TABLE 3.

Critical knowledge gaps in tuberculosis (TB) epidemiology and the potential use of environmental sampling for Mycobacterium tuberculosis

Epidemiological areas related to TB	Potential use of environmental sampling and ideas for further investigation
Where does TB transmission occur?	Characterising M. tuberculosis abundance in various congregate settings, including public transit, schools, churches, restaurants, bars and workplaces
How much interindividual heterogeneity is there in community transmission?	Compare abundance of M. tuberculosis genotypes across settings
How does dose of exposure influence risk of TB progression?	Compare abundance of M. tuberculosis in household with risk of progression among household contacts
How long are individuals infectious prior to detection?	Whole genome sequencing of environmental samples and comparing dates of detection in the environment with date of diagnosis
How does an individual’s infectiousness change over time?	Assess rates of environmental contamination with specific isolates, identified by whole genome sequencing, over time
Was an intervention successful at reducing transmission?	Assess changes in M. tuberculosis abundance in congregate settings (e.g. hospitals, prisons, mines, schools] over time
Was an individual infectious when a potential exposure occurred?	Conduct environmental sampling at sites of potential exposure (e.g. hospital rooms]