Table 4 Findings and recommendations

Suggested SNP thresholds for evidence of transmission are heterogeneous and sensitive to the finding of epidemiological links, SNP calling protocols and culturing/sampling, thus potentially are not transferrable between settings and/or studies

When setting study-specific SNP thresholds consider the time between samples, mutation rate, evolutionary pressure the strain may have been subjected to, and the endemicity of strains. Consider alternative approaches for determining transmission, including Bayesian approaches

The distinction between relapse and re-infection for repeated instances of TB disease has been made empirically (by examining the distribution of SNP distances between the initially infecting and subsequently infecting strains)

While existing thresholds appear adequate for clinical trials, consideration of epidemiological and clinical data is important, as well as a better idea of the within-host mutation rate when more accurate classification is required

The lack of diversity within M.tb complicates the use of WGS for inferring transmission patterns (17/25 studies found identical samples). Recent case studies show that there may be more diversity that is not identified by commonly used WGS methods

Deep sequencing, multiple samples and looking at shared minor variants (mutations present at low frequencies) will enhance detection of diversity. Epidemiological data, and consideration of associated uncertainty due to missing contact information, will also be necessary

Examining resistance-conferring mutations shared by phylogenetic clusters is a common method for identifying transmission of drug-resistant strains. However, phylogenetic clusters do not necessarily correspond to transmission clusters

Reconstruction of the transmission tree followed by an examination of the drug resistance patterns between linked individuals may be more appropriate