Dataset Information

Whole genome sequencing for tuberculosis in Victoria, Australia: A genomic implementation study from 2017 to 2020.

ABSTRACT:

Background

Whole genome sequencing (WGS) is increasingly used by tuberculosis (TB) programs to monitor Mycobacterium tuberculosis (Mtb) transmission. We aimed to characterise the molecular epidemiology of TB and Mtb transmission in the low-incidence setting of Victoria, Australia, and assess the utility of WGS.

Methods

WGS was performed on all first Mtb isolates from TB cases from 2017 to 2020. Potential clusters (≤12 single nucleotide polymorphisms [SNPs]) were investigated for epidemiological links. Transmission events in highly-related (≤5 SNPs) clusters were classified as likely or possible, based on the presence or absence of an epidemiological link, respectively. Case characteristics and transmission settings (as defined by case relationship) were summarised. Poisson regression was used to examine associations with secondary case number.

Findings

Of 1844 TB cases, 1276 (69.2%) had sequenced isolates, with 182 (14.2%) in 54 highly-related clusters, 2-40 cases in size. Following investigation, 140 cases (11.0% of sequenced) were classified as resulting from likely/possible local-transmission, including 82 (6.4%) for which transmission was likely. Common identified transmission settings were social/religious (26.4%), household (22.9%) and family living in different households (7.1%), but many were uncertain (41.4%). While household transmission featured in many clusters (n = 24), clusters were generally smaller (median = 3 cases) than the fewer that included transmission in social/religious settings (n = 12, median = 7.5 cases). Sputum-smear-positivity was associated with higher secondary case numbers.

Interpretation

WGS results suggest Mtb transmission commonly occurs outside the household in our low-incidence setting. Further work is required to optimise the use of WGS in public health management of TB.

Funding

The Victorian Tuberculosis Program receives block funding for activities including case management and contact tracing from the Victorian Department of Health. No specific funding for this report was received by manuscript authors or the Victorian Tuberculosis Program, and the funders had no role in the study design, data collection, data analysis, interpretation or report writing.

SUBMITTER: Dale K

PROVIDER: S-EPMC9405109 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature

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Publications

Whole genome sequencing for tuberculosis in Victoria, Australia: A genomic implementation study from 2017 to 2020.

Dale Katie K Globan Maria M Horan Kristy K Sherry Norelle N Ballard Susan S Tay Ee Laine EL Bittmann Simone S Meagher Niamh N Price David J DJ Howden Benjamin P BP Williamson Deborah A DA Denholm Justin J

The Lancet regional health. Western Pacific 20220818

<h4>Background</h4>Whole genome sequencing (WGS) is increasingly used by tuberculosis (TB) programs to monitor <i>Mycobacterium tuberculosis</i> (<i>Mtb</i>) transmission. We aimed to characterise the molecular epidemiology of TB and <i>Mtb</i> transmission in the low-incidence setting of Victoria, Australia, and assess the utility of WGS.<h4>Methods</h4>WGS was performed on all first <i>Mtb</i> isolates from TB cases from 2017 to 2020. Potential clusters (≤12 single nucleotide polymorphisms [SN ...[more]

PMID: 36034164

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Dataset Information

Whole genome sequencing for tuberculosis in Victoria, Australia: A genomic implementation study from 2017 to 2020.

Background

Methods

Findings

Interpretation

Funding

Publications

Whole genome sequencing for tuberculosis in Victoria, Australia: A genomic implementation study from 2017 to 2020.

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