In order to use Windows Authentication with sqlalchemy and mssql, the following connection string is required:
ODBC Driver:
engine = sqlalchemy.create_engine('mssql://*server_name*/*database_name*?trusted_connection=yes')
SQL Express Instance:
engine = sqlalchemy.create_engine('mssql://*server_name*\\SQLEXPRESS/*database_name*?trusted_connection=yes')