Encode sequences of integers for randomness testing

I need to test the randomness of multiple sequences of integers. All sequences have the same number of integers, all integers are of range [0, 55439] (including 0 and 55439). I'm planning to test them with the NIST test suite (http://csrc.nist.gov/rng).

The NIST test suite only accept binary streams, so I must encode those integers into binary strings of the same length. Since 55440 isn't a power of 2, I cannot use the binary representation of these integers. If the binary representation is used, the most significant bit of the the representation is more likely to be 0, which will result in false negatives.

How should those integers be encoded ?