Molecular characterisation and associated drug susceptibility patterns of Mycobacterium tuberculosis isolates from South African children

Abstract

According to the World Health Organization, South Africa is ranked the third highest country (0.4-0.6 million), after India and China, with a tuberculosis burden, coupled with drug resistance that is threatening tuberculosis control efforts. Understanding the genetic diversity and drug resistance patterns of Mycobacterium tuberculosis is crucial. The purpose of this study was to describe the molecular characterisation and associated drug susceptibility patterns of M. tuberculosis isolates from South African children. M. tuberculosis strains from children from four South African provinces were characterised and the drug resistance patterns determined. One hundred and four isolates that were culture positive in the Bactec Mycobacterium Growth Indicator Tube 960Reg. and positively identified by AccuProbeReg. assay as M. tuberculosis were used. To ensure purity, the samples were subcultured on Lowenstein-Jensen medium agar slants. Spoligotyping was performed according to the manufacturer's instructions. The international spoligotyping database 4 (SpolDB4) was used to analyse the genotypic data. First-line drugs, excluding pyrazinamide, were tested using the Middlebrook 7H11 AgarReg. proportion method. Twenty-one genotype families were identified in 93 isolates: Beijing (39%), T1 (14%), T2 (3%), T3 (1%), T4-CEU1 (1%), LAM3 (8%), LAM3 and S/convergent (1%), LAM4 (2%), LAM9 (1%), LAM11-ZWE (5%), H1 (2%), H2 (1%), H3 (1%), CAS (1%), CAS-KILI (1%), MANU2 (1%), EAI1-SOM (1%), EAI7-BGD2 (1%), S (3%), X3 (2%) and Bovis1-BCG (2%). Eleven (11%) isolates could not be assigned within the SpolDB4. The Beijing family was the most dominant in Gauteng (27%), followed by Mpumalanga (5%), North West (5%) and Limpopo (2%). The Beijing family was observed in 19 (18%) of isolates from children aged 0-5 years, and in 22 (21%) of isolates from children aged 6-12 years. Ninety-five (91%) isolates were susceptible to all drugs. Overall, of the 104 isolates, 3 (3%) were multidrug-resistant tuberculosis, one each from the Beijing family, T2 and LAM3. The Beijing family was the most dominant genotype, with most cases being from Gauteng, followed by T1. The Beijing genotype was distributed equally between children aged 0-5 years and those aged 6-12 years. The high prevalence of the Beijing genotype poses a serious threat to tuberculosis control owing to its high virulence and association with multi-drug resistance. Continuous surveillance programmes are needed to control tuberculosis, especially in areas with high tuberculosis and human immunodeficiency virus rates, such as those where the study was conducted.