Whole genome sequencing of clinical samples reveals extensively drug resistant tuberculosis (XDR TB) strains from the Beijing lineage in Nigeria, West Africa

Abstract

Multi-drug (MDR) and extensively drug-resistant (XDR) tuberculosis (TB) continues to be a global public health problem especially in high TB burden countries like Nigeria. Many of these cases are undetected and go on to infect high risk individuals. Clinical samples from positive rifampicin resistant Xpert®MTB/Rif assay were subjected to direct whole genome sequencing and bioinformatics analysis to identify the full antibiotics resistance and lineage profile. We report two (2) XDR TB samples also belonging to the East-Asian/Beijing family of lineage 2 Mycobacterium tuberculosis complex from clinical samples in Nigeria. Our findings further reveal the presence of mutations that confer resistance to first-line drugs (rifampicin, isoniazid, ethambutol and pyrazanimide), second-line injectables (capreomycin, streptomycin, kanamycin and/or amikacin) and at least one of the fluoroquinolones (ofloxacin, moxifloxacin, levofloxacin and/or ciprofloxacin) in both samples. The genomic sequence data from this study not only provide the first evidence of XDR TB in Nigeria and West Africa, but also emphasize the importance of WGS in accurately detecting MDR and XDR TB, to ensure adequate and proper management treatment regimens for affected individuals. This will greatly aid in preventing the spread of drug resistance TB in high burden countries.

Clinical utility of target amplicon sequencing test for rapid diagnosis of drug-resistant Mycobacterium tuberculosis from respiratory specimens

“…While these studies have demonstrated the feasibility of NGS in TB drug resistance diagnosis, the sequencing platforms are either obsoleted (Colman et al, 2016), or the study only focused on AFB positive specimens with limited variability in drug resistance patterns (Smith et al, 2020). More importantly, as most platform focused on whole genome sequencing data, high-quality genomic DNA prepared from MTB isolates are usually required (Lam et al, 2021;Olawoye et al, 2021). The long turnaround time of MTB culture would not be in favor of rapid MTB resistance analysis.…”

Comprehensive clinical assays for molecular diagnostics of gliomas: the current state and future prospects

“…Nevertheless, the sequencing of drug-resistant tuberculosis strains was performed utilizing Illumina iSeq 100 at Redeemer’s University, in Ede, Nigeria. ( Olawoye et al, 2021 ). The sequencing capacity of North Africa is concentrated in Egypt; for instance, Cairo University (Cairo, Egypt) possesses Illumina MiSeqDx and Ion Proton System, while Suez Canal University (Ismailia, Egypt) exploits Illumina MiSeq.…”

Diagnostic Modalities of Tuberculosis- Then and Now

“…The clinical research trials are still ongoing in Asian [72,73,74,75]and African [76,77,78,79] LMICs to study the sensitivity and specificity of these future-promising techniques with the purpose of including them into national diagnostic methods.…”