Table 2.

Methods studies used to confirm direction of transmission

Journal article	How was direction of transmission determined?
Didelot et al. [25]	Epidemiological data and WGS used in a Bayesian inference framework to construct a transmission tree
Gardy et al. [12]	Social network analysis and contact tracing posed putative transmission, timing of infection and smear status was used to narrow down possible direction and WGS to remove transmission events involving cases with different lineages
Kato-Maeda et al. [26]	Contact tracing and accumulation of SNPs
Luo et al. [16]	Epidemiological links and timing of infection and symptoms helped propose direction of transmission between isolates in the same WGS-based cluster. Transmission of mutant alleles from case with mixed base calls
Mehaffy et al. [13]	Genomic and epidemiological information (i.e. SNP pattern, contact information, year of diagnosis and infectiousness based on smear and chest X-ray results)
Pérez-Lago et al. [31]	In one case direction was proposed by the transmission of mutant alleles from a case with mixed base calls
Roetzer et al. [14]	Contact tracing revealed transmission chains and accumulation of variation is mentioned, although not clear if this resolved the order of the chain
Schürch et al. [24]	Accumulation of SNPs
Smit et al. [27]	Accumulation of SNPs and period of infectiousness