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Justin Edinburgh praised his players’ resilience after recovering from a double injury blow to beat Southend again on Tuesday night.
For the second time in four days they left Roots Hall 3-1 winners, this time in the first round of the League Cup.
Gillingham lost Max Ehmer to concussion and Bradley Dack to a knee injury, shortly before Southend went ahead.
But Cody McDonald levelled the scored after the break and Jay Emmanuel-Thomas’ brace clinched the win.
Edinburgh said: “It was a difficult night for us again, in terms of injuries and disruption, but credit to the players. They showed great resilience and got the victory.
“We were disappointed to have gone behind in the game. The two injuries really disrupted us so early in the game but it was brilliant to overcome that and win the game.”
Gillingham must now wait to learn the extent of both players’ injuries.
For the second time in four days the Gills found themselves a goal down. Keeper Stuart Nelson was unable to prevent Southend’s Stephen McLaughlin from prodding the ball out of his grasp.
Nelson had let a McLaughlin shot slip under him at the weekend.
Edinburgh said: “The players showed their spirit and that they are determined enough not to let that affect them and to make sure we help our team-mates out if there is an error or costly mistake.
“I said to Stuart, ‘it is best to get them out of the way when they are not costly’, which they haven’t been. The team pulled themselves up and at times looked really fluent and affective going forward.”
Emmanuel-Thomas came off the bench to score the winning goals, making it three goals in two games for the on-loan QPR man.
Edinburgh said: “They were classy finishes...that’s what we brought him here for.”