Genetic diversity of Mycobacterium tuberculosis clinical isolates in Blantyre, Malawi

Victor Ndhlovu,Anmol Kiran,Derek Sloan,Wilson Mandala,Konstantina Kontogianni,Mercy Kamdolozi,Maxine Caws,Gerry Davies

doi:10.1016/j.heliyon.2019.e02638

Abstract

Despite the high burden of tuberculosis (TB) worldwide, specific factors influencing disease transmission remain elusive. Long term epidemiological studies and in vitro experimental models provide evidence of variable relative fitness of Mycobacterium tuberculosis (Mtb) strains but few such studies are available. Large sequence polymorphisms (LSP) are a robust molecular marker and are feasible as an epidemiological investigative tool. Few Mtb molecular epidemiological studies have been reported in Malawi owing to lack of laboratories with molecular tools. We characterized the genetic diversity of Mtb clinical isolates amongst TB patients in Blantyre, Malawi. We genotyped 64 Mtb clinical isolates using LSP-PCR, assigned specific lineages and confirmed 18 of the isolates using SMRT sequencing. The 64 isolates clustered into 4 lineages (L1-L4) with L4 predominating. There were 10/64 (16%) isolates belonging to L1, 6/64 (9%) belonging to L2, 2/64 (3%) belonging to L3 and 46/64 (72%) belonging to L4. Comparison with a previous study done in Karonga revealed concordance in L1 and L4 but discodance in L2 and L3. The phylogenetic tree constructed, comprised of 3/4 lineages present in Blantyre with 3/18 belonging to L1, 3/18 belonging to L2 and 12/18 belonging to L4. Four Mtb lineages were present in Blantyre with L4 predominating. Larger studies are needed to understand the molecular epidemiology of TB in Blantyre in light of increased bi-directional migration with South Africa.

Highlights

There were 10 million new cases and 1.3 million deaths due to tuberculosis (TB) with a further 0.4 million due to coinfection with HIV in 2017 [1]
Sixty-four bacteriologically culture confirmed Mycobacterium tuberculosis (Mtb) positive samples were selected based on the first to be successfully revived from a total of 133 isolates and subjected to genomic deletion analysis
The analysis revealed 6 (9%) East Asian lineage (L2) (RD 105 deleted) strains generating a deleted product ~785bp on gel electrophoresis, 10 (16%) (L1) Indo-oceanic lineage (RD 239 deleted) strains, 2 (3%) East African/ Indian lineage (L3) (RD750 deleted) strains and 46 (L4) (72%) EuroAmerican lineage strains (Fig. 1)

Summary

Introduction

There were 10 million new cases and 1.3 million deaths due to tuberculosis (TB) with a further 0.4 million due to coinfection with HIV in 2017 [1]. Africa remains the hardest hit in terms of rates of active TB per capita [2, 3, 4] and the highest proportion of TB cases co-infected with HIV are in Africa (31%) with Southern Africa bearing the greatest burden (>50%) [5]. Malawi is among the top 20 high TB burden countries with the highest estimated number of incident TB cases among people living with HIV [4]. A lack of laboratories with molecular tools has hampered efforts to conduct Mycobacterium tuberculosis (Mtb) molecular epidemiology studies in Malawi and in most other low resource settings. Mtb molecular epidemiological data for the rest of the country is lacking. Knowledge of changes in the predominant circulating Mtb strains in Blantyre may aid in understanding the local TB epidemic and refining TB control strategies

Methods

Results

Conclusion