Shotgun for the diagnosis of tuberculosis
Tuberculosis was diagnosed in two days
The so-called "shotgun method" allows relatively quickly to identify and determine the characteristics of the causative agent of the disease, eliminating the need for long-term cultivation of bacteria in the laboratory. The work was published in the journal PeerJ (Doughty et al., Culture-independent detection and characterization of Mycobacterium tuberculosis and M. africanum in sputum samples using shotgun metagenomics on a benchtop sequencer).
The disadvantages of the standard laboratory diagnosis of tuberculosis, which has not changed since the 1880s, include not only the duration of the process (cultivation of sputum samples can take weeks and months), but also the difficulty of determining the strains of the causative agent of infection using a conventional microscope, as well as the difficulty of diagnosis in the case of mixed infection. Professor Mark Pallen from the School of Medicine at the University of Warwick (UK) and his colleagues propose to replace this outdated method with modern metagenomics methods that allow avoiding all these disadvantages.
To determine the bacterial genome, Pallen and his collaborators used the "shotgun method" used in sequencing long sections of DNA. Its essence consists in splitting the genome into random fragments, which are then sequenced by conventional methods. The overlapping nucleotide sequences obtained in this way are then assembled using special programs into a single whole. Using the Illumina MiSeq desktop sequencer, scientists identified the DNA of a tuberculosis bacterium in all eight sputum samples studied and were able to determine the strain of the pathogen in seven of them. The process took one or two days.
The study was designed to fundamentally confirm the possibility of using the method for the diagnosis of tuberculosis. Now Pallen's group plans to continue exploring its capabilities on a wider range of samples.
Portal "Eternal youth" http://vechnayamolodost.ru24.09.2014