Fig. 3: Comparison of the major attributes of each of the methods used to determine genetic similarity.
The number of isolate pairs below the intrapatient threshold was determined individually for each of the genomic methods and the epidemiological classification of isolate pairs only occurred for pairs below the threshold. The epidemiological classification process of the isolate pairs is detailed in the Supplementary Fig. 10. Pairwise comparison using de novo references (PCDR) was used as the gold standard genomic comparison method.
