Title: Using genomic approaches to understand drug resistance evolution of Mycobacterium tuberculosis

Author: Stefan Niemann^1,2

Affiliations: ¹Molecular and Experimental Mycobacteriology, Research Center Borstel, Parkallee 1, 23845 Borstel, Germany; ²German Center for Infection Research, Borstel Site, Borstel, Germany

Abstract: Multidrug resistant (MDR), Pre-extensively drug resistant (Pre-XDR), and XDR Mycobacterium tuberculosis complex (MTBC) strains have emerged worldwide and represent a serious challenge for global tuberculosis (TB) control. In several areas of the world, high rates of MDR TB have been associated with strains of particular phylogenetic MTBC lineages such as L2 (Beijing). Detailed data on the genetic diversity of particular MDR-TB outbreak strains, possible transmission networks and on their evolution are urgently needed esp. in light of implementation of the new WHO MDR TB treatment regimens.

Here, Next Generation Sequencing (NGS) based whole genome sequencing (WGS) allows for completely new approaches by analysing nearly complete genome sequences of clinical MTBC strains. This allows for high-resolution strain typing e.g. for outbreak analysis or even for comprehensive molecular epidemiological studies in combination with information on virtually all target genes involved in resistance development (resistome analysis).

We applied WGS to investigate population structure, transmission dynamics and evolution of MDR/XDR MTBC strains in different settings of the world. Besides previous assumptions that suggested a lower virulence of MDR strains, clonal expansion of particular outbreak strains and step-wise fixation of resistance mediating mutations appear to be an important factor driving the MDR TB epidemic in different settings of the world such as Eastern Europe, and India. Particular MDR outbreak clones have gained high resistance levels even to new WHO group A MDR TB treatment drugs in line with compensatory mutations that obviously allow for effective transmission.

The data obtained argue for the implementation of rapid molecular diagnostics linked to individualized MDR TB treatment to ensure effective MDR TB therapy and breaking transmission chains. Prospective genome based surveillance is essential to detect emergence of new MTBC MDR clones and to closely monitor resistance levels.