Your baby is likely to be suffering from hyper pigmentation post infection which will disappear with time.
However you mentioned a lump below the skin lesion ; maybe the infection has not yet got corrected.
Does the skin lump painful on touch ? If it is then you need to get him examined again by his doctor for oral antibiotics
or topical cream.
There is a limitation on diagnosing skin condition on mere history one needs to have a closer look,hence kindly get in touch with his doctor.