Diversity of Mycobacterium tuberculosis Complex Lineages Associated with Pulmonary Tuberculosis in Southwestern, Uganda

Mycobacterium tuberculosis Lineage Distribution Using Whole-Genome Sequencing and Bedaquiline, Clofazimine, and Linezolid Phenotypic Profiles among Rifampicin-Resistant Isolates from West Java, Indonesia

Tuberculosis (TB) is caused by Mycobacterium tuberculosis infection. Indonesia is ranked second in the world for TB cases. New anti-TB drugs from groups A and B, such as bedaquiline, clofazimine, and linezolid, have been shown to be effective in curing drug resistance in TB patients, and Indonesia is already using these drugs to treat patients. However, studies comparing the TB strain types with anti-TB resistance profiles are still relevant to understanding the prevalent strains in the country and their phenotypic characteristics. This study aimed to determine the association between the TB lineage distribution using whole-genome sequencing and bedaquiline, clofazimine, and linezolid phenotypic profile resistance among M. tuberculosisrifampicin-resistant isolates from West Java. M. tuberculosis isolates stock of the Department of Microbiology, Faculty of Medicine, Universitas Indonesia, was tested against bedaquiline, clofazimine, and linezolid using a mycobacteria growth indicator tube liquid culture. All isolates were tested for M. tuberculosis and rifampicin resistance using Xpert MTB/RIF. The DNA genome of M. tuberculosis was freshly extracted from a Löwenstein-Jensen medium culture and then sequenced. The isolates showed phenotypically resistance to bedaquiline, clofazimine, and linezolid at 5%, 0%, and 0%, respectively. We identified gene mutations on phenotypically bedaquiline-resistant strains (2/3), and other mutations also found in phenotypically drug-sensitive strains. Mykrobe analysis showed that most (88.33%) of the isolates could be classified as rifampicin-resistant TB. Using Mykrobe and TB-Profiler to determine the lineage distribution, the isolates were found to belong to lineage 4 (Euro-American; 48.33%), lineage 2 (East Asian/Beijing; 46.67%), and lineage 1 (Indo-Oceanic; 5%). This work underlines the requirement to increase the representation of genotype-phenotype TB data while also highlighting the importance and efficacy of WGS in predicting medication resistance and inferring disease transmission.

Multi-ancestry meta-analysis of host genetic susceptibility to tuberculosis identifies shared genetic architecture

The heritability of susceptibility to tuberculosis (TB) disease has been well recognized. Over 100 genes have been studied as candidates for TB susceptibility, and several variants were identified by genome-wide association studies (GWAS), but few replicate. We established the International Tuberculosis Host Genetics Consortium to perform a multi-ancestry meta-analysis of GWAS, including 14,153 cases and 19,536 controls of African, Asian, and European ancestry. Our analyses demonstrate a substantial degree of heritability (pooled polygenic h2 = 26.3%, 95% CI 23.7-29.0%) for susceptibility to TB that is shared across ancestries, highlighting an important host genetic influence on disease. We identified one global host genetic correlate for TB at genome-wide significance (p<5 × 10-8) in the human leukocyte antigen (HLA)-II region (rs28383206, p-value=5.2 × 10-9) but failed to replicate variants previously associated with TB susceptibility. These data demonstrate the complex shared genetic architecture of susceptibility to TB and the importance of large-scale GWAS analysis across multiple ancestries experiencing different levels of infection pressure.

Detection of Mycobacterium tuberculosis multiple strains in sputum samples from patients with pulmonary tuberculosis in south western Uganda using MIRU-VNTR

Infections with multiple strains of Mycobacterium tuberculosis are now widely recognized as a common occurrence. Identification of patients infected with multiple strains provides both insight into the disease dynamics and the epidemiology of tuberculosis. Analysis of Mycobacterial Interspersed Repetitive Unit-Variable-Number Tandem Repeats (MIRU-VNTR) has been shown to be highly sensitive in detecting multiple M. tuberculosis strains even in sputum. The goal of this study was to identify cases of multiple M. tuberculosis strain infections among patients diagnosed with pulmonary tuberculosis in Southwestern Uganda and assessment of factors associated with multiple strain infections. DNA extracted directly from 78 sputum samples, each from an individual patient, was analyzed using the standard 24 loci MIRU-VNTR typing. Five (6.4%) of the 78 patients were infected with multiple strains of M. tuberculosis with all of them being the newly diagnosed cases while two-thirds of them were co-infected with HIV. Exact regression analysis projected that the natives were more likely to harbor multiple strains (OR; 0.981, 95% CI 0–7.926) as well as those with a high microbial load (OR; 0.390, 95% CI 0–3.8167). Despite these findings being not statistically significant due to the small sample size, this points to a critical component of disease dynamics that has clinical implications and emphasizes a need for a study using a larger cohort. It is also essential to study the potential factors associated with higher risk of exposure to newly diagnosed and HIV positive patients at the community level. In addition, our ability to detect multiple M. tuberculosis strains using the standard 24 loci MIRU-VNTR typing especially with allelic diversity in loci 2059 and 3171, which are excluded from the 15-locus MIRU-VNTR, lead us to recommend the use of this genotyping technique, especially in areas with tuberculosis endemicity similar to this study.

Ethnobotanical plants used in the management of symptoms of tuberculosis in rural Uganda

BACKGROUND

Tuberculosis (TB) caused by Mycobacterium tuberculosis is the 13th leading cause of death worldwide. The emergence of multidrug-resistant TB (MDR-TB) poses a major health security threat. Plants have traditionally been used as a source of medicine, since olden days and 80% of the communities in Africa still rely on herbal medicines for their healthcare. In many parts of Uganda, some plants have shown ethno-pharmacological prospects for the treatment of TB, and yet they have not been fully researched.

AIM

This study aimed to document plant species used traditionally by the herbalists and non-herbalist communities of Kitgum and Pader districts for managing symptoms of TB.

METHODS

An ethnobotanical study was carried out in 42 randomly selected villages in Kitgum and Pader districts between August 2020 and January 2021. Information was obtained by administering semi-structured questionnaires to 176 respondents identified by snowball and random sampling methods. Data were analysed and presented using descriptive statistics and Informant Consensus Factor (ICF).

RESULTS

Overall, only 27% of the respondents were knowledgeable about plants used for managing symptoms of TB. Nine plant species belonging to six families (Mimosaceae, Apiaceae, Lamiaceae, Rutaceae, Loganiaceae and Rubiaceae) were used to manage symptoms of TB. The most representative family was Rutaceae with three species, followed by Rubiaceae (two species) and the rest of the families were represented by one species each. The most frequently recorded species were Steganotaenia araliacea Hochst. (8.5%), Gardenia ternifolia Schumach. & Thonn (6.8%) and Albizia adianthifolia (Schum.) W.Wight (6.8%). Most of the medicinal plants were trees, and roots (69%) were the most frequently plant part used, followed by the bark (16%) and leaves (15%). The most common method of preparation was by pounding and mixing concoction with water. The administration of the concoctions was mostly done orally.

CONCLUSIONS

The results established the existence of few medicinal plants for managing symptoms of TB among the Acholi communities which could be used in developing new, effective plant-based antimycobacterial drugs. The few plants mentioned might face conservation threats due to exploitations of the roots. Phytochemical and toxicological studies are recommended to identify active compounds responsible for antimycobacterial activity.