Molecular typing using repetitive sequenced-based PCR (rep-PCR) and sequencing were applied to a collection of diverse complex isolates. To determine the most practical method for reference laboratories, we analyzed 71 complex isolates from sporadic and outbreak occurrences originating from 4 geographic areas. While rep-PCR was more discriminating, sequencing provided a broader and a more objective geographical tracking method similar to multilocus sequence typing (MLST). In addition, we suggest that MLST may have higher discriminative power compared to sequencing, although rep-PCR remains the most discriminative method for local outbreak investigations. In addition, rep-PCR can be an effective and inexpensive method for local outbreak investigation.