Mycobacterium tuberculosis (MTB) complex is comprising of pathogenic mycobacteria responsible for human and animal tuberculosis, a major public health problem in Niger. Although infected individuals are paramount sources of contamination, nevertheless alternative, neglected sources may play some role in minority forms of the infection. Accordingly, we investigated the presence of Mycobacterium tuberculosis complex in soil samples in Niger. A total of 103 soil samples were collected in six different areas in Niger in October and November 2018 and April and May 2020 from residential areas of tuberculosis patients. Screening PCR targeting M. tuberculosis complex CRISPR-Csm4 and Xpert MTB/RIF Ultra assay were applied to detect the M. tuberculosis complex. M. tuberculosis DNA was positively detected in five of 103 (5/103; 4.8%) soil samples (Dosso: one sample, Zinder: one sample and Niamey: three samples) using the CRISPR-Csm4 system. CRISPR-Csm4 gene sequence identified four M. tuberculosis sensu stricto (may be lineages 1, 3 or 4) and one M. tuberculosis L2 lineage (Beijing). Moreover, the five positive samples were confirmed by Xpert MTB/RIF Ultra assay as rifampicin-susceptible M. tuberculosis complex strains. However, culture remained negative after 42 days. In this study, we announced for the first time the presence of M. tuberculosis sensu stricto in the soil of Niger. Moreover, these detected lineages were identical to the dominant M. tuberculosis lineages in patients. The presence of common lineages of M. tuberculosis between the soil and human highlight the risk of transmission from the soil to human.

Mycobacterium bovis (M. bovis), a Mycobacterium tuberculosis complex species responsible for tuberculosis in cattle and zoonotic tuberculosis in humans, is present in Algeria. In Algeria however, the M. bovis population structure is unknown, limiting understanding of the sources and transmission of bovine tuberculosis. In this study, we identified the whole genome sequence (WGS) of 13 M. bovis strains isolated from animals exhibiting lesions compatible with tuberculosis, which were slaughtered and inspected in five slaughterhouses in Algeria. We found that six isolates were grouped together with reference clinical strains of M. bovis genotype-Unknown2. One isolate was related to M. bovis genotype-Unknown7, one isolate was related to M. bovis genotype-Unknown4, three isolates belonged to M. bovis genotype-Europe 2 and there was one new clone for two M. bovis isolates. Two isolates from Blida exhibited no pairwise differences in single nucleotide polymorphisms. None of these 13 isolates were closely related to four zoonotic M. bovis isolates previously characterized in Algeria. In Algeria, the epidemiology of bovine tuberculosis in cattle is partly driven by cross border movements of animals and animal products.

The whole-genome sequence comparison of the Mycobacterium tuberculosis complex (MTC) genomic sequences that are available in the NCBI database identified a unique, specific gene to be used directly on clinical diagnostic samples to detect MTC against all species of mycobacteria and to differentiate between MTC species, lineages, and sublineages.

Background: Among other West African countries experiencing the high endemicity of deadly tuberculosis, the situation in Niger is poorly evidenced by microbiological investigations. Methodology/Principal findings: The study of 42 isolates of Mycobacterium tuberculosis from Niger by whole genome sequencing using Illumina iSeq technology yielded four M. tuberculosis lineages: Indo-Oceanic L1 (n = 1) (2.3%), East-Asian (n = 1) (2.3%), East-African Indian L3 (n = 2) (4.7%) and Euro-American L4 (n = 38) (90.4%). The sub-lineage L4.1.3 comprising 18 isolates (47.3%) was predominant, followed by the L4.6.2.2 sub-lineage (Cameroon genotype, n = 13 isolates) (34.2%). Investigating drug resistance profile for 12 antibiotics found 8/42 (19%) pan-susceptible isolates and 34/42 (81%) resistant isolates; with 40/42 (95.2%) isolates being susceptible to clofazimine-bedaquiline. Conclusions/Significance: These unprecedented data from Niger highlight the dynamics of tuberculosis transmission and drug resistance in Niger and may assist tuberculosis control in this country which continues to support a high burden of tuberculosis.

The capacity of the 49 sub-Saharan African countries, which account for 85% of tuberculosis cases in Africa (WHO, 2025), to monitor the genomic dynamics of Mycobacterium tuberculosis complex strains responsible for the disease was examined for the period 2000-2025. A total of 8141 GenBank entries, supplemented by 163 as yet unreported whole genome sequences prepared at the Institut Hospitalier-Universitaire, Marseille, France and the Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formation, Dakar, Sénégal were analysed using TB-Profiler. M. tuberculosis sub-lineage L2.2.1 dominated the sub-continent, while other lineages and sub-lineages featured a discrete pattern of geographical distribution, here illustrated by interactive maps. Although three-quarters of the genomes showed a predicted antibiotic-susceptibility, the predicted resistant recovered in 80% countries largely comprised multidrug-resistant (MDR) genomes (12.19% of genomes), followed by Rifampicin-susceptible, isoniazid-resistant (HR-TB) genomes (4.47%), Rifampicin-resistant TB (RR-TB) genomes (3.31%), extensively drug-resistant (XDR) genomes (1.78%), and pre-XDR genomes (0.64%). Resistance to second-line antibiotics was observed with prevalence lower than that of first-line drugs. This review gives an updated, accurate, and interactive overview of tuberculosis in sub-Saharan Africa and provides a strong basis for following the current evolution of tuberculosis in African regions.

Background: We implanted WGS as the routine method to profile the antibiotic susceptibility of M. tuberculosis isolates focusing on in silico resistance to antileprosy drugs that we recently proposed to reposition for the treatment of pulmonary tuberculosis. Methods: We prospectively performed WGS of 112 M. tuberculosis isolates recovered from respiratory tract samples of 106 patients diagnosed with pulmonary tuberculosis between 2017 and 2019 and defined their antibiotic susceptibility profile to 17 antibiotics including antileprotics drugs. Results: We incidentally observed 08 sequence variations in 07 genes, specific to seven sublineages. Altogether, we observed 09 (8%) rifampicin-resistant, 05 (4.4%) multidrug-resistant and 02 (1.7%) extensively-drug resistant isolates; whereas only one isolate exhibited in silico resistance to clofazimine. Conclusion: These results support repurposing of antileprosis antibiotics as antituberculosis; and offer new targets for genotyping M. tuberculosis .