Phylogenomic Assessment of Drug-Resistant Mycobacterium tuberculosis Strains from Beira, Mozambique

Background: Mozambique is one of the high-burden tuberculosis (TB) countries where drug resistant tuberculosis (DR-TB) is rising. Whole genome sequencing (WGS) comprehensively describes the molecular epidemiology of TB and allows for the prediction of DR-TB phenotypes, recognition of genetically related strainsstrain lineage identification, and resolution of TB transmission.Objective: To describe genetic diversity of M. tuberculosis strains causing DR-TB in Beira, Mozambique.Methods: This was a descriptive cross-sectional study. 35 strains were genotyped using MTBDRplusTM and MTBDRslTM. All isolates resistant to isoniazid (INH), rifampicin (RMP) or both were submitted subjected to WGS, using the Nextera-XT library kit., Vvariant identification, drug resistance prediction, phylogenetic analysis and strain relatedness were investigated. WGS and MTBDR genotyping results were compared.Findings: The 35 strains belong to: Lineage 4: 25(71.4%); Lineage 1: 5(14.3%); and Lineage 2 Beijing family: 5(14.3%). Among these 35 strains, 32 (91.6%) had resistance to at least one drug resistance, of these, 5 (15.6%) were pre-XDR strains and 1 (3.1%) fulfilled criteria for XDR-TB.Conclusion: DR-TB in Beira Mozambique, is mainly caused by three of seven major M. tuberculosis lineages: Lineage 4.3, Lineage 2 (Beijing) and Lineage 1 (EAI). Genetically related strains are infecting people sharing health facilities.