Tuberculosis (TB) diagnosis has got a major boost with researchers developing a new approach that relies on direct sequencing of DNA extracted from sputum to detect and characterize the bacteria that cause TB. This method eliminates the need for long drawn-out processes of culturing bacteria in the laboratory.

The new technique is known as metagenomics, defined as the study of genetic material collected directly from environmental samples. It involves applying genomic techniques to study microbial communities in their natural environments without the need to culture or cultivate them in the lab. In this case, the sample would be the sputum of the patient suspected of having TB. The technique was developed by researchers working in the UK and Gambia. A paper on it has been published Tuesday in the journal PeerJ.

While conventional laboratory diagnosis to identify TB takes weeks or months, metagenomics would take just up to a few hours, says Professor Mark Pallen, director of the research. “Relying on laboratory culture means using techniques that date back to the 1880s! Metagenomics using the latest high-throughput sequencing technologies and some smart bioinformatics, allows us to detect and characterize the bacteria that cause TB in a matter of a day or two, without having to grow the bacteria, while also giving us key insights into their genome sequences and the lineages that they belong to,” he said in a statement.

Great diversity exists among species Mycobacterium, and rapid identification of the pathogenic strain is a must for effective treatment of tuberculosis. The researchers, with the help of metagenomics, detected sequences from the TB bacteria in all eight sputum samples they investigated and were able to assign the bacteria to a known lineage in seven of the samples. Two samples were found to contain sequences from Mycobacterium africanum, a species of Mycobacterium most commonly found in West African countries.

In spite of being a preventable disease, TB still affects millions of people in underdeveloped and developing countries. According to the World Health Organization, in 2012 an estimated 8.6 million people developed TB and 1.3 million died from the disease.

The team is confident that this new technique can help develop new diagnostic tools for detecting TB. The team earlier used metagenomics to successfully isolate pathogenic strains from human samples. For example, they successfully identified the genome of E.Coli, which caused an infectious outbreak last year. Metagenomics was also used on historical samples when the team isolated the genome of Brucella melitensis, a bacterium which causes an infection called brucellosis in livestock and humans, from a 700-year-old skeleton from Sardinia, Italy.

While more improvements are needed to fully integrate metagenomics in the diagnosis and analysis of infectious pathogens, the research team says that successful identification of the TB lineages provides proof of its effectiveness.

Source: Doughty E, Sergeant M, Adetifa I, Antonio M, Pallen M. Culture independent detection and characterisation of Mycobacterium tuberculosis and M. africanum in sputum samples using shotgun metagenomics on a bench top sequencer. PeerJ. 2014.