Identifying missing links - an ongoing outbreak of a novel tuberculosis strain in regional Queensland

Tuberculosis (TB) is a global public health problem, and community outbreaks occur. We report an outbreak of TB with an unusual MPT64 negative status, first detected in North Queensland, Australia, in 2017-2018.

A retrospective epidemiological and laboratory investigation into potentially linked cases was undertaken. Whole genome sequencing (WGS) phylogenetic and cluster analysis was performed. A confirmed outbreak case was defined as genomically closely related and a probable case as epidemiologically linked to a confirmed case, in the absence of WGS. Demographic characteristics and risk factors of outbreak cases were compared to other Australian-born cases in Queensland using univariate analysis. The aim of this study was to describe the outbreak, identify any associated risk factors and compare the epidemiological and genomic links between cases.

Between 2002-2023, a total of 47 outbreak cases were identified: 44 (94%) were genomically linked and three (6%) were epidemiologically linked. Cases were all adults; 29 (64%) were male; 40 (89%) had pulmonary TB, of whom 30 (75%) were sputum smear positive. Compared to other Australian born cases, outbreak cases were more likely to be aged 25-44 years; to be Aboriginal and Torres Strait Islander peoples (First Nations peoples); to be residents of Central and Northern Queensland; and to experience a less successful TB treatment outcome (p < 0.05). Homelessness, previous incarceration, and substance use were significantly associated with being an outbreak case (p < 0.01). WGS analysis provided links for ten cases (24%) where no epidemiological links were identified.

Ongoing local transmission of a unique TB strain has persisted in Queensland's First Nations communities and presents an opportunity to reconfigure TB prevention and care efforts in partnership with local communities. This study demonstrates the importance of integrating genomic data with traditional case investigation and contact tracing information, enhancing public health surveillance and targeted interventions to optimise TB management in high-risk populations.