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Biomedicines Apr 2022The upper respiratory tract (URT) microbiome can contribute to the acquisition and severity of respiratory viral infections. The described associations between URT...
The upper respiratory tract (URT) microbiome can contribute to the acquisition and severity of respiratory viral infections. The described associations between URT microbiota and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are limited at microbiota genus level and by the lack of functional interpretation. Our study, therefore, characterized the URT bacterial microbiome at species level and their encoded pathways in patients with COVID-19 and correlated these to clinical outcomes. Whole metagenome sequencing was performed on nasopharyngeal samples from hospitalized patients with critical COVID-19 ( = 37) and SARS-CoV-2-negative individuals ( = 20). Decreased bacterial diversity, a reduction in commensal bacteria, and high abundance of pathogenic bacteria were observed in patients compared to negative controls. Several bacterial species and metabolic pathways were associated with better respiratory status and lower inflammation. Strong correlations were found between species biomarkers and metabolic pathways associated with better clinical outcome, especially and pathways of vitamin K biosynthesis. Our study demonstrates correlations between the URT microbiome and COVID-19 patient outcomes; further studies are warranted to validate these findings and to explore the causal roles of the identified microbiome biomarkers in COVID-19 pathogenesis.
PubMed: 35625719
DOI: 10.3390/biomedicines10050982 -
MSphere Jan 2021nasal carriage provides the bacterial reservoir for opportunistic infection. In comparing the nasal microbiomes of culture-defined persistent carriers versus...
nasal carriage provides the bacterial reservoir for opportunistic infection. In comparing the nasal microbiomes of culture-defined persistent carriers versus noncarriers, we detected DNA in all noses, including those with an established history of negativity based on culture. Colonization with , including , , , and select spp., was associated with noncarriage. We next developed physiological competition assays for testing anti- activity of isolated nasal species, utilizing medium modeling the nutrient-limited fluid of the nasal mucosa, polarized primary nasal epithelia, and nasal secretions. from the nose of an noncarrier demonstrated >99% inhibition of recovery in all assays, even when was coincubated in 9-fold excess. Secreted inhibitory proteins from and were heat-stable and <30 kDa, fitting the profile of antimicrobial peptides. , , , and inhibited recovery on nasal epithelia in a contact-dependent manner, while several other species either had no effect or promoted growth. Collectively, this project is one of the first to identify resident nasal microbial species that impede survival, and it implies that detectable nasal results from shifts in microbial community composition. Nasal carriage of is a risk factor for infection, but it is not yet understood why some individuals carry nasal persistently, intermittently, or seemingly not at all when tested via culture methods. This study compared the nasal microbiomes of established carriers and noncarriers, identified species associated with noncarriage, and tested them for anti- activity using assays developed to model the nutrient-limited nasal mucosa. We determined that all nostril swabs contain DNA, even swabs from hosts considered to be long-term noncarriers. Select members of the class were more prevalent in noncarrier than carrier nostrils and demonstrated potent activity against multiple strains of The results described here provide a better understanding of how the nasal microbiome controls growth and viability and may be useful in the design of improved decolonization strategies.
Topics: Anti-Bacterial Agents; Antibiosis; Carrier State; Cells, Cultured; Epithelial Cells; Gammaproteobacteria; Humans; Microbiota; Nasal Cavity; Staphylococcus aureus
PubMed: 33408227
DOI: 10.1128/mSphere.01015-20 -
Microbial Genomics Oct 2021Acute respiratory infections (ARIs) constitute one of the leading causes of antibiotic administration, hospitalization and death among children <5 years old. The upper...
Acute respiratory infections (ARIs) constitute one of the leading causes of antibiotic administration, hospitalization and death among children <5 years old. The upper respiratory tract microbiota has been suggested to explain differential susceptibility to ARIs and modulate ARI severity. The aim of the present study was to investigate the relation of nasopharyngeal microbiota and other microbiological parameters with respiratory health and disease, and to assess nasopharyngeal microbiota diagnostic utility for discriminating between different respiratory health statuses. We conducted a prospective case-control study at Hospital Sant Joan de Deu (Barcelona, Spain) from 2014 to 2018. This study included three groups of children <18 years with gradual decrease of ARI severity: cases with invasive pneumococcal disease (IPD) (representative of lower respiratory tract infections and systemic infections), symptomatic controls with mild viral upper respiratory tract infections (URTI), and healthy/asymptomatic controls according to an approximate case-control ratio 1:2. Nasopharyngeal samples were collected from participants for detection, quantification and serotyping of pneumococcal DNA, viral DNA/RNA detection and 16S rRNA gene sequencing. Microbiological parameters were included on case-control classification models. A total of 140 subjects were recruited (IPD=27, URTI=48, healthy/asymptomatic control=65). Children's nasopharyngeal microbiota composition varied according to respiratory health status and infection severity. The IPD group was characterized by overrepresentation of , higher frequency of invasive pneumococcal serotypes, increased rate of viral infection and underrepresentation of potential protective bacterial species such as and . Microbiota-based classification models differentiated cases from controls with moderately high accuracy. These results demonstrate the close relationship existing between a child's nasopharyngeal microbiota and respiratory health, and provide initial evidence of the potential of microbiota-based diagnostics for differential diagnosis of severe ARIs using non-invasive samples.
Topics: Adolescent; Bacteria; Carnobacteriaceae; Case-Control Studies; Child; Child, Preschool; Female; Health Status; Humans; Male; Microbiota; Moraxella; Nasopharynx; Pneumococcal Infections; Prospective Studies; RNA, Ribosomal, 16S; Respiratory System; Respiratory Tract Infections; Streptococcus pneumoniae
PubMed: 34699345
DOI: 10.1099/mgen.0.000661