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Flu alters the gut microbiota and its resistance to common antibiotics

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A study coordinated by researchers from Universidad CEU San Pablo, from the Virology and Innate Immunity Groups (VII), and MICROAMB-Environmental Bacterial Biotechnology, together with researchers from the Geneva Center of Inflammation Research, the School of Medicine at the University of Geneva and the Icahn School of Medicine at Mount Sinai Hospital in New York have published a paper in the American Association for Microbiology's journal Microbiology Spectrum demonstrating that infection with the influenza A virus changes the lung and gut microbiota. This, in turn, affects its resistance to common antibiotics such as those used for ear or throat infections.

The analysis also reveals that, during the first days after infection, the ability of the gut microbiota to metabolise sugars is reduced, something that is recovered five to seven days later. As one of the main authors, virologist Estanislao Nistal, explains that: “We have analysed changes related to antibiotic resistance in gut bacterial communities of mice infected with a flu virus. It has been observed that resistance to families of antibiotics as common as cephalosporins that are used for ear and throat infections, pneumonia, or meningitis, among other diseases, temporarily increases in the gut microbiota”.

Traditionally, the study of antibiotic resistance is carried out using populations of bacteria isolated from a patient. Our approach studies this resistance in bacterial communities, in which many bacteria together determine the resistance of the community. This strategy would allow a better choice of antibiotics in more individualised treatments. Knowing the behaviour of a microbial community (such as gut bacteria) could allow us to anticipate therapeutic failure due to the application of an ineffective antibiotic for a patient”, explains Pedro Jiménez, co-lead author of the study.

Knowledge of antibiotic resistance in bacterial communities has been limited due to the complexity associated with its interpretation. Resistance to a given antibiotic can vary depending on which bacteria and which resistance mechanisms are present in a community. This study shows that influenza infections not only alter the composition of the gut microbiota, but also its metabolic capacity and response to certain antibiotics. Diseases affecting the gut microbiota can alter its activity and metabolic function, including resistance to orally administered antibiotics. “Functional characterization of these complex communities is essential, although currently it is largely limited to taxonomic descriptions. Knowing the functional changes could significantly influence treatment strategies, especially in infections caused by several microbes at the same time,” explain Marina Robas and Jesús Presa, first signatories of the study.

Some organs in our body host a complex and dynamic microscopic world known as the microbiota, where bacteria play a key role. “Thanks to advanced genomic sequencing techniques, we can now identify the bacteria present in our body, even those that are difficult to study in the laboratory due to their resistance to being cultured; in this study we propose techniques to study their 'group response', beyond their traditional use ”, states Nistal.

This advance has served to improve the treatment of inflammatory bowel diseases such as Crohn's disease and ulcerative colitis, and is transforming our understanding of dysbiosis and its relationship with conditions such as neurological diseases and cancer, among others. However, despite being able to know which bacteria are present, most research does not focus on what determines their group behaviour and its consequences. This study goes a step further by trying to understand how bacteria behave in groups, something that remains a challenge, especially when trying to interpret the relationship between such behaviour and its connection to different diseases and the way to treat them.

More information:

Robas M, Presa J, Arranz-Herrero J, Yildiz S, Rius-Rocabert S, Llinares-Pinel F, Probanza A, Schmolke M, Jiménez PA, Nistal-Villan E. Influenza A virus infection alters the resistance profile of gut microbiota to clinically relevant antibiotics. Microbiol Spectr. 2023 Dec 5:e0363522. doi: 10.1128/spectrum.03635-22. Epub ahead of print. PMID: 38051056.

Palabras clave Flu Research Microbiology Medicine Pharmacy