A new approach quickly diagnoses tuberculosis by relying on direct sequencing of DNA taken from sputum. The technique, called metagenomics, detects and characterizes the bacteria that cause TB without taking several weeks for bacterial cultures.
“Laboratory diagnosis of TB using conventional approaches is a long drawn-out process, which takes weeks or months,” says Mark Pallen, professor of microbial genomics at University of Warwick Medical School.
“Plus, 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.”
In the new study, published in the journal PeerJ, researchers worked to develop and exploit novel sequencing and analytic approaches.
“TB is still a big problem in Africa and across the world. It is exciting to be involved in the development of new diagnostic approaches for this deadly disease,” says Martin Antonio, head of the TB diagnostics laboratory at the Medical Research Council Unit in The Gambia.
The team 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 variety of the TB bacterium that is particular to West Africa.
The researches have used shotgun metagenomics before to detect bacterial pathogens in contemporary and historical human material. Last year, they used metagenomics to obtain an outbreak strain genome from stool samples from an E. coli outbreak and to recover TB genomes from Hungarian mummies approximately 200 years-old.
Earlier this year, they recovered the genome of Brucella melitensis, which causes an infection called brucellosis in livestock and humans, from a 700-year-old skeleton from Sardinia, Italy.
The researchers aim to test the metagenomics technique on a wide range of samples—and hope it will help detect mixed infections caused by more than one kind of bacterium. But metagenomics is still some way from routine diagnostic use, Pallen says.
“We have provided proof-of-principle here, but we still need to make metagenomics more sensitive and improve our workflows.”
Source: University of Warwick