2024-09-09 09:15:55
Scientists have managed to sequence, from the type of secretions released by the patient, the complete genome of the bacteria that causes the disease, and compare it with bacterial cultures.
The breakthrough is the work of a group led by Carla Mariner-Llicer, from the Institute of Biomedicine of Valencia (IBV), based at the Higher Council for Scientific Research (CSIC) in Spain.
This new genomic sequencing method is much faster than other traditional methods and makes it possible to quickly diagnose tuberculosis from the patient’s sputum, an easy way to get samples.
The new method, in addition to having the ability to speed up the diagnosis of the disease, allows to obtain a complete genetic profile of the tuberculosis bacillus, which, unlike the molecular methods currently used, offers complete information on drug resistance and mutations.
The method was modified and tested with samples from patients in Mozambique and Georgia.
Using genetic sequencing techniques, members of the IBV Tuberculosis Genomics Unit compared the genetic diversity of Mycobacterium tuberculosis, the bacteria that causes tuberculosis, found in patient sputum samples, with their corresponding cultures. .
This method of growing bacteria from patient samples is more than a century old, but it is still the most used to diagnose asthma in countries where the disease is limited.
According to data from the World Health Organization (WHO), tuberculosis is the second most deadly infectious disease after COVID-19, and in 2022 it will cause 1.3 million deaths.
“Some studies suggest that the culture process may not capture all the genetic diversity of the patient sample due to the presence of lines or strains that are better suited to growth in in vitro conditions,” explains Carla Mariner, CSIC researcher at IBV and first author of the work. “We use cultures not only for diagnosis, but also to study the genes of bacteria, therefore, if this hypothesis is true, it will show the inconsistency in the tests and the scientific results that can lead to to a mistake,” he said. researcher
To investigate if this is true, the IBV group has designed the aforementioned technique to collect and analyze the genome of Mycobacterium tuberculosis from sputum and by direct sequencing, and compare it with their respective cultures. “Getting direct sequencing of the complete genome of a sample such as sputum is complicated, because the presence of bacteria in the sample is minimal compared to commensal microbiota or human cells,” argues Mariana Gabriela López, one of the CSIC researchers who lead .the work. “We have developed procedures that allow direct derivation and, therefore, we have been able to compare the difference of sputum with that of culture.”
Mycobacterium tuberculosis. (Photo: NIAID/CDC)
Rely on seed genetics
The IBV team analyzed samples from two countries with high and medium incidence of tuberculosis, Mozambique and Georgia, and validated the method with three previously published data sets of samples from the countries. various. The results show that the genetic diversity of tuberculosis bacteria obtained by sequencing is expressed in culture in all the scenarios analyzed. “The genetic differences between the culture and the sputum are minimal, which indicates that the culture does not change the genetic information,” Mariner summarizes. “In addition, when we compared the drug resistance profile by sputum sequencing and cultures we found no differences, which supports the reliability of the culture.”
“Working with sputum is a challenge because these are complex samples with a small amount of M. tuberculosis. Despite this, it provides a great advantage, since it is fast to get results from weeks to days,” said said Iñaki Comas, director of the Tuberculosis Genomics Unit of the IBV. For this reason, there is a great interest in the development of culture-free sequencing techniques, although until now studies have not obtained sufficient reference quality to analyze in depth the genetic diversity present in the samples and compare it with traditions, treat scientist from. the CSIC.
Treatment lasts a few days instead of weeks
This study is the first in which 61 sputum has been successfully collected, including samples with 1% of bacteria. “The genetic sequencing of M. tuberculosis allows us to have all the information that we can compare with the molecular analysis methods or the sequencing of the genes recommended by the WHO for the diagnosis of tuberculosis,” says Comas. . “On the other hand, by knowing the complete genome with the physiological process we can identify many potential antibiotic mutations and even carry out epidemiological studies.”
The biggest disadvantage of cultures is the slow growth of bacteria, which can delay the reception of results for more than a month, during which time the patient will not receive adequate treatment. “With the sputum extract, the diagnosis will be done more quickly, not only identifying the bacteria but also obtaining its resistance profile. This will allow better treatment to be given to the patient in a few days instead of waiting weeks,” Comas summarized.
Although the current direct sputum analysis technique is not optimized for use in clinical practice, especially in terms of costs, this study marks an important step towards its future implementation, CSIC researchers emphasize. Therefore, the IBV Tuberculosis Genomics Unit is designing the next steps to bring the method closer to clinical practice.
Experts from the Barcelona Institute for Global Health (ISGlobal) collaborated in the study; Swiss Institute of Public and Tropical Health (Swiss TPH), Manhiça Health Research Center (CISMM) in Mozambique; and the National Center for Tuberculosis and Lung Diseases in Tbilisi, Georgia.
The study is titled “Genetic variation between sputum samples is demonstrated in the culture of Mycobacterium tuberculosis across different settings.” And it was published in the academic journal Nature Communications. (Source: Isidoro García / CSIC)
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