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The Journal of Allergy and Clinical... Mar 2024The respiratory microbiome has been associated with the etiology and disease course of asthma.
BACKGROUND
The respiratory microbiome has been associated with the etiology and disease course of asthma.
OBJECTIVE
We sought to assess the nasopharyngeal microbiota in children with a severe asthma exacerbation and their associations with medication, air quality, and viral infection.
METHODS
A cross-sectional study was performed among children aged 2 to 18 years admitted to the medium care unit (MCU; n = 84) or intensive care unit (ICU; n = 78) with an asthma exacerbation. For case-control analyses, we matched all cases aged 2 to 6 years (n = 87) to controls in a 1:2 ratio. Controls were participants of either a prospective case-control study or a longitudinal birth cohort (n = 182). The nasopharyngeal microbiota was characterized by 16S-rRNA-gene sequencing.
RESULTS
Cases showed higher Shannon diversity index (ICU and MCU combined; P = .002) and a distinct microbial community composition when compared with controls (permutational multivariate ANOVA R = 1.9%; P < .001). We observed significantly higher abundance of Staphylococcus and "oral" taxa, including Neisseria, Veillonella, and Streptococcus spp. and a lower abundance of Dolosigranulum pigrum, Corynebacterium, and Moraxella spp. (MaAsLin2; q < 0.25) in cases versus controls. Furthermore, Neisseria abundance was associated with more severe disease (ICU vs MCU MaAslin2, P = .03; q = 0.30). Neisseria spp. abundance was also related with fine particulate matter exposure, whereas Haemophilus and Streptococcus abundances were related with recent inhaled corticosteroid use. We observed no correlations with viral infection.
CONCLUSIONS
Our results demonstrate that children admitted with asthma exacerbations harbor a microbiome characterized by overgrowth of Staphylococcus and "oral" microbes and an underrepresentation of beneficial niche-appropriate commensals. Several of these associations may be explained by (environmental or medical) exposures, although cause-consequence relationships remain unclear and require further investigations.
PubMed: 38467291
DOI: 10.1016/j.jaci.2024.02.020 -
PLoS Pathogens Feb 2024
Topics: Gram-Positive Cocci; Carnobacteriaceae
PubMed: 38300905
DOI: 10.1371/journal.ppat.1011955 -
Scientific Reports Nov 2023Crohn's disease (CD) is a chronic inflammatory bowel disease. An imbalanced microbiome (dysbiosis) can predispose to many diseases including CD. The role of oral...
Crohn's disease (CD) is a chronic inflammatory bowel disease. An imbalanced microbiome (dysbiosis) can predispose to many diseases including CD. The role of oral dysbiosis in CD is poorly understood. We aimed to explore microbiome signature and dysbiosis of the salivary microbiome in CD patients, and correlate microbiota changes to the level of inflammation. Saliva samples were collected from healthy controls (HC) and CD patients (n = 40 per group). Salivary microbiome was analyzed by sequencing the entire 16S rRNA gene. Inflammatory biomarkers (C-reactive protein and calprotectin) were measured and correlated with microbiome diversity. Five dominant species were significantly enriched in CD, namely Veillonella dispar, Megasphaera stantonii, Prevotella jejuni, Dolosigranulum pigrum and Lactobacillus backii. Oral health had a significant impact on the microbiome since various significant features were cariogenic as Streptococcus mutans or periopathogenic such as Fusobacterium periodonticum. Furthermore, disease activity, duration and frequency of relapses impacted the oral microbiota. Treatment with monoclonal antibodies led to the emergence of a unique species called Simonsiella muelleri. Combining immunomodulatory agents with monoclonal antibodies significantly increased multiple pathogenic species such as Salmonella enterica, Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa. Loss of diversity in CD was shown by multiple diversity indices. There was a significant negative correlation between gut inflammatory biomarkers (particularly calprotectin) and α-diversity, suggesting more inflammation associated with diversity loss in CD. Salivary dysbiosis was evident in CD patients, with unique microbiota signatures and perturbed species that can serve as disease biomarkers or potential targets for microbiota modulation. The interplay of various factors collectively contributed to dysbiosis, although each factor probably had a unique effect on the microbiome. The emergence of pathogenic bacteria in the oral cavity of CD patients is alarming since they can disturb gut homeostasis and induce inflammation by swallowing, or hematogenous spread of microbiota, their metabolites, or generated inflammatory mediators.
Topics: Humans; Crohn Disease; Dysbiosis; RNA, Ribosomal, 16S; Gastrointestinal Microbiome; Microbiota; Inflammation; Biomarkers; Antibodies, Monoclonal; Leukocyte L1 Antigen Complex
PubMed: 37932491
DOI: 10.1038/s41598-023-46714-8 -
IDCases 2023is an anaerobic, gram-positive coccus rarely identified as a pathogenic organism. However, case reports have suggested as a causative pathogen in bacteremia,...
is an anaerobic, gram-positive coccus rarely identified as a pathogenic organism. However, case reports have suggested as a causative pathogen in bacteremia, nosocomial pneumonia, ventilator-associated pneumonia, synovitis, cholecystitis, and ophthalmologic infections. Herein, we present the first case of causing native mitral valve infective endocarditis. With the exception of erythromycin, the isolate displayed favorable minimum inhibitory concentrations (MIC) to all other antibiotics tested, including beta-lactams, levofloxacin, and vancomycin. The patient was successfully treated with a 6-week course of intravenous (IV) ceftriaxone followed by robotically assisted cardiac valve repair.
PubMed: 37645537
DOI: 10.1016/j.idcr.2023.e01818 -
Design and validation of Dolosigranulum pigrum specific PCR primers using the bacterial core genome.Scientific Reports Apr 2023Dolosigranulum pigrum-a lactic acid bacterium that is increasingly recognized as an important member of the nasal microbiome. Currently, there are limited rapid and...
Dolosigranulum pigrum-a lactic acid bacterium that is increasingly recognized as an important member of the nasal microbiome. Currently, there are limited rapid and low-cost options for confirming D. pigrum isolates and detecting D. pigrum in clinical specimens. Here we describe the design and validation of a novel PCR assay targeting D. pigrum that is both sensitive and specific. We designed a PCR assay targeting murJ, a single-copy core species gene identified through the analysis of 21 D. pigrum whole genome sequences. The assay achieved 100% sensitivity and 100% specificity against D. pigrum and diverse bacterial isolates and an overall 91.1% sensitivity and 100% specificity using nasal swabs, detecting D. pigrum at a threshold of 1.0 × 10 D. pigrum 16S rRNA gene copies per swab. This assay adds a reliable and rapid D. pigrum detection tool to the microbiome researcher toolkit investigating the role of generalist and specialist bacteria in the nasal environment.
Topics: Humans; RNA, Ribosomal, 16S; Gram-Positive Bacterial Infections; Gram-Positive Cocci; Polymerase Chain Reaction; DNA Primers; DNA, Bacterial
PubMed: 37059715
DOI: 10.1038/s41598-023-32709-y -
Clinical Ophthalmology (Auckland, N.Z.) 2023The Covid-19 pandemic introduced significant changes in our daily life, including the widespread use of face masks. The purpose of this study was to assess if...
PURPOSE
The Covid-19 pandemic introduced significant changes in our daily life, including the widespread use of face masks. The purpose of this study was to assess if significant changes occurred in the microbiological profile of infectious keratitis.
PATIENTS AND METHODS
A retrospective study was performed, based on a survey review of the electronic medical records of all patients with presumed infectious keratitis, between March 2020 and October 2021. The microbiological isolates in this sample (pandemic group) were compared with those obtained in our center between 2009 and 2018 (pre-pandemic group).
RESULTS
A total of 194 samples were included in the pandemic group. We obtained a culture-positivity rate of 43.3%, which was significantly higher when compared with the pre-pandemic data (35.15%, p = 0.033). Several further significant differences were found between the pandemic and the pre-pandemic groups: the proportion of bacteria, including gram-positive and gram-negative groups, was higher in our sample (pre-pandemic vs pandemic: 76.78% vs 83.33%, p = 0.010; 53.35% vs 60.71%, p = 0.016; 23.43% vs 34.52%, p = 0.005, respectively); two populations of Gram-positive bacteria found in this study were not isolated in the pre-pandemic sample - and spp.; and two bacterial isolates were significantly increased in our sample - spp. (18.41% vs 29.76%, p = 0.003) and (9.00% vs 16.66%, p = 0.012).
CONCLUSION
In conclusion, significant changes were found in the microbiological profile of infectious keratitis in our center during the Covid-19 pandemic. While these changes could be related to face mask use, more observational and experimental studies are needed to explore this possible association.
PubMed: 36798798
DOI: 10.2147/OPTH.S395877 -
Frontiers in Cellular and Infection... 2022The human nose harbors various microbes that decisively influence the wellbeing and health of their host. Among the most threatening pathogens in this habitat is ....
The human nose harbors various microbes that decisively influence the wellbeing and health of their host. Among the most threatening pathogens in this habitat is . Multiple epidemiological studies identify as a likely beneficial bacterium based on its positive association with health, including negative associations with . Carefully curated GEMs are available for both bacterial species that reliably simulate their growth behavior in isolation. To unravel the mutual effects among bacteria, building community models for simulating co-culture growth is necessary. However, modeling microbial communities remains challenging. This article illustrates how applying the fosters our understanding of two microbes' joint growth conditions in the nasal habitat and their intricate interplay from a metabolic modeling perspective. The resulting community model combines the latest available curated GEMs of and . This uses case illustrates how to incorporate genuine GEM of participating microorganisms and creates a basic community model mimicking the human nasal environment. Our analysis supports the role of negative microbe-microbe interactions involving examined experimentally in the lab. By this, we identify and characterize metabolic exchange factors involved in a specific interaction between and as an candidate factor for a deep insight into the associated species. This method may serve as a blueprint for developing more complex microbial interaction models. Its direct application suggests new ways to prevent disease-causing infections by inhibiting the growth of pathogens such as through microbe-microbe interactions.
Topics: Humans; Staphylococcus aureus; Methicillin-Resistant Staphylococcus aureus; Nose; Staphylococcal Infections; Bacteria; Microbiota
PubMed: 36605126
DOI: 10.3389/fcimb.2022.925215 -
Scientific Reports Nov 2022Nasal decolonization procedures against the opportunistic pathogen Staphylococcus aureus rely on topical antimicrobial drug usage, whose impact on the nasal microbiota...
Nasal decolonization procedures against the opportunistic pathogen Staphylococcus aureus rely on topical antimicrobial drug usage, whose impact on the nasal microbiota is poorly understood. We examined this impact in healthy S. aureus carriers and noncarriers. This is a prospective interventional cohort study of 8 S. aureus carriers and 8 noncarriers treated with nasal mupirocin and chlorhexidine baths. Sequential nasal swabs were taken over 6 months. S. aureus was detected by quantitative culture and genotyped using spa typing. RNA-based 16S species-level metabarcoding was used to assess the living microbial diversity. The species Dolosigranulum pigrum, Moraxella nonliquefaciens and Corynebacterium propinquum correlated negatively with S. aureus carriage. Mupirocin treatment effectively eliminated S. aureus, D. pigrum and M. nonliquefaciens, but not corynebacteria. S. aureus recolonization in carriers occurred more rapidly than recolonization by the dominant species in noncarriers (median 3 vs. 6 months, respectively). Most recolonizing S. aureus isolates had the same spa type as the initial isolate. The impact of mupirocin-chlorhexidine treatment on the nasal microbiota was still detectable after 6 months. S. aureus recolonization predated microbiota recovery, emphasizing the strong adaptation of this pathogen to the nasal niche and the transient efficacy of the decolonization procedure.
Topics: Humans; Mupirocin; Staphylococcus aureus; Chlorhexidine; Prospective Studies; Cohort Studies; Carrier State; Staphylococcal Infections; Microbiota
PubMed: 36396730
DOI: 10.1038/s41598-022-21453-4 -
Bioscience of Microbiota, Food and... 2022On March 11, 2020, the World Health Organization declared a pandemic of coronavirus infectious disease 2019 (COVID-19) caused by severe acute respiratory syndrome... (Review)
Review
On March 11, 2020, the World Health Organization declared a pandemic of coronavirus infectious disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and imposed the biggest public health challenge for our civilization, with unforeseen impacts in the subsequent years. Similar to other respiratory infections, COVID-19 is associated with significant changes in the composition of the upper respiratory tract microbiome. Studies have pointed to a significant reduction of diversity and richness of the respiratory microbiota in COVID-19 patients. Furthermore, it has been suggested that , and are associated with severe COVID-19 cases, while and are significantly more abundant in asymptomatic subjects or with mild disease. These results have stimulated the search for new microorganisms from the respiratory microbiota with probiotic properties that could alleviate symptoms and even help in the fight against COVID-19. To date, the potential positive effects of probiotics in the context of SARS-CoV-2 infection and COVID-19 pandemics have been extrapolated from studies carried out with other viral pathogens, such as influenza virus and respiratory syncytial virus. However, scientific evidence has started to emerge demonstrating the capacity of immunomodulatory bacteria to beneficially influence the resistance against SARS-CoV-2 infection. Here we review the scientific knowledge regarding the role of the respiratory microbiota in viral infections in general and in the infection caused by SARS-CoV-2 in particular. In addition, the scientific work that supports the use of immunomodulatory probiotic microorganisms as beneficial tools to reduce the severity of respiratory viral infections is also reviewed. In particular, our recent studies that evaluated the role of immunomodulatory strains in the context of SARS-CoV-2 infection are highlighted.
PubMed: 35846832
DOI: 10.12938/bmfh.2022-009 -
Zhejiang Da Xue Xue Bao. Yi Xue Ban =... Dec 2021To explore the application value of nanopore sequencing technique in the diagnosis and treatment of secondary infections in patients with severe coronavirus disease 2019...
To explore the application value of nanopore sequencing technique in the diagnosis and treatment of secondary infections in patients with severe coronavirus disease 2019 (COVID-19). A total of 77 clinical specimens from 3 patients with severe COVID-19 were collected. After heat inactivation, all samples were subjected to total nucleic acid extraction based on magnetic bead enrichment. The extracted DNA was used for DNA library construction, then nanopore real-time sequencing detection was performed. The sequencing data were subjected to Centrifuge software database species matching and R program differential analysis to obtain potential pathogen identification. Nanopore sequencing results were compared with respiratory pathogen qPCR panel screening and conventional microbiological testing results to verify the effectiveness of nanopore sequencing detection. Nanopore sequencing results showed that positive pathogen were obtained in 44 specimens (57.1%). The potential pathogens identified by nanopore sequencing included , , and , et al. , , were also detected in clinical microbiological culture-based detection; was detected in respiratory pathogen screening qPCR panel; was only detected by the nanopore sequencing technique. Comprehensive considerations with the clinical symptoms, the patient was treated with antibiotics against , and the infection was controlled. Nanopore sequencing may assist the diagnosis and treatment of severe COVID-19 patients through rapid identification of potential pathogens.
Topics: COVID-19; Coinfection; Humans; Nanopore Sequencing; Nanopores; Sequence Analysis, DNA
PubMed: 35347908
DOI: 10.3724/zdxbyxb-2021-0158