Human genetic ancestry, Mycobacterium tuberculosis diversity and tuberculosis disease severity in Dar es Salaam, Tanzania

Reviewer #1 (Public review):

Summary:

This Tanzanian study focused on the relationship between human genetic ancestry, Mycobacterium tuberculosis complex (MTBC) diversity, and tuberculosis (TB) disease severity. The authors analyzed the genetic ancestry of 1,444 TB patients and genotyped the corresponding MTBC strains isolated from the same individuals. They found that the study participants predominantly possess Bantu-speaking genetic ancestry, with minimal European and Asian ancestry. The MTBC strains identified were diverse and largely resulted from introductions from South or Central Asia. Unfortunately, no associations were identified between human genetic ancestry, the MTBC strains, or TB severity. The authors suggest that social and environmental factors are more likely to contribute to TB severity in this setting.

Strengths:

In comparison to other studies investigating the role of human genetics in TB phenotypes, this study is relatively large, with more than 1,400 participants.

The matched human-MTBC strain collection is valuable and offers the opportunity to address questions about human-bacterium co-evolution.

Weaknesses:

Although the authors had genome-wide genotyping and whole genome sequencing data, they only compared the associations between human ancestry and MTBC strains. Given the large sample size, they had the opportunity to conduct a genome-wide association study similar to that of Muller et al. (https://doi.org/10.1016/j.ygeno.2021.04.024).

The authors tested whether human genetic ancestry is associated with TB severity. However, the basis for this hypothesis is unclear. The studies cited as examples all focused on progression to active TB (from a latent infection state), which should not be conflated with disease severity. It is difficult to ascertain whether the role of genetic ancestry in disease severity would be detectable through this study design, as some participants might simply have been sicker for longer before being diagnosed (despite the inquiry about cough duration). This delay in diagnosis would not be influenced solely by human genetics, which is the conclusion of the study.

Additionally, the study only included participants who attended the TB clinic.

Including healthy controls from the general population would have provided an interesting comparison to see if ancestry proportions differ.

Although the authors suggest that social and environmental factors contribute to TB severity, only age, smoking, and HIV status were characterised in the study.

Reviewer #2 (Public review):

Summary:

This manuscript reports the results of an observational study conducted in Dar es Salaam, Tanzania, investigating potential associations between genetic variation in M. tuberculosis and human host vs. disease severity. The headline finding is that no such associations were found, either for host / bacillary genetics as main effects or for interactions between them.

Strengths:

Strengths of the study include its large size and rigorous approaches to classification of genetic diversity for host and bacillus.

Weaknesses:

(1) There are some limitations of the disease severity read-outs employed: X-ray scores and Xpert cycle thresholds from sputum analysis can only take account of pulmonary disease. CXR is an insensitive approach to assessing 'lung damage', especially when converted to a binary measure. What was the basis for selection of Ralph score of 71 to dichotomise patients? If outcome measures were analysed as continuous variables, would this have been more sensitive in capturing associations of interest?

(2) There is quite a lot of missing data, especially for TB scores - could this have introduced bias? This issue should be mentioned in the discussion.

(3) The analysis adjusted for age, sex, HIV status, age, smoking and cough duration - but not for socio-economic status. This will likely be a major determinant of disease severity. Was adjustment made for previous TB (i.e. new vs repeat episode) and drug-sensitivity of the isolate? Cough duration will effectively be a correlate/consequence of more severe disease - thus likely highly collinear with disease severity read-outs - not a true confounder. How does removal of this variable from the model affect results? Data on socioeconomic status should be added to models, or if not possible then lack of such data should be noted as a limitation.

(4) Recruitment at hospitals may have led to selection bias due to exclusion of less severe, community cases. The authors already acknowledge this limitation in the Discussion however.

(5) Introduction: References refer to disease susceptibility, but the authors should also consider the influences of host/pathogen genetics on host response - both in vitro (PMIDs 11237411, 15322056) and in vivo (PMID 23853590). The last of these studies encompassed a broader range of ethnic variation than the current study, and showed associations between host ancestry and immune response - null results from the current study may reflect the relative genetic homogeneity of the population studied.