Genetic Diversity and Drug-Resistance Patterns of Mycobacteriumtuberculosis from Pulmonary Tuberculosis Patients in the Southwest and Littoral Regions of Cameroon
Background: In Cameroon, data on Mycobacteriumtuberculosis (MTB) lineage diversity, drug-resistance burden and on-going disease transmission are lacking. Existing-reports are derived from conventional genotyping and phenotyping methods, with limited power to discriminate between MTB sub-lineages. Therefore, we used Whole-Genome Sequencing (WGS) to investigate MTB lineage diversity and drug-resistance patterns in Pulmonary TB patients in the Southwest and Littoral Regions of Cameroon, relevant to Tuberculosis (TB) prevention and control. Methods: Sputum samples were collected from 552 Pulmonary Tuberculosis (PTB) patients and cultured on Lowenstein-Jensen (LJ) medium. DNA was extracted from the MTB isolates and whole genome sequenced. A total of 88 high quality MTB sequence reads were obtained and used to generate a Variant Calling File (VCF), which was analyzed using TB-Profiler pipeline to predict MTB lineage diversity and drug-resistance pattern. Results: Three MTB lineages were identified. The most abundant being the L4-Euro-American lineage (98%), followed by L2-East Asian (1%) and L3-East-Asian India (1%). Nine sub-lineages were identified: L4-LAM_10 Cameroon (45%), L4-Haarlem (20%), L4-Euro-American (10%), L4-Mainly T (6%), L4-Uganda II (2%), L4-LAM (1%), L3-Delhi-CAS (1%), L4-Congo type (1%) and the L2-Beijing genotype (1%). Notably, no isolates of the West African strains (L5 or L6) were found. Three isolates were Rifampicin resistant (3.4%); one was isoniazid resistant (1.1%); one was streptomycin resistant (1.1%) and four (4.5%) were resistant to second-line drugs. No Multi-Drug-Resistant (MDR) MTB was identified. Conclusion: This study revealed that the MTB Complex population in the Littoral and Southwest Regions of Cameroon is diverse, indicating ongoing transmission. There also appears to be marked regression of Mycobacteriumafricanum in favor of the LAM_10 Cameroon. Further investigation could provide insight into the genetics, epidemiology, and transmission dynamics of the LAM_10 Cameroon genotype.
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