Mycobacterium tuberculosis

Although Australia has a low and stable Mycobacterium tuberculosis incidence rate, there is ongoing risk of imported cases from countries that have a high incidence¹. With Australia committed to eliminating Mycobacterium tuberculosis, genomic investigation will be required to enhance identification and analysis of transmission among Australian cases. This disease will be led by a team of clinical and public health microbiologists, genomic epidemiologists, and representatives from the National TB Advisory Committee (NTAC).

¹ health.gov.au

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Projects

Establish national surveillance system to identify Mycobacterium tuberculosis (MTB) clusters and antimicrobial resistance (AMR) (MTB surveillance system)

Aim: To establish a centralised national surveillance system for MTB and integrate onto AusTrakka.

1. To transition national surveillance protocols onto AusTrakka (e.g. Core-genome multilocus sequence typing (cgMLST) and AMR tools).
2. Undertake pilot project to identify MTB transmission clusters and characterise AMR trends.

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Validate high resolution typing scheme for identifying MTB clusters (MTB) typing scheme)

Aim: Validate a harmonised MTB cgMLST scheme for MTB genomic surveillance.

1. Using national retrospective MTB genomes and metadata, assess if cgMLST is concordant with core genome SNPs, lineages and MTB clusters.
2. Characterise cgST trends over time and if cgSTs correlate with geography or source.

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Genomics informed AMR detection for MTB

Aim: To develop a genomic tool for harmonised in silico detection of MTB AMR and assess predictive capacity towards first and second line anti-tuberculous drugs.

1. Collate characterised MTB AMR conferring mutations into AMR tool
2. Undertake pilot project to assess predictive capacity of AMR tool and identify and characterise MTB AMR and determine AMR patterns using national MTB datasets

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