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Frontiers in Microbiology 2021Microbiome mediates early life immune deviation in asthma development. Recurrent wheeze (RW) in pre-school years is a risk factor for asthma diagnosis in school-age...
Microbiome mediates early life immune deviation in asthma development. Recurrent wheeze (RW) in pre-school years is a risk factor for asthma diagnosis in school-age children. Dysbiosis exists in asthmatic airways, while its origin in pre-school years and relationship to RW is not clearly defined. This study investigated metagenomics of nasopharyngeal microbiome in pre-school children with RW. We applied whole-genome shotgun sequencing and human rhinovirus (HRV) detection on nasopharyngeal samples collected from three groups of pre-school children: (i) RW group: 16 children at-risk for asthma who were hospitalized for RW, (ii) inpatient control (IC): 18 subjects admitted for upper respiratory infection, and (iii) community control (CC): 36 children without respiratory syndromes. Sequence reads were analyzed by MetaPhlAn2 and HUMAnN2 algorithm for taxonomic and functional identification. Linear discriminant analysis effect size (LEfSe) analysis was used to identify discriminative features. We identified that and were predominant species in nasopharynx. RW had lower alpha diversity (Shannon diversity index) than CC (0.48 vs. 1.07; = 0.039), characterized by predominant Proteobacteria. LEfSe analysis revealed was the only discriminative species across groups (LDA = 5.57, = 0.002), with its relative abundance in RW, IC, and CC being 9.6, 14.2, and 37.3%, respectively ( < 0.05). LEfSe identified five (ribo)nucleotides biosynthesis pathways to be group discriminating. Adjusting for HRV status, pre-school children with RW have lower nasopharyngeal biodiversity, which is associated with Proteobacteria predominance and lower abundance of . Along with discriminative pathways found in RW and CC, these microbial biomarkers help to understand RW pathogenesis.
PubMed: 35250904
DOI: 10.3389/fmicb.2021.792556 -
Microorganisms Jun 2021Previously, we demonstrated that the nasal administration of 040417 differentially modulated the respiratory innate immune response triggered by the activation of...
Previously, we demonstrated that the nasal administration of 040417 differentially modulated the respiratory innate immune response triggered by the activation of Toll-like receptor 2 in infant mice. In this work, we aimed to evaluate the beneficial effects of 040417 in the context of infection and characterize the role of alveolar macrophages (AMs) in the immunomodulatory properties of this respiratory commensal bacterium. The nasal administration of 040417 to infant mice significantly increased their resistance to pneumococcal infection, differentially modulated respiratory cytokines production, and reduced lung injuries. These effects were associated to the ability of the 040417 strain to modulate AMs function. Depletion of AMs significantly reduced the capacity of the 040417 strain to improve both the reduction of pathogen loads and the protection against lung tissue damage. We also demonstrated that the immunomodulatory properties of are strain-specific, as 030918 was not able to modulate respiratory immunity or to increase the resistance of mice to an infection. These findings enhanced our knowledge regarding the immunological mechanisms involved in modulation of respiratory immunity induced by beneficial respiratory commensal bacteria and suggested that particular strains could be used as next-generation probiotics.
PubMed: 34207076
DOI: 10.3390/microorganisms9061324 -
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 -
Cureus Aug 2020In this report, we describe a case of a 61-year-old male patient who had the bacterium growing in a blood culture. It was susceptible to ampicillin, ceftriaxone,...
In this report, we describe a case of a 61-year-old male patient who had the bacterium growing in a blood culture. It was susceptible to ampicillin, ceftriaxone, levofloxacin, and vancomycin but was intermediately resistant to erythromycin. The patient did not have a negative outcome as a consequence of this bacterium, which retrospectively could have been predicted based on the epidemiological data within the patient's profile.
PubMed: 32953288
DOI: 10.7759/cureus.9770 -
Journal of Clinical Microbiology Jun 2000We evaluated three rapid identification systems-The Biomerieux rapid ID 32 STREP (ID32), the BBL Crystal rapid gram-positive identification (Crystal), and the Remel IDS... (Comparative Study)
Comparative Study
We evaluated three rapid identification systems-The Biomerieux rapid ID 32 STREP (ID32), the BBL Crystal rapid gram-positive identification (Crystal), and the Remel IDS RapID STR (IDS) systems-for their ability to identify 7 strains of Alloiococcus otitidis, 27 strains of Dolosigranulum pigrum, 3 strains of Ignavigranum ruoffiae, and 18 strains of 4 different Facklamia species. Since none of these six species of gram-positive cocci are included in the identification databases for these systems, the correct identification for the strains tested should be "unacceptable ID" for the ID32 and Crystal systems or "no choice" for the IDS system. The ID32 system identified all 27 strains of D. pigrum, 6 of 18 Facklamia species, and 2 of 3 cultures of I. ruoffiae as "unacceptable ID." The Crystal system identified 10 of 27 D. pigrum, 2 of 18 Facklamia species, and 2 of 3 I. ruoffiae strains as "unacceptable ID." The IDS system identified only 1 culture of D. pigrum as "no choice," but it also identified 2 cultures of D. pigrum as a "questionable microcode" and 19 cultures of D. pigrum as an "inadequate ID, E. faecalis 90%, S. intermedius 9%." A total of 2 of the 18 cultures of Facklamia and all 3 of the I. ruoffiae cultures were correctly identified as "no choice." The most common misidentifications of Facklamia species by the ID32 and IDS systems were as various Streptococcus species and as Gemella species. In the Crystal system, the most common erroneous identification was Micrococcus luteus. These data indicate the need for the commercial manufacturers of these products to update their databases to include newly described species of gram-positive cocci.
Topics: Bacterial Typing Techniques; Databases, Factual; Evaluation Studies as Topic; Gram-Positive Bacterial Infections; Gram-Positive Cocci; Humans; Reagent Kits, Diagnostic
PubMed: 10834950
DOI: 10.1128/JCM.38.6.2037-2042.2000 -
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 -
Microbiology Spectrum Oct 2021The objective of this study was to examine the nasal microbiota in relation to otitis media (OM) status and nose health in Indigenous Australian children. Children 2 to...
The objective of this study was to examine the nasal microbiota in relation to otitis media (OM) status and nose health in Indigenous Australian children. Children 2 to 7 years of age were recruited from two northern Australian (Queensland) communities. Clinical histories were obtained through parent interviews and reviews of the medical records. Nasal cavity swab samples were obtained, and the children's ears, nose, and throat were examined. DNA was extracted and analyzed by 16S rRNA amplicon next-generation sequencing of the V3/V4 region, in combination with previously generated culture data. A total of 103 children were recruited (mean age, 4.7 years); 17 (16.8%) were healthy, i.e., normal examination results and no history of OM. The nasal microbiota differed significantly in relation to OM status and nose health. Children with historical OM had greater relative abundance of , compared to healthy children, despite both having healthy ears at the time of swabbing. Children with healthy noses had greater relative abundance of Staphylococcus aureus, compared to those with rhinorrhea. was correlated with in healthy children. Haemophilus and Streptococcus were correlated across phenotypes. was absent or was present with low relative abundance in healthy children and clustered around otopathogens. It correlated with and and form a synergism that promotes upper respiratory tract (URT)/ear health in Indigenous Australian children. likely represents " Ornithobacterium hominis" and in this population is correlated with a novel bacterium that appears to be related to poor URT/ear health. Recurring and chronic infections of the ear (OM) are disproportionately prevalent in disadvantaged communities across the globe and, in particular, within Indigenous communities. Despite numerous intervention strategies, OM persists as a major health issue and is the leading cause of preventable hearing loss. In disadvantaged communities, this hearing loss is associated with negative educational and social development outcomes, and consequently, poorer employment prospects and increased contact with the justice system in adulthood. Thus, a better understanding of the microbial ecology is needed in order to identify new targets to treat, as well as to prevent the infections. This study used a powerful combination of 16S rRNA gene sequencing and extended culturomics to show that Dolosigranulum pigrum, a bacterium previously identified as a candidate protective species, may require cocolonization with Corynebacterium pseudodiphtheriticum in order to prevent OM. Additionally, emerging and potentially novel pathogens and bacteria were identified.
Topics: Australia; Bacteria; Child; Child, Preschool; Ear; Female; Health Status; Humans; Male; Microbiota; Nasal Cavity; Nasal Mucosa; Nasopharynx; Native Hawaiian or Other Pacific Islander; Otitis Media; Persistent Infection; RNA, Ribosomal, 16S; Respiratory System
PubMed: 34668729
DOI: 10.1128/Spectrum.00367-21 -
Scientific Reports Jun 2018Selecting appropriate tools providing reliable quantitative measures of individual populations in biofilms is critical as we now recognize their true polymicrobial and...
Selecting appropriate tools providing reliable quantitative measures of individual populations in biofilms is critical as we now recognize their true polymicrobial and heterogeneous nature. Here, plate count, quantitative real-time polymerase chain reaction (q-PCR) and peptide nucleic acid probe-fluorescence in situ hybridization (PNA-FISH) were employed to quantitate cystic fibrosis multispecies biofilms. Growth of Pseudomonas aeruginosa, Inquilinus limosus and Dolosigranulum pigrum was assessed in dual- and triple-species consortia under oxygen and antibiotic stress. Quantification methods, that were previously optimized and validated in planktonic consortia, were not always in agreement when applied in multispecies biofilms. Discrepancies in culture and molecular outcomes were observed, particularly for triple-species consortia and antibiotic-stressed biofilms. Some differences were observed, such as the higher bacterial counts obtained by q-PCR and/or PNA-FISH (≤4 log cells/cm) compared to culture. But the discrepancies between PNA-FISH and q-PCR data (eg D. pigrum limited assessment by q-PCR) demonstrate the effect of biofilm heterogeneity in method's reliability. As the heterogeneity in biofilms is a reflection of a myriad of variables, tailoring an accurate picture of communities´ changes is crucial. This work demonstrates that at least two, but preferentially three, quantification techniques are required to obtain reliable measures and take comprehensive analysis of polymicrobial biofilm-associated infections.
Topics: Anti-Bacterial Agents; Biofilms; Carnobacteriaceae; Cystic Fibrosis; Humans; In Situ Hybridization, Fluorescence; Rhodospirillaceae
PubMed: 29934504
DOI: 10.1038/s41598-018-27497-9 -
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