Mycobacterium tuberculosis clinical care and transmission - insights gained using whole genome sequencing

Abstract

The aim of the research presented in this thesis was to improve laboratory, public health & clinical aspects of tuberculosis care & control using advances in genome sequencing, bioinformatic & statistical methods.

I compared the performance of mycobacterial interspersed repetitive unit (MIRU) typing with whole genome sequencing for tracking transmission of Mycobacterium tuberculosis. Subsequently, I investigated the processes contributing to false MIRU clustering among the modern lineages of M. tuberculosis. My analysis confirmed the presence of extensive homoplasy, but found no evidence of natural selection.

I explored the limits of whole-genome sequencing to track transmission pathways within a cluster of tuberculosis cases in NSW, using high-depth sequencing, de novo assembly, inclusion of small indels, placement of reference sequences as outliers, & combined analysis of the cluster phylogeny together with epidemiologic data.

Using the first case report of extensively drug-resistant (XDR) tuberculosis in the state of NSW, I demonstrated that resistance profiles derived from whole-genome sequencing could provide actionable & timely information to clinicians.

I investigated source & contact demographic, clinical & epidemiologic parameters associated with tuberculosis transmission to child household contacts. We found the expected association between source case sputum smear status & infection in close child contacts, as measured by tuberculin skin test (TST) reactivity, but the strongest association was with Bacille Calmette Guérin (BCG) vaccination. BCG was also associated with chest clinic decisions to treat contacts for latent tuberculosis infection (LTBI) or active disease, & this association was mediated by TST reactivity.

The findings of my research have helped inform strategies adopted in NSW during transition from legacy MIRU & phenotypic susceptibility testing to routine prospective whole genome sequencing of all M. tuberculosis isolates.