2023-12-11 12:15:59
Antibiotic-resistant bacteria are one of the world’s main public health problems. Among the 10 bacteria that cause the most deaths due to their resistance to antibiotics is Mycobacterium tuberculosis, the cause of tuberculosis, the most lethal infectious disease on the planet until the appearance of COVID-19. An estimated 200,000 people will die in 2022 from some form of multidrug-resistant (multidrug-resistant) tuberculosis. Added to this is the cost for health systems: treating a case of susceptible tuberculosis costs 180 euros in European countries, but can reach 200,000 in cases with more complicated resistance.
Having diagnostics that quickly and accurately detect antibiotic resistance is vital to personalize treatment and prevent the development of additional resistance. The method currently used in hospitals is based on the culture of samples from the infected patient, which in the case of Mycobacterium tuberculosis takes weeks, to obtain the resistance profile of the bacteria (its phenotype). These resistances are caused by genetic mutations, so that specific changes in DNA are always associated with resistance to specific antibiotics. In 2021, the WHO published the first catalog of mutations associated with resistance of Mycobacterium tuberculosis, being the most complete study to date.
Iñaki Comas, from the Higher Council for Scientific Research (CSIC) in Spain, participated in its preparation. His group at the Institute of Biomedicine of Valencia (IBV), headed by researcher Victoria Furió, has now used massive sequencing techniques of the genetic material (DNA) of this bacteria to predict which antibiotics it is resistant to and how this prediction could improve the diagnosis and treatment of the disease. Massive sequencing techniques allow the DNA sequence of any living being to be determined quickly and accurately, and their main advantage is that they can be used on a large scale.
“Our project consists of evaluating our ability to predict resistance using the WHO catalogue, particularly in an environment of low resistance such as the Valencian Community,” explains Victoria Furió. “To do this, we sequence the DNA extracted from samples of tuberculosis patients and obtain the resistance profile of the drugs used in the treatment through genomic prediction. Subsequently, we compare the resistance profile obtained with massive sequencing with that obtained through phenotypic testing, which is the current reference method, and we check how accurate the prediction is and the improvement it can represent in the diagnosis.”
Scanning electron micrograph of bacteria of the species Mycobacterium tuberculosis (colored in red and yellow). This species causes tuberculosis. (Image: NIAID)
The project has been carried out with the collaboration of 25 hospitals in the Valencian Community, which have provided the 785 clinical samples included in the study, as well as the resistance data of the reference method that they apply in clinical laboratories. The samples were processed in the biosafety laboratory of the Foundation for the Promotion of Health and Biomedical Research of the Valencian Community (Fisabio). The IBV researchers (attached to the CSIC) studied the four first-line antibiotics for the treatment of tuberculosis, obtaining a specificity greater than 99.5% and a sensitivity range between 85 and 50% depending on the antibiotic through sequencing. massive DNA.
“We found great complementarity between the two methods,” says Iñaki Comas. “Although genomics correctly predicts the vast majority of resistances, there were examples only detected by cultivation. We also found examples in the other direction, where genomics outperformed the standard method. In fact, thanks to genomic prediction we were able to detect two new cases of multidrug-resistant tuberculosis and eleven cases of fluoroquinolone-monoresistant tuberculosis,” says the CSIC researcher.
According to Comas, the main advantages of using massive sequencing in the diagnosis of resistance are the speed, “if it is carried out at the moment a positive culture for tuberculosis is detected”, and the large number of applications that access to the complete genome provides. of the bacteria. This allows, simultaneously, to establish the resistance profile for the entire spectrum of drugs (not just the four main ones); identify cases of antibiotic resistance that are missed by the reference method; and obtain information to carry out epidemiological and transmission analyses. “With a single determination of the genome we can predict resistance and epidemiological relationships between cases,” summarizes Comas.
This IBV team belongs to the Networked Biomedical Research Center for Epidemiology and Public Health (CIBERESP) in Spain and the Interdisciplinary Thematic Platform for Global Health of the CSIC, and was a pioneer in Spain in the use of these massive sequencing techniques to determine the variants in the coronavirus associated with successive waves in the recent COVID-19 pandemic.
The study is titled “Role of the first WHO mutation catalog in the diagnosis of antibiotic resistance in Mycobacterium tuberculosis in the Valencia Region, Spain: a retrospective genomic analysis.” It has been published in the academic journal The Lancet Microbe. And the first signatory is Ana María García-Marín, from the Institute of Biomedicine of Valencia. (Source: Isidoro García / CSIC)
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