Genetic characterization of <em>Mycobacterium tuberculosis</em> complex isolates circulating in Abuja, Nigeria

Abstract

ObjectiveNigeria ranks fourth among the high tuberculosis (TB) burden countries. This study describes the prevalence of drug resistance and the genetic diversity of Mycobacterium tuberculosis in Abuja’s Federal Capital Territory.Materials and methodsTwo hundred and seventy-eight consecutive sputum samples were collected from adults with presumptive TB during 2013–2014. DNA was extracted from Löwenstein–Jensen cultures and analyzed for the identification of nontuberculous mycobacteria species, detection of drug resistance with line probe assays, and high-throughput spacer oligonucleotide typing (spoligotyping) using microbead-based hybridization.ResultsTwo hundred and two cultures were positive for M. tuberculosis complex, 24 negative, 38 contaminated, and 15 positive for nontuberculous mycobacteria. Five (2.5%) M. tuberculosis complex isolates were resistant to rifampicin (RIF) and isoniazid (multidrug resistant), nine (4.5%) to RIF alone, and 15 (7.4%) to isoniazid alone; two RIF-resistant isolates were also resistant to fluoroquinolones and ethambutol, and one multidrug resistant isolate was also resistant to ethambutol. Among the 180 isolates with spoligotyping results, 164 (91.1%) were classified as lineage 4 (Euro-American), 13 (7.2%) as lineage 5 (West African 1), two (1.1%) as lineage 2 (East Asia), and one (0.6%) as lineage 6 (West African 2). One hundred and fifty-six (86.7%) isolates were grouped in 17 clusters (2–108 isolates/cluster), of which 108 (60.0%) were grouped as L4.6.2/Cameroon (spoligotype international type 61).ConclusionThe description of drug resistance prevalence and genetic diversity of M. tuberculosis in this study may be useful for improving TB control in Nigeria.

Prevalence and molecular characterization of Mycobacterium tuberculosis complex in cattle and humans, Maiduguri, Borno state, Nigeria: a cross-sectional study

“…Notably, the study also reported M. tuberculosis strains belonging to spoligotypes SIT 838 and 61 both of the international family LAM10_CAM. Earlier reports have identified LAM10_CAM in humans in Nigeria [ 28 , 64 , 72 – 74 ] and other countries in Africa including Cameroon [ 75 ], Burkina Faso [ 76 ], Sierra Leone [ 77 ], Niger and Ivory Coast and parts of Europe [ 68 ]. Previous reports showed the LAM10-CAM family as the most predominant circulating clade in Nigeria [ 28 , 72 – 74 , 78 , 79 ] The LAM10-CAM was first described in Cameroon, where it represented 34% of the M. tuberculosis isolates in 2003 [ 75 ] and has recently emerged as a dominant strain in the western province of Cameroon.…”

“…Earlier reports have identified LAM10_CAM in humans in Nigeria [ 28 , 64 , 72 – 74 ] and other countries in Africa including Cameroon [ 75 ], Burkina Faso [ 76 ], Sierra Leone [ 77 ], Niger and Ivory Coast and parts of Europe [ 68 ]. Previous reports showed the LAM10-CAM family as the most predominant circulating clade in Nigeria [ 28 , 72 – 74 , 78 , 79 ] The LAM10-CAM was first described in Cameroon, where it represented 34% of the M. tuberculosis isolates in 2003 [ 75 ] and has recently emerged as a dominant strain in the western province of Cameroon. Importantly, a study demonstrated LAM 10 as part of spoligotype families including LAM 1 and Beijing families which had the highest sensitivities when compared with isolates belonging to other spoligotype families; suggesting their highly clonal and homogeneous nature [ 80 ].…”

An updated evolutionary history and taxonomy ofMycobacterium tuberculosislineage 5, also calledM. africanum

“…The 25 newly sequenced M.africanum (numbered CUS0000001-CUS0000025) were recovered from well-characterized human TB cases from archive DNAfrom previous published studies whose DNA had previously been sent between 2007 to 2019 to the Infection Genetics and Evolution of Emerging Pathogens research team (IGEPE, Institute of Integrative Cell Biology, Gif sur Yvette) (Lawson et al, 2012; Molina-Moya et al, 2018a; Molina-Moya et al, 2018b). Another origin of samples is culture positive L5-L6 isolates from the French national TB reference-associated laboratory in Bichat Hospital Paris, France.…”

“…CUS0000001 and 0000008 represent isolates from Lawson et al . 2012 collection, while the remaining eleven are from collections either recovered from Molina-Moya et al ., 2018a or 2018b collections. In this study, newly recruited L5-L6 DNAs from Nigeria were selected from patients with a microbiological diagnosis of TB characterized by the presence of 2 copies of MIRU24 as assessed by MIRU-VNTR analysis.…”

Early detection of Pre-XDR TB with line probe assay in a high TB burden country

“…All procedures were carried out according to the National Standard operating procedure (SOP) for LJ Culture/DST LPA LPA is based on PCR amplification of rpo B (RIF), katG and the promoter of inhA (INH), gyrA and gyrB (FLQ), and rrs and the promoter of eis (KAN, AMK, CAP) and subsequent detection of mutations through hybridization to probes immobilized to a nitrocellulose membrane. 6…”