Molecular epidemiology and genetic diversity of Mycobacterium tuberculosis complex in the Cross River State, Nigeria

• Published in: Infection, genetics and evolution genetics and evolution, 2012-06, Vol.12 (4), p.671-677
• Main Authors: Thumamo, Benjamin P., Asuquo, Anne E., Abia-Bassey, Lydia N., Lawson, Lovett, Hill, Véronique, Zozio, Thierry, Emenyonu, Nnamdi, Eko, Francis O., Rastogi, Nalin
• Format: Article
• Language: English
• Subjects: Adolescent; Adult; Aged; Bacteriology; Cluster Analysis; cross contamination; Cross River State; DNA, Bacterial; drug resistance; Drug Resistance, Multiple, Bacterial - genetics; Epidemiology; Evolution, Molecular; Genetic Variation; genotyping; Humans; Life Sciences; Microbiology and Parasitology; Middle Aged; Minisatellite Repeats; MIRU–VNTRs; molecular epidemiology; Molecular Typing; Mycobacterium africanum; Mycobacterium tuberculosis; Mycobacterium tuberculosis - classification; Mycobacterium tuberculosis - genetics; Mycobacterium tuberculosis - isolation & purification; Nigeria; Nigeria - epidemiology; patients; Phylogeny; Spoligotyping; streptomycin; Tuberculosis - epidemiology; Young Adult
• ISSN: 1567-1348; 1567-7257
• DOI: 10.1016/j.meegid.2011.08.011

► This study provides with a first insight on Mycobacterium tuberculosis complex epidemiology and genetic diversity in the Cross River State, Nigeria. ► Majority of the clustered isolates were phylogeographically specific of West Africa; 52% belonged to the LAM10-CAM (Cameroon lineage) of M. tuberculosis, and 33% to the AFRI_2 sublineage of M. africanum. ► Apparently the proportion of evolutionary ancestral M. africanum is gradually decreasing in West-Africa. These strains are being replaced by more successful, evolutionary recent M. tuberculosis, particularly the LAM10-CAM lineage; a significant proportion (10%) was concomittantly multidrug-resistant in this study. This study provides with a first insight on Mycobacterium tuberculosis complex epidemiology and genetic diversity in the Cross River State, Nigeria. Starting with 137 smear positive patients recruited over a period of 12months (June 2008 to May 2009), we obtained 97 pure mycobacterial isolates out of which 81 (83.5%) were identified as M. tuberculosis complex. Genotyping revealed a total of 27 spoligotypes patterns with 10 clusters (n=64% or 79% of clustered isolates, 2–32 isolates/cluster), with patients in the age group range 25–34years being significantly associated with shared-type pattern SIT61 (p=0.019). Comparison with SITVIT2 database showed that with the exception of a single cluster (SIT727/H1), all other clusters observed were representative of West Africa; the two main lineages involved were LAM10-CAM (n=42/81% or 51.8%) of M. tuberculosis and AFRI_2 sublineage of Mycobacterium africanum (n=27/81% or 33.3%). Subsequent 12-loci MIRU typing resulted in a total of 13 SIT/MIT clusters (n=52 isolates, 2–9 isolates per cluster), with a resulting recent n−1 transmission rate of 48.1%. Available drug-susceptibility testing (DST) results for 58/81 clinical isolates revealed 6/58% or 10.4% cases of multiple drug-resistance (MDR); 5/6 MDR cases were caused by strains belonging to LAM10-CAM lineage (a specific cluster SIT61/MIT266 in 4/6 cases, and an orphan spoligotype pattern in 1/6 case). Additionally, MIT266 was associated with streptomycin resistance (p=0.016). All the six MDRTB isolates were concomitantly resistance to streptomycin and ethambutol; however, 4/6 MDR strains with identical MIRU patterns were characterized by consecutive strain numbers hence the possibility of laboratory cross contamination could not be excluded in 3/4 serial cases. The present preliminary study underlines th