Table 1 PubMed Search terms and inclusion and exclusion criteria

Identify studies of Pathogen Biology using whole genome sequencing and analysis

`genome sequencing AND `tuberculosis AND (`drug resistance OR `virulence OR `immunogenicity OR `transmissibility OR `fitness)

All abstracts describing the use of WGS data to identify genes related to pathogen immunogenicity, virulence, transmissibility, drug resistance, or fitness

(1) Review articles

(2) Studies that published new sequence data only

(3) Studies that did not study MTB bacteria and its biology

In all PubMed fields

(4) Studies that only assess mutation rates in non-clinical settings