Validation of potential mutations identified in the complete genome sequence of isolate 3 relative to isolate 2 as well as both reference strains.

Potential mutations were prioritized using the product quality score (see Methods). Primers used for amplification and sequencing are indicated. The nine highest quality scores (above ‘…..’) as well as several mutations with lower scores (below ‘…..’) were validated. ‘Correct’ indicates that the mutation found by complete genome sequencing was validated using conventional PCR and sequencing methods; ‘incorrect’ indicates isolate 3 did not differ from isolate 2.