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Cell Host & Microbe Sep 2022Neisseria species are frequently identified in the bronchiectasis microbiome, but they are regarded as respiratory commensals. Using a combination of human cohorts,...
Neisseria species are frequently identified in the bronchiectasis microbiome, but they are regarded as respiratory commensals. Using a combination of human cohorts, next-generation sequencing, systems biology, and animal models, we show that bronchiectasis bacteriomes defined by the presence of Neisseria spp. associate with poor clinical outcomes, including exacerbations. Neisseria subflava cultivated from bronchiectasis patients promotes the loss of epithelial integrity and inflammation in primary epithelial cells. In vivo animal models of Neisseria subflava infection and metabolipidome analysis highlight immunoinflammatory functional gene clusters and provide evidence for pulmonary inflammation. The murine metabolipidomic data were validated with human Neisseria-dominant bronchiectasis samples and compared with disease in which Pseudomonas-, an established bronchiectasis pathogen, is dominant. Metagenomic surveillance of Neisseria across various respiratory disorders reveals broader importance, and the assessment of the home environment in bronchiectasis implies potential environmental sources of exposure. Thus, we identify Neisseria species as pathobionts in bronchiectasis, allowing for improved risk stratification in this high-risk group.
Topics: Animals; Bronchiectasis; Humans; Metagenome; Mice; Microbiota; Neisseria
PubMed: 36108613
DOI: 10.1016/j.chom.2022.08.005 -
Frontiers in Microbiology 2022Resistance acquisition natural transformation is a common process in the genus. Transformation has played an important role in the emergence of resistance to many...
Resistance acquisition natural transformation is a common process in the genus. Transformation has played an important role in the emergence of resistance to many antimicrobials in and . In a previous study, we found that currently circulating isolates of had acquired an gene that has been found to result in macrolide resistance in other bacteria but never found in species before. To determine if this resistance mechanism is transferable among species, we assessed if we could transform the gene into other commensal and pathogenic under low dose azithromycin pressure. Intraspecies recombination in commensal was confirmed with PCR and resulted in high-level macrolide resistance. Whole-genome sequencing of these transformed strains identified the complete uptake of the integration fragment. Sequence analysis showed that a large fragment of DNA (5 and 12 kb) was transferred through a single horizontal gene transfer event. Furthermore, uptake of the gene had no apparent fitness cost. Interspecies transformation of from to was, however, not successful.
PubMed: 35432273
DOI: 10.3389/fmicb.2022.855482 -
Microbiology Spectrum Jun 2023Orofacial granulomatosis (OFG) is a chronic inflammatory disease characterized by nontender swelling of the orofacial tissues, the underlying cause of which remains...
Orofacial granulomatosis (OFG) is a chronic inflammatory disease characterized by nontender swelling of the orofacial tissues, the underlying cause of which remains unknown. Our previous study demonstrated that tooth apical periodontitis (AP) is involved in the development of OFG. To characterize the AP bacterial signatures of OFG patients and identify possible pathogenic bacteria that cause OFG, the compositions of the AP microbiotas in OFG patients and controls were compared using 16S rRNA gene sequencing. Pure cultures of putative bacterial pathogens were established by growing bacteria as colonies followed by purification, identification, and enrichment and then were injected into animal models to determine the causative bacteria contributing to OFG. A specific AP microbiota signature in the OFG patients was shown, characterized by the predominance of phyla and , notably members of the genera Streptococcus, , and , were found. Streptococcus spp., Lactobacillus casei, Neisseria subflava, Veillonella parvula, and spp. from OFG patients were isolated and successfully cultured and then injected into mice. Ultimately, footpad injection with elicited granulomatous inflammation. Infectious agents have long been considered to play a role in the initiation of OFG; however, a direct causal relationship between microbes and OFG has not yet been established. In this study, a unique AP microbiota signature was identified in OFG patients. Moreover, we successfully isolated candidate bacteria from AP lesions of OFG patients and assessed their pathogenicity in laboratory mice. Findings from this study may help provide in-depth insights into the role of microbes in OFG development, providing the basis for targeted therapeutic approaches for OFG.
Topics: Animals; Mice; Granulomatosis, Orofacial; RNA, Ribosomal, 16S; Crohn Disease; Chronic Disease; Bacteria
PubMed: 37227290
DOI: 10.1128/spectrum.02266-22 -
Microbiology Spectrum Mar 2023The microbial metagenome in cystic fibrosis (CF) airways was investigated by whole-genome shotgun sequencing of total DNA isolated from nasal lavage samples,...
The microbial metagenome in cystic fibrosis (CF) airways was investigated by whole-genome shotgun sequencing of total DNA isolated from nasal lavage samples, oropharyngeal swabs, and induced sputum samples collected from 65 individuals with CF aged 7 to 50 years. Each patient harbored a personalized microbial metagenome unique in microbial load and composition, the exception being monocultures of the most common CF pathogens Staphylococcus aureus and Pseudomonas aeruginosa from patients with advanced lung disease. The sampling of the upper airways by nasal lavage uncovered the fungus Malassezia restricta and the bacterium Staphylococcus epidermidis as prominent species. Healthy and CF donors harbored qualitatively and quantitatively different spectra of commensal bacteria in their sputa, even in the absence of any typical CF pathogen. If P. aeruginosa, S. aureus, or Stenotrophomonas maltophilia belonged to the trio of the most abundant species in the CF sputum metagenome, common inhabitants of the respiratory tract of healthy subjects, i.e., Eubacterium sulci, Fusobacterium periodonticum, and Neisseria subflava, were present only in low numbers or not detectable. Random forest analysis identified the numerical ecological parameters of the bacterial community, such as Shannon and Simpson diversity, as the key parameters that globally distinguish sputum samples from CF and healthy donors. Cystic fibrosis (CF) is the most common life-limiting monogenetic disease in European populations and is caused by mutations in the gene. Chronic airway infections with opportunistic pathogens are the major morbidity that determines prognosis and quality of life in most people with CF. We examined the composition of the microbial communities of the oral cavity and upper and lower airways in CF patients across all age groups. From early on, the spectrum of commensals is different in health and CF. Later on, when the common CF pathogens take up residence in the lungs, we observed differential modes of depletion of the commensal microbiota in the presence of S. aureus, P. aeruginosa, S. maltophilia, or combinations thereof. It remains to be seen whether the implementation of lifelong CFTR (cystic fibrosis transmembrane conductance regulator) modulation will change the temporal evolution of the CF airway metagenome.
PubMed: 36892308
DOI: 10.1128/spectrum.03633-22 -
Frontiers in Microbiology 2021The taxonomy of the genus remains confusing, particularly regarding and In 2012, ribosomal multi-locus sequence typing reclassified both as , but data concerning 17...
Confirmation of the Need for Reclassification of and Using Average Nucleotide Identity Blast and Phylogenetic Analysis of Whole-Genome Sequencing: Hinted by Clinical Misclassification of a Strain.
The taxonomy of the genus remains confusing, particularly regarding and In 2012, ribosomal multi-locus sequence typing reclassified both as , but data concerning 17 strains remain available in GenBank. The continuous progress of high-throughput sequencing has facilitated ready accessibility of whole-genome data, promoting vigorous development of average nucleotide identity (ANI) and high-resolution phylogenetic analysis. Here, we report that a isolate, which caused native-valve endocarditis and multiple embolic brain infarcts in a patient with congenital heart disease, was misidentified as by VITEK MS. This isolate was reclassified as by ANI blast (ANIb) and by phylogenetic analysis using whole-genome data yielded by the PacBio Sequel and Illumina NovaSeq PE150 platforms. The confusion evident in the GenBank and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) databases suggests that ( = 13) and ( = 16) in GenBank should be reclassified using ANIb and high-resolution phylogenetic analysis. The whole-genome data of 30 strains (including the clinical isolate) were compared with the data of 27 type strains (including one and two type strains) as a genomic index. In total, 25 (8 originally identified as and 17 originally identified as ) and 7 (1 originally identified as and 6 originally identified as ) strains were reclassified into the and groups, respectively; 1 residual strain was reclassified as . In conclusion, a combination of ANIb and robust phylogenetic analysis reclassified strains originally identified as and into (principally) the group and the group. The misclassified and strains in the GenBank and MALDI-TOF MS databases were supposed to be corrected. Updated genomic classification strategy for originally identified and strains was recommended to be adopted in GenBank.
PubMed: 35281306
DOI: 10.3389/fmicb.2021.780183 -
Case Reports in Neurology 2018We report a rare case of meningitis due to a combination of and . An 80-year-old female had a 4-year history of type II diabetes mellitus (DM) and an 11-year history of...
We report a rare case of meningitis due to a combination of and . An 80-year-old female had a 4-year history of type II diabetes mellitus (DM) and an 11-year history of rheumatoid arthritis, which was treated with prednisolone, tacrolimus, and methotrexate. One month after the removal of a dental implant, she complained of a disturbance of consciousness and suffered a convulsion. A cerebrospinal fluid culture was found to be positive for both and . After 14 days of antibiotic treatment with 4 g/day ceftriaxone, her stiff neck, somnolence, and laboratory data greatly improved, and she was successfully discharged at 27 days after admission. Although both and are generally considered to be benign bacteria, they can cause meningitis in patients with the following risk factors: older age, on immunosuppressive treatment, DM, or dental treatment.
PubMed: 30140217
DOI: 10.1159/000490695 -
Scientific Reports Apr 2022Tobacco use is the leading preventable cause of cancer, and affects the respiratory, oral, fecal, and duodenal mucosa-associated microbiota. However, the effects of...
Tobacco use is the leading preventable cause of cancer, and affects the respiratory, oral, fecal, and duodenal mucosa-associated microbiota. However, the effects of smoking on the duodenal luminal microbiome have not been studied directly. We aimed to compare the duodenal luminal microbiome in never-smokers, current smokers, and ex-smokers who quit ≥ 10 years ago. In a cross-sectional study, current smokers (CS, n = 24) were identified and matched to never-smokers (NS, n = 27) and ex-smokers (XS, n = 27) by age (± 5 years), body mass index (BMI, ± 3 kg/m), and sex. Current antibiotic users were excluded. The duodenal luminal microbiome was analysed in 1 aspirate sample per subject by 16S rRNA gene sequencing. Relative abundances (RA) of families associated with increased duodenal microbial diversity, Prevotellaceae, Neisseriaceae, and Porphyromonadaceae, were significantly lower in CS vs. NS. This was driven by lower RA of unknown Prevotella and Porphyromonas species, and Neisseria subflava and N. cinerea, in CS. In contrast, RA of Enterobacteriaceae and Lactobacillaceae (associated with decreased diversity), were significantly higher in CS, due to higher RA of Escherichia-Shigella, Klebsiella and Lactobacillus species. Many of these changes were absent or less pronounced in XS, who exhibited a duodenal luminal microbiome more similar to NS. RA of taxa previously found to be increased in the oral and respiratory microbiota of smokers were also higher in the duodenal luminal microbiome, including Bulledia extructa and an unknown Filifactor species. In conclusion, smoking is associated with an altered duodenal luminal microbiome. However, ex-smokers have a duodenal luminal microbiome that is similar to never-smokers.
Topics: Cross-Sectional Studies; Humans; Microbiota; RNA, Ribosomal, 16S; Smoking; Tobacco Smoking
PubMed: 35422064
DOI: 10.1038/s41598-022-10132-z -
Journal of Bacteriology Feb 2001Neisserial lipooligosaccharides (LOSs) are a family of complex cell surface glycolipids. We used mass spectrometry techniques (electrospray ionization, collision-induced... (Comparative Study)
Comparative Study
Neisserial lipooligosaccharides (LOSs) are a family of complex cell surface glycolipids. We used mass spectrometry techniques (electrospray ionization, collision-induced dissociation, and multiple step), combined with fluorophore-assisted carbohydrate electrophoresis monosaccharide composition analysis, to determine the structure of the two low-molecular-mass LOS molecules (LOSI and LOSII) expressed by Neisseria subflava 44. We determined that LOSI contains one glucose on both the alpha and beta chains. LOSII is structurally related to LOSI and differs from it by the addition of a hexose (either glucose or galactose) on the alpha chain. LOSI and LOSII were able to bind monoclonal antibody (MAb) 25-1-LC1 when analyzed by Western blotting experiments. We used a set of genetically defined Neisseria gonorrhoeae mutants that expressed single defined LOS epitopes and a group of Neisseria meningitidis strains that expresses chemically defined LOS components to determine the structures recognized by MAb 25-1-LC1. We found that extensions onto the beta-chain glucose of LOSI block the recognition by this MAb, as does further elongation from the LOSII alpha chain. The LOSI structure was determined to be the minimum structure that is recognized by MAb 25-1-LC1.
Topics: Animals; Antibodies, Bacterial; Antibody Specificity; Carbohydrate Sequence; Electrophoresis, Polyacrylamide Gel; Lipopolysaccharides; Mass Spectrometry; Mice; Mice, Inbred BALB C; Molecular Sequence Data; Monosaccharides; Neisseria; Species Specificity
PubMed: 11208793
DOI: 10.1128/JB.183.3.942-950.2001 -
Microbial Genomics Apr 2023Complete Type VI Secretion Systems were identified in the genome sequence data of isolates sourced from throat swabs of human volunteers. The previous report was the...
Complete Type VI Secretion Systems were identified in the genome sequence data of isolates sourced from throat swabs of human volunteers. The previous report was the first to describe two complete Type VI Secretion Systems in these isolates, both of which were distinct in terms of their gene organization and sequence homology. Since publication of the first report, Type VI Secretion System subtypes have been identified in spp. The characteristics of each type in are further investigated here and in the context of the other spp., including identification of the lineages containing the different types and subtypes. Type VI Secretion Systems use VgrG for delivery of toxin effector proteins; several copies of and associated effector / immunity pairs are present in spp. Based on sequence similarity between strains and species, these core Type VI Secretion System genes, , and effector / immunity genes may diversify via horizontal gene transfer, an instrument for gene acquisition and repair in spp.
Topics: Humans; Type VI Secretion Systems; Bacterial Proteins
PubMed: 37052605
DOI: 10.1099/mgen.0.000986 -
Revista Chilena de Infectologia :... Aug 2017Neisseria subflava belongs to Neisseriaceae family, is considered a comensal specie, however in certain host, mainly inmunosuppresed patientes and children, the... (Review)
Review
Neisseria subflava belongs to Neisseriaceae family, is considered a comensal specie, however in certain host, mainly inmunosuppresed patientes and children, the literature has documented invasive infections. We present a case of a bacteriemia due to N. subflava in a newborn, treated with cefotaxime with good outcome. In newborns, the most common Neisseria bacteria to cause invasive infections are N. meningitidis, with highly fatal clinical course and N. gonorrhoeae which compromise the eye, oftalmia neonatorum, with uncommon invasive infections. It's very important the adequate microbiological diagnosis because the biochemical tests may be inconclusive. MALDITOF mass spectrometry technique is a useful tool.
Topics: Bacteremia; Humans; Immunocompromised Host; Infant, Newborn; Male; Neisseria; Neisseriaceae Infections
PubMed: 29165520
DOI: 10.4067/s0716-10182017000400389