Researchers at the University of Melbourne’s Microbiological Diagnostic Unit Public Health Laboratory (MDU PHL) at the Doherty Institute have developed an open-access genomic software tool that enables clinicians to accurately detect antibiotic resistance in tuberculosis (TB) and use the results to guide patient care.
By supporting faster diagnosis and more targeted treatment, the tool, known as tbtAMR, helps improve patient outcomes and strengthens antibiotic stewardship in the global fight against drug-resistant TB.
The world’s first ISO-accredited tool of its kind, tbtAMR analyses the genome of Mycobacterium tuberculosis, the TB-causing bacterium, to identify drug-resistance mutations and reports the results in a clinician-ready format. By sequencing the bacteria, the software pinpoints the most effective treatment options for each patient and rapidly relays this information to treating doctors.
TB remains one of the leading causes of death from infectious diseases globally and rising rates of drug-resistant TB make accurate and timely treatment decisions increasingly critical.
While whole-genome sequencing has transformed TB research, its clinical use has been limited by the lack of validated and accredited testing pipelines that laboratories can confidently use for patient care. tbtAMR, described in a new study in The Lancet Digital Health, is changing this.
The University of Melbourne’s Dr Kristy Horan, a Bioinformatician at the Doherty Institute and first author of the paper, said the tool is efficient and uniquely designed for real-world use in frontline clinical laboratories, including settings with no dedicated bioinformatics expertise.
“In our study, tbtAMR correctly identified resistance to first-line TB drugs in almost 95 per cent of cases, while also accurately detecting drug-susceptible infections more than 97 per cent of the time. Its performance matched or exceeded other widely used genomic tools,” said Dr Horan.
“It’s already in routine clinical use at the Doherty Institute and produces results within timeframes comparable to traditional laboratory testing.
“The tool accepts standard sequencing files, detects a wide range of genetic changes associated with antibiotic resistance and rapidly reports which drugs are most likely to be effective for each patient, making it a useful resource to control and treat drug-resistant TB, especially in low-resource settings.”
Large-scale testing using over 15,000 TB genome sequences from public databases and accredited laboratories, showed that tbAMR reliably detects resistance mutations and identifies TB lineages across diverse samples, validating its effectiveness in real-world conditions.
The University of Melbourne’s Associate Professor Norelle Sherry, Deputy Director at MDU PHL at the Doherty Institute and senior author of the paper, said the team also developed thorough processes to ensure laboratories are able to use tbAMR accurately, giving doctors and patients confidence in the results.
“Our goal was not just to build a powerful tool, but to make sure it could be trusted in real clinical settings and readily accessible,” said Associate Professor Sherry.
To support widespread use of the new tool, the MDU PHL team has made tbtAMR freely and publicly available on the Centre for Pathogen Genomics portal. It runs on a user-friendly Windows-based format and does not require command-line expertise, therefore making high-quality genomic testing far more accessible globally.
Additionally, the tbtAMR validation datasets, reporting templates and accreditation methods have also been made available for other labs to use to implement and accredit tbtAMR in their own settings.
“Free and public access to tbAMR allows laboratories worldwide, particularly those in low- and middle-income countries, to easily analyse TB genomic data, with outputs that are ready to report back to clinicians to guide optimal patient management,” added Associate Professor Sherry.
More updates and news from the Doherty Institute
Public Health
