Insertion Element IS6110 based characterisation of Nepalese tuberculosis strains into different genetic lineages

Kartyk Moganeradj,Timothy D Mchugh,Dunstan Rajendram,Ibrahim Abubakar,Deanna A Hagge,Murdo Macdonald,Pam Sonnenberg,Saraswoti Khadge,Catherine Arnold

doi:10.15761/cmid.1000101

Abstract

Nepal is geographically located between India and China, a region containing significant Tuberculosis (TB) and Multi-Drug Resistance (MDR-TB) burdens. However, limited information is available on the phylogenetic diversity of Mycobacterium tuberculosis (Mtb) in Nepal. To gain further insight into the diversity of Mtb in Nepal, consecutive clinical samples from 176 newly diagnosed pulmonary tuberculosis patients were collected from two hospitals in Nepal. Insertion Site IS6110 Fluorescent Amplified Fragment Length Polymorphism (FAFLP) PCR and rpoB sequence analysis were carried out on genomic DNA extracts of cultured strains to assign them to accepted genetic lineages and identify MDR-TB. In this study, the IS6110 based characterisation showed a prevalence of 36.36% Central Asian Strain (CAS), 18.75% Beijing, 7.95 % Haarlem, 3.97% X, 2.2% each of Latin American Mediterranean (LAM), T-Uganda and T, 1.7% S and 24.4% were unassigned. Further, 3.9% of total M. tuberculosis isolates were of rifampicin resistant genotypes thus indicating that the prevalence of MDR could be higher than the country wide prevalence of MDR among new TB cases (2.2%) as reported by the national drug resistance survey carried out in 2011/2012.

Highlights

TB is ranked as the sixth leading cause of death among the top 20 causes of death in Nepal
Sputum samples from 176 consecutive new TB patients over one year were collected between 2007 and 2008 and cultured alongside routine diagnostics from two Nepalese tuberculosis reference centres located in the Kathmandu valley: the National Tuberculosis Centre (NTC) and the German Nepal Tuberculosis Project (GENETUP)
Our results indicate that the prevalence of Rifampicin (RIF) resistant TB was higher than the nationally reported 2.2% MDR in new untreated cases

Summary

Introduction

TB is ranked as the sixth leading cause of death among the top 20 causes of death in Nepal. According to National Tuberculosis Control Programme (NTCP) in Nepal, in 2014 37,025 TB cases were registered and among them 15,947 (43%) cases were new sputum smear positive TB cases. It was estimated by WHO [1] that 4.6 (2.1-7.5) thousand people in Nepal died from TB in 2014. Even though short course TB drug treatment regimen could cure around 89% of cases, TB mortality was still unacceptably high in Nepal. Drug resistant TB (DR-TB) still threatens national TB control and is a major public health concern. The proportion of MDR-TB cases in new cases was 2.2% and retreatment cases were 15.4%. Even though the Millennium Development Goal (MDG) to halt and reverse TB incidence has been achieved in all six WHO regions, work remains to be done to prevent the deaths from this dreadful disease [1]

Methods

Discussion

Conclusion