Persistent Legionnaires’ Disease and Associated Antibiotic Treatment Engender a Highly Disturbed Pulmonary Microbiome Enriched in Opportunistic Microorganisms

Abstract

Despite the importance of pneumonia to public health, little is known about the composition of the lung microbiome during infectious diseases, such as pneumonia, and how it evolves during antibiotic therapy. To study the possible relation of the pulmonary microbiome to the severity and outcome of this respiratory disease, we analyzed the dynamics of the pathogen and the human lung microbiome during persistent infections caused by the bacterium Legionella pneumophila and their evolution during antimicrobial treatment. We collected 10 bronchoalveolar lavage fluid samples from three patients during long-term hospitalization due to pneumonia and performed a unique longitudinal study of the interkingdom microbiome, analyzing the samples for presence of bacteria, archaea, fungi, and protozoa by high-throughput Illumina sequencing of marker genes. The lung microbiome of the patients was characterized by a strong predominance of the pathogen, a low diversity of the bacterial fraction, and an increased presence of opportunistic microorganisms. The fungal fraction was more stable than the bacterial fraction. During long-term treatment, no genomic changes or antibiotic resistance-associated mutations that could explain the persistent infection occurred, according to whole-genome sequencing analyses of the pathogen. After antibiotic treatment, the microbiome did not recover rapidly but was mainly constituted of antibiotic-resistant species and enriched in bacteria, archaea, fungi, or protozoa associated with pathogenicity. The lung microbiome seems to contribute to nonresolving Legionella pneumonia, as it is strongly disturbed during infection and enriched in opportunistic and/or antibiotic-resistant bacteria and microorganisms, including fungi, archaea, and protozoa that are often associated with infections. IMPORTANCE The composition and dynamics of the lung microbiome during pneumonia are not known, although the lung microbiome might influence the severity and outcome of this infectious disease, similar to what was shown for the microbiome at other body sites. Here we report the findings of a comprehensive analysis of the lung microbiome composition of three patients with long-term pneumonia due to L. pneumophila and its evolution during antibiotic treatment. This work adds to our understanding of how the microbiome changes during disease and antibiotic treatment and points to microorganisms and their interactions that might be beneficial. In addition to bacteria and fungi, our analyses included archaea and eukaryotes (protozoa), showing that both are present in the pulmonary microbiota and that they might also play a role in the response to the microbiome disturbance.

Interkingdom Gut Microbiome and Resistome of the Cockroach Blattella germanica

“…In fact, we identified some keystone species, which deserve further research to clarify their role in the equilibrium of the gut microbiome. The network groups showed a phylogenetic signal as they tend to contain bacteria belonging mainly to one phylum, a trend that has also been found in the human bacterial microbiome (56,57). The cooccurrence of closely related microorganisms indicates that cooperation predominates over competition in these taxonomic groups.…”

Altered Ecology of the Respiratory Tract Microbiome and Nosocomial Pneumonia

“…The detection of microbial eukaryotes (fungi and protozoa), archaea, and viruses have been neglected in RTM research. However, through the application of “omics,” the RTM composition of non-bacterial microorganisms is starting to be described (Koskinen et al, 2017 ; Xu et al, 2017 ; Pérez-Cobas et al, 2020a ). The mycobiome and virome should be considered a high priority due to the contribution of viruses and fungi in the development of respiratory infections (Wu and Segal, 2018 ).…”

“…The mycobiome and virome should be considered a high priority due to the contribution of viruses and fungi in the development of respiratory infections (Wu and Segal, 2018 ). In pneumonia and other infectious diseases, intra- (bacteria-bacteria, fungi-fungi) and inter-kingdom interactions (bacteria-fungi, bacteria-viruses) seem to influence the severity of the infections and might have a role in host-microbiome equilibrium restoration after disease remission (Molyneaux et al, 2013 ; Pérez-Cobas et al, 2020a ). Since the microbial ecosystem works as a network of connections, it is wise to consider bacteria and their interactions with other kingdoms to treat infections.…”

“…Marker genes derived data provided a vision on the relative abundance of the taxa; however, the absolute abundance values are often not estimated. Therefore, the marker genes approach combined with quantification methods of the selected fractions such as qPCR, spikes, or droplet-digital PCR will be relevant to have a more accurate picture of the microbiome evolution during disease, considering not only the relative abundance but the biomass dynamics (Dickson et al, 2020 ; Pérez-Cobas et al, 2020a ).…”

Evolution of Animal Microbial Communities in Response to Environmental Stress

“…The detection of microbial eukaryotes (fungi and protozoa), archaea, and viruses have been neglected in RTM research. However, through the application of "omics, " the RTM composition of non-bacterial microorganisms is starting to be described (Koskinen et al, 2017;Xu et al, 2017;Pérez-Cobas et al, 2020a). The mycobiome and virome should be considered a high priority due to the contribution of viruses and fungi in the development of respiratory infections (Wu and Segal, 2018).…”