Pulmonary tuberculosis (TB), a disease of public health importance, is caused by pathogenic members of the Mycobacterium tuberculosis complex (MTBC), such as M. africanum (Maf) and M. tuberculosis sensu stricto (Mtbss). Each species comprising several clades of specific strains show variable virulence and disease-causing mechanisms (Yeboah-Manu et al., 2011; Delogu et al., 2013; Reiling et al., 2013; Brites and Gagneux, 2015). While Maf is restricted to West African countries including Ghana, Mtb is responsible for TB cases worldwide (Gagneux and Small, 2007). As a disease transmitted through aerosol, (Delogu et al., 2013), it is expected that susceptible immunocompetent individuals who come into contact with aerosol(s) containing viable bacteria will be equally infected. However, in about 90% of infected individuals, the host immune system can wall off the site of infection in a granuloma (Ghon complex) (Malik and Godfrey-Faussett, 2005; Gagneux et al., 2008; Yeboah-Manu et al., 2011). However, with the remaining 10%, only 5% will potentially develop active TB disease within 2–3 years of infection, while the remaining 5% may develop TB later in their life (Sakamoto, 2012; Fattorini et al., 2013; Narasimhan et al., 2013). This unique differential infection propensity depends on the interplay between the genetic makeup of the human host (Thye et al., 2010; Oki et al., 2011; Thye et al., 2012; Chimusa et al., 2014; Kinnear et al., 2017), the environment, and socioeconomic factors (Cheng et al., 2017; Mohidem et al., 2018).

In recent years, genetic association studies between important genes and susceptibility to infectious diseases such as TB, Malaria, and HIV using linkage and genome-wide association (GWAS) have been reported (Comstock, 1978; Pydi et al., 2013; McHenry et al., 2020). With these studies, several genes have been reported to be associated with TB, including Toll-like receptors (TLRs), cytokines/chemokines, and their receptors leukocyte antigens (HLAs), SLC11A1, major histocompatibility complex-(MHC), mannose-binding lectin (MBL), vitamin D Receptor (VDR), etc. (Søborg et al., 2003; Salie et al., 2013). For instance, in 2012, Pydi et al. reported on inhibitory genes, such as KIR3DL1 and KIR2DL3, that confer susceptibility toward TB in individuals.

Although these studies provide useful insights into the disease etiology, very few of these studies investigated the association between these gene variants and specific MTBC strains (McHenry et al., 2020). For example, in a cohort study of 1,916 sputum-positive Ghanaian TB patients genotyped for the ALOX5 g.760G > A variant, individuals with heterozygous alleles were found to be at increased risk for developing TB (Herb et al., 2008). Through stratification by MTBC lineage, this association was mainly driven by patients harboring the exonic variant (g.760A) and infected with Maf [OR = 1.70 (95% CI: 1.2–2.6)] (Herb et al., 2008). Conversely, a protective association [OR = 0.60 (95% CI: 0.4–0.9)] was identified among the occurrence of TB caused by Maf but not Mtb and the mannose-binding lectin (MBL2) G57E variant in another cohort of Ghanaian patients (Thye et al., 2011). Moreover, this latter study also found that Maf binds human recombinant MBL more efficiently, perhaps leading to an improved uptake of Maf by macrophages and selection of deficient MBL variants among human populations exposed to Maf.

Comparative analysis of HLA alleles and the Mtb strains isolated from pulmonary TB patients in a South African study found a significant association of HLA-B27 allele with decreased risk of TB caused by the Beijing strain (Salie et al., 2013). Using a candidate gene approach, from a cohort of 237 adult Vietnamese TB patients, Caws et al. concluded that individuals carrying the C allele of the Toll-like receptor-2 (TLR2) T597C polymorphism were significantly more likely to develop TB caused by mycobacteria belonging to the East-Asian/Beijing strain family [OR = 1.57 (95% CI 1.15–2.15)] (Caws et al., 2008). Similar studies have been conducted to understand the coevolution of MTBC and its human host, with regard to the association between different MTBC strains and disease severity. Findings from one such study in Uganda reported an interaction between a single-nucleotide polymorphism (SNP) in SLC11A1 and the lineage (L) L4 of Mtb with several IL12B polymorphisms associated with disease severity (McHenry et al., 2020).

Even though the Sub-Saharan African continent is home to the highest diversity of humans as well as the MTBC, studies to explore the potential association of specific host gene variants and susceptibility to strains of the MTBC are limited (Mboowa, 2014; Omae et al., 2017; McHenry et al., 2020). Thus, host genetics and susceptibility to distinct MTBC lineages cannot be overlooked. Findings from two independent molecular epidemiological studies by our group and other groups (Asante-Poku et al., 2015; Asante-Poku et al., 2016) showed a strong association between Maf (driven by lineage 5) and a native West African ethnic group. To improve our understanding of the genetic susceptibility to the MTBC clades, this current study thence explored genotyping data from the host and pathogen to screen for clade-specific genetic associations in cohorts originating from Ghana.

Host factors are increasingly being recognized as critical for TB control considering the diversity of the outcome of interaction between MTBC and distinct human host populations. This study sought to explore potential host genetic factor (s) that may confer susceptibility or protection to distinct MTBC lineages, toward understanding crucial mechanisms of host–pathogen interaction. From this study, the most significant findings of the association analysis were two statistically significant protective SNPs: rs17235409 in SLC11A1 against Mtb only and rs955263 in SORBS2 against Mtb and Maf together. In addition, we found multiple marginally significant protective variants including in SLC11A1 and MBL2, and younger patients <35 years and patients >65 years are associated with active TB in Ghana.

Solute carrier family 11A Member 1 (SLC11A1) (OMIM: 600266), formerly NRAMP1, a bivalent antiporter located on chromosome 2q35, delivers metal cations from the cytosol into acidic endosomal and lysosomal compartments where Fenon and Haber–Weiss reaction generates toxic antimicrobial radicals for direct antimicrobial activity against infectious microorganisms such as mycobacteria (Mulero et al., 2002; Sobota et al., 2016). SLC11A1 also appears to have multiple functions, having a role in both the resolution of infections; thus, any polymorphism in the gene may influence the function of the gene, primarily affecting the survival of the TB pathogen after phagocytosis (O'Brien et al., 2008). Of the most assessed SLC11A1 variants, the polymorphic (GT)_n microsatellite repeat has been shown to alter the level of SLC11A1 expression and is, therefore, a strong candidate for influencing disease incidence. Several alleles of different repeat lengths have been identified, with (GT)_n allele 2 conferring lower SLC11A1 expression compared with the more commonly occurring (GT)_n allele 3 (Zaahl et al., 2004).

Earlier studies analyzing (GT)_n allele 2 in humans with TB in West Africans have primarily focused on four or five polymorphisms distributed across the gene: A GT_n repeat in the 5′ promoter region, a four base-pair (TGTG) insertion/deletion (rs17235416) in the 3′ untranslated region (UTR), and two single-nucleotide polymorphisms (SNPs) in intron 4 (rs3731865). These mutations were found to be significantly associated with pulmonary TB. This association has been replicated in studies from Guinea-Conakry (Cervino et al., 2000) and Gambia (Yakubu et al., 2014). Bellamy et al. (Bellamy, 1998; Taype et al., 2006) found a significant association between heterozygous GC, GA, and +del genotypes, of INT4, D543N, and 3′UTR, respectively, and pulmonary TB patients, in a case-control study in Gambia. Similarly, case-control studies found an association between GA and +del genotypes, of D543N, and 3′UTR, and lung TB in Cambodia. All these genotypes were associated with resistance to TB. However, in contrast, this study identified a protective association with the more commonly occurring (GT)_n allele 3, exon 15 (rs17235409, D543N).

Although there are several studies on the rs17235409 variant, the role of the variant in the pathobiology of TB remains unclear. A study by Liu et al. associated the variant with treatment failure of pulmonary TB in the Chinese (Yajie et al., 2021) and Mexican populations (Salinas-Delgado et al., 2015). Among the Tibetan population in Qinghai, the variant has been associated with TB susceptibility (Xiying et al., 2016). The variant was not only associated with TB but also was implicated in other diseases as well. The rs17235409 variant was among the list of host factors associated with susceptibility to leishmaniasis (Ates et al., 2009) and rheumatoid arthritis (Niño-Moreno et al., 2017; Braliou et al., 2019). Our analysis shows that rs17235409 might be a promotor/repression gene mutation, which could lead to significant phenotypic consequences. Mutations in this gene might eventually make the phagocytic cells less toxic, thus, providing the patients with more protection from infections by Mtb. It has, therefore, been hypothesized that allele 3 would provide protection against infectious disease by driving high SLC11A1 expression and resulting in Th1-mediated immune response. It was also suspected that the intronic position of this polymorphism might affect posttranscriptional modification of the affected gene, hence, potentially affecting the resulting SLC11A1 protein. Further analysis of the mechanism of action of NRAMP1 and its genetic variants may lead to new approaches in controlling tuberculosis, which kills more people than any other disease caused by an infectious pathogen.

Sorbin and sh3 domain-containing protein 2 (SORBS2) gene (OMIM: 616,349) located on chromosome 4q35.1 is responsible for the regulation of many cell signaling pathways. It is involved in several biological processes such as apoptosis, mitochondrial dysfunction, and innate immunity. Our study found a protective association of rs955263 in SORBS2 against Mtb and Maf together. Contrary to the protective value of rs955263 observed within the Ghanaian population, the variant was associated with active TB in a combined cohort from Uganda and Tanzania (36). Similar to our finding, a study from China reported an inconsistent risk association between SNPs in the SORBS2 gene and active TB cases with respect to the data published from Uganda and Tanzania (Qi et al., 2017). The inconsistency maybe explained by different host factors that may modify the activity of the gene as well as genetic diversity observed in the different populations. There seems to be some level of population specificity, which needs to be investigated from different populations to fully understand the role of SORBS2 gene variants in the development of active TB.

Associations between MTBC lineages and human ethnicities have been reported. Indeed, lineages 1, 2, and 4 are reported to be strongly associated with Filipino, Chinese, and “white” ethnicities, respectively (Gagneux et al., 2006; Asante-Poku et al., 2016). Likewise, in China, Hui ethnicity was found to be associated with the Beijing family of MTBC (Pang et al., 2012). Indeed, human genetic diversity has been linked to an increased or reduced susceptibility to TB. Recent studies have reported human genetic polymorphisms that influence the susceptibility to TB caused by Maf but Mtbss or vice versa. These studies indicate that human genetic susceptibility to TB is further influenced by the MTBC genotype. Conversely, a human polymorphism that reported recently on mannose-binding lectin (MBL) was associated with protection against TB caused by Maf (23). Moreover, this latter study also found Maf to bind to human recombinant MBL more efficiently, perhaps leading to an improved uptake by macrophages and selection of deficient MBL variants among human populations exposed to Maf. Although our study did not find a significant association between ethnicity and MTBC lineages, our study suggests that host genetics play an important role in TB pathogenesis, hence, the need for newer approaches to TB therapy such as host-directed immune-therapy, which have the potential to shorten the TB treatment and prevent resistance by promoting autophagy.

In conclusion, we found SLC11A1 as a potential susceptibility gene of substantial interest for TB caused by M. africanum, which is an important pathogen in West Africa. Given the odds ratio specified in the sample size calculation method (which effectively powers the study to detect loci that increase TB susceptibility), it implies that further studies on larger case-control sample sizes are needed to confirm the resistance loci observed in this study.