What is already known
Bacterial pneumonia is a lung infection caused by certain bacteria, and it can be life-threatening in young children, people older than 65 and individuals with weakened immune systems. Previous research has suggested that the respiratory tract microbiota may protect against pathogens, but the effects of this bacterial community on pneumonia remain unclear.
What this research adds
Researchers analyzed the respiratory microbiota of 38 hospitalized people with pneumonia caused by Legionella pneumophila. The microbiotas of people with pneumonia were characterized by an enrichment in Microbacteriaceae, Stenotrophomonas, Pseudomonas and Mycoplasma, a low bacterial diversity and the presence of opportunistic pathogens such as the fungus Candida albicans. The researchers also identified a group of bacteria associated with a healthy respiratory tract microbiota, which they dubbed “commensal” cluster, and a group of bacteria enriched with pathogens, which they dubbed “pathogenic” cluster. The levels of Legionella were associated with disease severity, with fungi, archaea and protozoa contributing to the progress of pneumonia. Clinical interventions such as mechanical ventilations were also associated with more severe disease.
Conclusions
The findings suggest that the interplay between the respiratory tract microbiota, the levels of bacterial pathogens and specific clinical interventions is a key factor in determining the outcome of bacterial pneumonia.
Bacterial pneumonia is a lung infection, caused by certain bacteria, that can be life-threatening in young children, people older than 65 and individuals with weakened immune systems. Now, researchers have found that high bacterial and fungal loads are a marker of alterations in the respiratory tract microbiota, and that the balance between a “commensal” and a “pathogenic” group of microbes in the respiratory tract can tip the scale towards recovery from bacterial pneumonia or severe disease.
The findings, published in Cell Reports Medicine, suggest that the interplay between the respiratory microbiota, the levels of bacterial pathogens and specific clinical interventions is a key factor in determining the outcome of bacterial pneumonia.
The effects of the respiratory tract microbiota on pneumonia remain unclear, although previous research has suggested that this microbial community may protect against pathogens.
To investigate whether the composition of the respiratory microbiota influences disease severity, researchers led by Ana Elena Pérez-Cobas at the Institut Pasteur in Paris analyzed the respiratory microbiota of 38 hospitalized people with pneumonia caused by Legionella pneumophila, a bacterium that was among the pathogens responsible for an estimated 7.7 million deaths globally in 2019.
Altered microbiota
The researchers found that the respiratory microbiotas of people with pneumonia were characterized by an enrichment in Microbacteriaceae, Stenotrophomonas, Pseudomonas and Mycoplasma, a low bacterial diversity and the presence of opportunistic pathogens such as the fungus Candida albicans.
The most abundant bacteria identified in people with pneumonia were Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria and Fusobacteria, with the most common genera including Escherichia coli, Haemophilus parainfluenzae, Legionella pneumophila, Staphylococcus aureus and Veillonella dispar.
The researchers identified a group of bacteria, which they dubbed “commensal” cluster, that was enriched in beneficial bacteria generally found in the respiratory microbiota of healthy individuals. This cluster included Prevotella, Streptococcus, Veillonella and Haemophilus. Another group of bacteria, including Staphylococcus, Stenotrophomonas, Enterobacteriaceae and Legionella, was dubbed the “pathogenic” cluster.
Microbial balance
Further analyses suggested that during hospitalization and therapy, Legionella bacteria were replaced by other potential pathogens that could occupy its niche in the lungs. What’s more, higher levels of Legionella were observed in men and people with weakened immune systems.
Specific clinical interventions also had an effect on disease severity. People that were helped to breathe with a mechanical ventilator had a different respiratory microbiota composition, with higher levels of Legionella and lower bacterial diversity and richness compared to people who were not on a mechanical ventilator. Other pathogens, including Staphylococcus and Mycoplasma, were associated with ventilation, the researchers found.
“The interaction of the [respiratory tract microbiota] equilibrium and the pathogen load dynamics, together with clinical interventions, are crucial factors in the severity and outcome of bacterial pneumonia,” the authors say.
