Characterization of Mycobacterium tuberculosis genotypes and their correlation to multidrug resistance in Lusaka, Zambia

Abstract Objectives The burden of multidrug resistant tuberculosis (MDR-TB) has been reported to be increasing in Zambia. The reasons for the increase are still unclear. This study determined the diversity ofMycobacterium tuberculosis genotypes among isolates in Lusaka, the capital city, and investigated their association with MDR-TB. Methods Spoligotyping, large sequence polymorphism (LSP) analysis and sequencing of MDR associated genes were performed on a total of 274 M. tuberculosis clinical isolates stored at the University Teaching Hospital from 2013 to 2017. Of these, 134 were MDR-TB while 126 were pan-susceptible. Results Spoligotyping showed LAM family as the most predominant genotype (149/274, 54.4%) followed by CAS family (44/274, 16.1%), T family (39/274, 14.2%) and minor proportions of X, S, Harleem, EAI and Beijing spoligofamilies were identified. Three M. bovis isolates were also observed. Among those, CAS1-Kili (SIT 21) and LAM1 (SIT 20) subfamilies showed propensity for MDR-TB with p =  0.0001 and p =  0.001, respectively. Conclusions This phenomenon might explain the future increase in the burden of MDR-TB caused by specific lineages in Zambia. It is therefore recommended that the National TB control program in the country complements conventional control strategies with molecular analysis for monitoring and surveillance of MDR-TB epidemiology.