Abstract
Viruses are responsible for most of both upper and lower acute respiratory infections (ARIs). The microbiome—the ecological community of microorganisms sharing the body space, which has gained considerable interest over the last decade—is modified in health and disease states. Even if most of these disturbances have been previously described in relation to chronic disorders of the gastrointestinal microbiome, after a short reminder of microbiome characteristics and methods of characterization, this review will describe the impact of the microbiome (mainly respiratory) on host responses to viral ARIs. The microbiome has a direct environmental impact on the host cells but also an indirect impact on the immune system, by enhancing innate or adaptive immune responses. In microbial infections, especially in viral infections, these dramatic modifications could lead to a dramatic impact responsible for severe clinical outcomes. Studies focusing on the microbiome associated with transcriptomic analyses of the host response and deep characterization of the pathogen would lead to a better understanding of viral pathogenesis and open avenues for biomarker development and innovative therapeutics.
Highlights
After a first period focusing on the characterization of the composition and the physiological variations of the “healthy” respiratory microbiome, most recent studies have focused on changes induced during a so-called “pathological” situation, infectious or not
Bacterial microbiota could interact directly with viral pathogens. Such an interaction has not been described in the respiratory tract but it is known that some enteric viruses bind bacterial lipopolysaccharides (LPS) to stabilize their entry into the target cells or to induce unresponsiveness to itself [27,28]
The development of Generation Sequencing (NGS) technologies has led to a dramatic increase in microbiome understanding in physiological and pathological situations
Summary
Acute respiratory infections (ARIs) are the most common type of acute infection worldwide in both adults and children and are mainly caused by viruses, including respiratory syncytial virus (RSV), human rhinovirus (hRV), influenza virus (IV), or metapneumovirus (hMPV). In Europe, lower respiratory tract infection is the eighth leading cause of disease in both adults and children [1]. ARIs account for an estimated 40% of all healthcare-associated infections in pediatric long-term care facilities [2]. Most of these viral infections could lead to very severe forms of respiratory diseases. It is estimated that 33.8 million new episodes of RSV-associated acute respiratory infection occurred worldwide in children younger than 5 years of age, during the 2005 epidemics, with at least. Attempts to prevent respiratory viral infections are currently limited to vulnerable high-risk groups such as immunocompromised patients, the elderly, or young children and include optimized vaccination, reduced exposure and prophylactic treatment. Vaccines 2017, 5, 40 presentation and the difficulties with anticipating clinical complications of respiratory infections, it is necessary to better understand their pathophysiology
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