Mycobacterium tuberculosis complex (MTBC) which is responsible for tuberculosis (TB) remains a global public health concern especially in low-income countries as it is the leading cause of death from a bacterial infectious disease 1. In 2019, it was estimated that ten million people worldwide contracted the tubercle disease and about 1.2 million (HIV negative) of these people died as a result of complications that arose from TB 1. MTBC is grouped into different lineages, known as M. tuberculosis sensu stricto (lineage 1, 2, 3, 4 and, 7), M. africanum (lineage 5 and 6), the recently discovered lineages 8, 9, 2,3, and, several other animal-associated habitat (M. bovis, M.microti, M.pinnipedii, M. orygis and, others) 4. Some of these lineages are geographically restricted, such as lineages 5, 6, 7 and, 9 2,5,6, whilst some are globally distributed such as lineages 1, 2, 3 and, 4 7.
Lineage 2, also known as the Beijing lineage is associated with the increased spread of multi-drug resistant TB in Eurasia and has since spread across the world in successive waves during human migration 8. Genome analysis have reported multiple introductions of the Beijing lineage in Africa dating back to 300 years 9. In addition, the Beijing lineage have been reported in the West African region, using spoligotyping and whole genome sequencing 10–12, but with no report in Nigeria yet using molecular techniques 13,14.
Multi-drug resistant TB (MDR TB) is the type of TB bacteria that is resistant to two of the most important drugs to treat TB also known as first-line drugs: isoniazid (INH) and rifampicin (RIF). The updated definition of extensively drug-resistant TB (XDR TB) is a rare type of MDR TB that is resistant to INH, RIF and any fluoroquinolone, and at least one additional Group A drug (levofloxacin, moxifloxacin bedaquiline and/or, linezolid) which are the most powerful second-line drugs used for drug resistant TB management 15. The emergence of drug resistant and extensively drug resistant MTBC worldwide has largely affected public health and global economy, as many cases go unreported or undetected in many low resource settings and cause further spread and misdiagnosis 16. In 2019, the incidence of MDR TB resistant to rifampicin (RR-TB) in Nigeria was estimated at 21,000 with 16 laboratory confirmed XDR TB cases, with reports that about 2% of global MDR TB cases acquire multiple resistance to antibiotics to become XDR TB 1. This statistics may be underplayed as many high burden TB countries do not have diagnostic capacities to capture the real scenario, as such it is crucial to use cutting edge technologies to screen drug-resistant (DR) or MDR TB samples for the presence of XDR acquiring mutations in these countries 17.
Just as many other West African countries, Nigeria has deployed rapid molecular techniques to detect RR-TB and MDR TB by using Xpert®MTB/Rif assay (Cephid, USA) and Line Probe Assay 18. However, these techniques come with limitations when compared to whole genome sequencing (WGS), as the latter can detect drug resistant mutations outside the target zone of rapid tests and produce much more reliable and robust drug resistance profile of TB 19.
In this study, we use whole genome sequencing to investigate TB positive clinical samples that were confirmed RR-TB with Xpert®MTB/Rif assay (Cephid, USA). We also use bioinformatics to classify the bacteria into lineages in order to identify the strains or clonal complexes present in Nigeria.