match against the Bundesliga leaders after failing to recover from an ankle injury, while Goal.com revealed on Tuesday morning that the Gunners are concerned that the midfielder's problem could be long term.
Arsene Wenger has also included Lukasz Fabianski, Abou Diaby, Andrey Arshavin and Kieran Gibbs to his 18-man squad for Wednesday night's fixture.
Arsenal suffered a 3-1 defeat at the hands of Bayern Munich in their last-16 first-leg clash at the Emirates on February 19.