Genetic diversity of drug resistant tuberculosis in Zambia

Zimba, Sharon

Genetic diversity of drug resistant tuberculosis in Zambia

Date

2021-03-04

Authors

Zimba, Sharon

Publisher

Kamuzu University of Health Sciences

Abstract

Type of study: A cross-sectional study Aim of the study: To establish the genetic diversity of drug resistant tuberculosis in Zambia Specific objectives: 1. To identify the circulating strains of Mtb in Zambia. 2. To classify the mycobacterium lineages associated with drug resistant TB in Zambia. 3. To determine the proportion of each mycobacterium lineage in drug resistant TB in Zambia. 4. To analyse the resistance trend among the circulating Mtb lineages in the past five (5) years in Zambia. Problem statement: Drug resistant tuberculosis has been reported to be an increasingly serious concern and a threat to public health due to its mode of spread and cost of treatment. In 2017, an estimated 3.5% of new cases and 18% of previously treated cases had MDR-TB globally with Africa reporting 2.7% in new cases and 14% in previously treated cases, and Zambia contributing about 1.1% in new cases and 18% in previously treated case although it is not classified as a high MDR-TB burden country (WHO, 2018). In 2018, about half a million new cases of rifampicin-resistant TB were reported, of which 78% had multidrug-resistant TB, worldwide. Of the new TB cases, 3.4% had drug resistant TB while 18% of previously treated cases had multidrug-resistant TB or rifampicin-resistant TB (WHO, 2019). In Zambia, there was an increase of drug resistant TB rate in new TB cases in 2018, from 1.1% reported in 2017 to 2.8% in 2018 while there was neither a decrease nor an increase in the MDR/RR rate in the previously treated TB cases as it remained unchanged at 18% (WHO, 2019). Despite the statistics and increase in the incidence and prevalence of MDR-TB in Zambia and Africa at large, there is inadequate documented literature on the association between the various strain and lineages in the Mycobacterium tuberculosis complex with drug resistant TB in Zambia, the proportion each lineage has contributed to the resistant strains and the trend of resistance patterns in each lineage over the past five (5) years. The study will be conducted in Zambia, on sputum samples with drug resistant TB archived at Chest Disease laboratory (CDL). The study units of 245 will be selected through Stratified sampling method. The samples will first be subdivided into strata based on the year of collection, and then the individual units will be collected from each stratum using simple random or systematic sampling. Data will be collected through the laboratory analysis of archived sputum samples. The analysis will include, liquid culture using the Mycobacteria Growth Indicator Tube (MGIT) system (to revive the mycobacterium) , Genotyping with a single nucleotide polymorphism (SNP) based PCR method using primers specific for each of regions of difference (L1), (L2) and (L3) and L4 according to Thermofisher Scientific Line probe assay and Single Nucleotide Pleomorphism (SNP) and Line probe assay will be performed using the Hain Life science technology. Data will be stored using MS excel database and analysed using SPSS version 21. Descriptive statistics will be presented in form of percentages, charts tables and graphs. Chi square test will be used to determine associations between categorical variables. Molecular data will be analysed using the taqMan Genotyper Software.