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

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Tuberculosis, caused by Mycobacterium tuberculosis (Mtb), remains a serious global healthproblem, with increasing drug resistance (DR-TB) complicating disease control. Less than 1/3of DR-TB cases are detected, contributing to the ongoing transmission and spread of resistantstrains [1]. Current methods for Mtb detection and DR-TB diagnosis are non-timely or useonly limited molecular markers [2]. Rapid tools to detect DR-TB, their transmission, andunderstand the genetic diversity of loci interacting with the human host, are urgentlyneeded. Transmission events can be identified by finding (near-)identical Mtb genomes [3],and we are applying whole genome sequencing (WGS), bioinformatic and phylogeneticanalysis techniques to understand DR-TB transmissibility globally (including in South Africaand Thailand). The proposed project will generate both portable Oxford Nanopore MinION"real-time" and high-throughput Illumina sequencing data with global partnering clinics andlaboratories. We will assess the performance of MinION technology to:(1) Characterise DR-TB in clinical samples, using both WGS and targeted amplicon candidateloci 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 interactwith 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 understandgenetic diversity in DR-TB loci. The MinION platform, molecular amplicon design tools, andbioinformatic pipelines are established in our laboratory [2]. The project will be supervised byTaane Clark (genomic epidemiology, PI on studies generating data), Susana Campino(microbiology, WGS), and Jody Phelan ((bio)informatics). This project uses cutting-edgesequencing technologies and "big data" bioinformatics methods, and it is expected tofacilitate the deployment of a MinION platform from bench to near-patient settings. Theproject will lead to scientific papers in journals of high standing that provide insights intotransmission and DR-TB genetics.