Table 1 Criteria for including and excluding articles in this study

M. tuberculosis studies

Other species of Mycobacteria

Human TB

Animal TB or zoonotic transmission of TB

Whole genome sequencing of at least three M. tuberculosis isolates from distinct people

Less than three isolates from distinct people sequenced and studies designed to investigate isolates from less than three possibly epidemiologically-linked people

Clustering analysis based on 12 or less SNP rule for clustering or possibility to identify clusters of 12 or less SNP of difference

Lack of clustering analysis or clustering analysis based on strains differing by more than 12 SNP, impossible to impose 12 or less rule for clustering

Cluster after sequencing containing three or more isolates

Largest cluster after sequencing containing less than three isolates or impossible to determine clusters of three and more isolates

English language

Any other language than English

Original analysis

Repurposed data or review manuscripts

Study not available in full text