19 Yr Old F. Thin-built (100 Lbs.) With Juvenile RA

19 yr old F. thin-built (100 lbs.) with Juvenile RA and hemolytic anemia (hgb=9) with elevated Alk Phase (750), normal bilirubin, elevated ALT (100), AST (300), gamma-GT(1456) and LDH(950). PT is normal and serology is negative. Albumin is decreased(2.2). She had been treated with Methotrexate (<6 months), on prednisone 30mg/day. No history of alcohol or ilicit drugs intake. Recently presented to ER with fever, found to have septicemia with MSSA, given Ancef . A few days later underwent EUS-Bx. of liver which showed mild to moderate fatty change and mild pericellular fibrosis without evidence of inflammation, septal or bridging fibrosis.
What is the most likely cause of her liver disease and reason for elevated Alk phosphatase? What is the best advice for her treatment?