An international team of scientists, led by researchers at the Yale School of Public Health, has adapted a technique originally used to track COVID-19 variants to rapidly sequence the genome of Mycobacterium tuberculosis, the bacteria that causes tuberculosis (TB). The method, called tiled amplicon sequencing, reduces the time required to analyze TB samples from weeks to days and lowers testing costs to under $20 per sample, according to a study published in the Journal of Clinical Microbiology.
The process involves preparing small pieces of DNA, known as amplicons, that copy specific parts of the TB genome. By overlapping these amplicons, researchers can reconstruct the complete genome without first culturing the bacteria – a traditionally time-consuming step. This approach proved effective even with samples containing low concentrations of bacteria or mixed with other microbial species, as demonstrated in tests using samples from patients in Moldova and Peru.
The World Health Organization (WHO) has emphasized the need for rapid, cost-effective TB diagnostics, particularly for drug-resistant strains. Next-generation sequencing (NGS) technologies, endorsed by the WHO, have improved the detection of drug-resistant TB, but the high cost of many sequencing systems has limited access in low- and middle-income countries. Portable sequencing technologies, coupled with tiled amplicon sequencing, offer a potential solution by reducing infrastructure requirements.
Researchers have successfully used a long-read sequencing approach, processing data with a bioinformatics pipeline designed for that purpose, to identify resistance-associated variants detected by more traditional short-read sequencing. While the long-read approach showed limitations in detecting low-frequency variants, it represents a significant step toward accessible genomic surveillance of TB.
The adaptation of tiled amplicon sequencing for TB builds on its earlier success in tracking viruses like Zika and, more recently, monitoring the evolution of SARS-CoV-2 during the COVID-19 pandemic. The technique allows public health authorities to tailor responses to TB outbreaks with greater precision, potentially transforming tuberculosis surveillance and care globally.
A study published in PubMed details the use of portable sequencing platforms alongside the tiled amplicon sequencing assay, demonstrating successful identification of high-frequency resistance-associated variants. Further research is ongoing to improve the detection of low-frequency variants, enhancing the sensitivity of the method.
