Molecular investigations of Mycobacterium tuberculosis strains circulating in four regions of Eswatini

Abstract Background: The tuberculosis (TB) epidemic remains a major global health problem and has high in Eswatini. Our study aimed to investigate the circulating genotypes in Eswatini and to determine genotype changes of susceptible Mycobacterium tuberculosis (Mtb) strains when they develop into Multidrug resistant (MDR)-TB strains during treatment. Methods: Participants were selected using a systematic random sampling method, and patient who met the inclusion criteria, were included in this quantitative descriptive cohort study ( n =103). A total of 206 Mtb strains at baseline and at follow-up detected by GeneXpert® MTB/RIF assay (Cephied, USA) and microscopy respectively. The decontaminated specimens were processed on the BACTEC™ MGIT™ 960 Mycobacteria Culture System (Becton Dickinson, USA), for culture drug sensitivity testing. DNA was extracted for spoligotyping, using GenoLyse (Hain LifeScience). The study results were analysed using the Statistical Package for the Social Sciences version 25 software and STATA. Results: Resistance to at least one first line drug was detected higher in baseline compared to follow-up specimens with most of them developed into MDR-TB. A total of 82.5% (170/206) strains had valid spoligotyping patterns, with four lineages and eighteen sublineages. The distribution of the lineages varied among the different regions in Eswatini. The Euro-American lineage was the most prevalent with 57.6% (98/170) followed by the East Asian with 28.8% (49/170); Indo-Oceanic at 11.2% (19/170) and Central Asian at 2.4% (4/170). Furthermore, a high proportion of the Beijing sublineage at 28.8% (49/170) and S sublineage at 20.0% (34/170) were detected. The Beijing sublineage strain was predominant found in follow-up strains of the Manzini region with 48.9% (23/47) which was significant (p=0.001). A significant proportion of follow-up specimens developed MDR-TB (p=0.001) with Beijing genotype being the major sublineage in most follow-up specimens (p<0.000). Conclusion: Eswatini has a high Mtb genotypic diversity. A significant proportion of the TB infected participants had the Beijing sublineage associated with MDR-TB in follow up specimens and thus indicate community wide transmission.