Rapid drug resistance and transmission profiling of tuberculosis using portable genome sequencing technology

Tuberculosis, caused by Mycobacterium tuberculosis (Mtb), remains a serious global health problem, with increasing drug resistance (DR-TB) complicating disease control. Less than 1/3 of DR-TB cases are detected, contributing to the ongoing transmission and spread of resistant strains [1]. Current methods for Mtb detection and DR-TB diagnosis are non-timely or use

only limited molecular markers [2]. Rapid tools to detect DR-TB, their transmission, and understand the genetic diversity of loci interacting with the human host, are urgently needed. Transmission events can be identified by finding (near-)identical Mtb genomes [3], and we are applying whole genome sequencing (WGS), bioinformatic and phylogenetic

analysis techniques to understand DR-TB transmissibility globally (including in South Africa and Thailand). The proposed project will generate both portable Oxford Nanopore MinION "real-time" and high-throughput Illumina sequencing data with global partnering clinics and laboratories. We will assess the performance of MinION technology to:

(1) Characterise DR-TB in clinical samples, using both WGS and targeted amplicon candidate loci assays; (2) Understand transmission patterns of DR-TB using phylogenetic-based analyses; (3) Assess genetic diversity in highly variable genes (e.g. pe/ppe families), which can interact with the human host and are potential vaccine candidates.

A large inhouse WGS dataset of ~37k global Mtb samples (with phenotypic DR-TB data) [2-5] is immediately available for "mining" using big-data methods, including to understand genetic diversity in DR-TB loci. The MinION platform, molecular amplicon design tools, and bioinformatic pipelines are established in our laboratory [2]. The project will be supervised by

Taane Clark (genomic epidemiology, PI on studies generating data), Susana Campino (microbiology, WGS), and Jody Phelan ((bio)informatics). This project uses cutting-edge sequencing technologies and "big data" bioinformatics methods, and it is expected to facilitate the deployment of a MinION platform from bench to near-patient settings. The

project will lead to scientific papers in journals of high standing that provide insights into transmission and DR-TB genetics.