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World Journal of Clinical Cases Jun 2023-induced meningitis and -induced meningitis concomitant with spinal canal infection are extremely rare. To the best of our knowledge, only 1 case of -induced central...
BACKGROUND
-induced meningitis and -induced meningitis concomitant with spinal canal infection are extremely rare. To the best of our knowledge, only 1 case of -induced central system infection has been reported. This is the second report on meningitis combined with spinal canal infection due to .
CASE SUMMARY
We report a case of a 9-year-old boy suffering from meningitis and spinal canal infection. The patient presented to the neurosurgery department with lumbosacral pain for 1 mo and headache and vomiting for 1 d. He had been treated with cephalosporin and nonsteroidal anti-inflammatory drugs for fever, otalgia and pharyngalgia in a local hospital 2 mo prior to this admission. During hospitalization, magnetic resonance imaging suggested meningitis and L3-S1 lumbosacral dural sac infection. The cerebrospinal fluid and blood cultures were negative, but the cerebrospinal fluid specimen indicated the presence of by metagenomic next-generation sequencing. Previous cases of infection were retrieved from PubMed to characterize the clinicopathological features and identify the prognostic factors and related antimicrobial treatment of infection due to .
CONCLUSION
This report shed light on the characteristics of infection and highlighted the role of metagenomic next-generation sequencing in pathogen detection.
PubMed: 37383115
DOI: 10.12998/wjcc.v11.i16.3830 -
Journal of Endodontics May 2024In this study, we used metatranscriptomics for the first time to investigate microbial composition, functional signatures, and antimicrobial resistance gene expression...
INTRODUCTION
In this study, we used metatranscriptomics for the first time to investigate microbial composition, functional signatures, and antimicrobial resistance gene expression in endodontic infections.
METHODS
Root canal samples were collected from ten teeth, including five primary and five persistent/secondary endodontic infections. RNA from endodontic samples was extracted, and RNA sequencing was performed on a NovaSeq6000 system (Illumina). Taxonomic analysis was performed using the Kraken2 bacterial database. Then, sequences with a taxonomic classification were annotated against the Universal Protein Knowledgebase for functional annotation and the Comprehensive Antibiotic Resistance Database for AR-like gene identification.
RESULTS
Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria represented the dominant phyla, whereas Fusobacteria, Spirochetes, and Synergistetes were among the nondominant phyla. The top ten species were mainly represented by obligate (or quasiobligate) anaerobes, including Gram-negative (eg, Capnocytophaga sp. oral taxon 323, Fusobacterium nucleatum, Prevotella intermedia, Prevotella oris, Tannerella forsythia, and Tannerella sp. oral taxon HOT-286) and Gram-positive species (eg, Olsenella uli and Parvimonas micra). Transcripts encoding moonlighting proteins (eg, glycolytic proteins, translational elongation factors, chaperonin, and heat shock proteins) were highly expressed, potentially affecting bacterial adhesion, biofilm formation, host defense evasion, and inflammation induction. Endodontic bacteria expressed genes conferring resistance to antibiotic classes commonly used in dentistry, with a high prevalence and expression of tetracycline and lincosamide resistance genes. Antibiotic efflux and antibiotic target alteration/protection were the main resistance mechanisms.
CONCLUSIONS
Metatranscriptomics revealed the activity of potential endodontic pathogens, which expressed putative virulence factors and a wide diversity of genes potentially involved in AR.
PubMed: 38719087
DOI: 10.1016/j.joen.2024.03.015 -
International Journal of Molecular... Jan 2024The activation of inflammasomes is thought to induce the inflammatory process around dental implants. No information is available on the correlation between microbiota...
The activation of inflammasomes is thought to induce the inflammatory process around dental implants. No information is available on the correlation between microbiota and inflammasomes in clinical samples from patients suffering peri-implantitis. For this cross-sectional study, 30 biofilm samples were obtained from 19 patients undergoing surgical treatment for peri-implantitis because of the presence of bleeding on probing, probing depth higher than 6 mm, and radiographic bone loss higher than 3 mm. Then, soft tissue samples from around the implant were also collected. The relative abundance of bacteria and alpha-diversity indexes were calculated after analyzing the 16S rRNA gene using next-generation sequencing. The soft-tissue samples were processed for evaluation of the inflammasomes NLRP3 and AIM2 as well as caspase-1 and IL-1β. The relative abundance (mean (SD)) of specific species indicated that the most abundant species were (10.95 (14.17)%), (10.93 (13.18)%), (5.89 (7.23)%), (3.88 (4.94)%), (2.91 (3.19)%), and (2.84 (4.15)%). Several correlations were found between the species and the immunohistochemical detection of the inflammasomes NLRP3 and AIM2 as well as caspase-1 and IL-1β, both in the epithelium and the lamina propria. A network analysis found an important cluster of variables formed by NLRP3 in the lamina propria and AIM2, caspase-1, and IL-1β in the lamina propria and the epithelium with , , , or . Thus, it could be concluded that inflammasomes NLRP3 and AIM2 and their downstream effectors caspase-1 and interleukin-1β can be significantly associated with specific bacteria.
Topics: Humans; Inflammasomes; NLR Family, Pyrin Domain-Containing 3 Protein; Peri-Implantitis; Cross-Sectional Studies; RNA, Ribosomal, 16S; Microbiota; Caspase 1
PubMed: 38256037
DOI: 10.3390/ijms25020961 -
Frontiers in Cellular and Infection... 2022The combination of maxillofacial infections (MI) with descending necrotizing mediastinitis (DNM) is a complex disease characterized by rapid development and high...
The combination of maxillofacial infections (MI) with descending necrotizing mediastinitis (DNM) is a complex disease characterized by rapid development and high mortality. Here, we performed metagenomic next-generation sequencing (mNGS) using samples from 21 patients with MI and eight patients with DNM. In this study, we found that the species richness of the DNM group was higher than that of the MI group, and the species diversity of the DNM group was higher than that of the MI group, with no statistically significant differences between groups (P > 0.05). LefSE analysis revealed that the main species differing between groups were , , , and ( and ). In addition, the PLS-DA analysis revealed that the dominant groups in the DNM group at the species level were , , , , , and . Next, we correlated the clinical characteristics of the patients with the relative abundance of the pathogens identified in the LefSe and PLS-DA analyses. The relative abundance of was positively correlated with C-reactive protein (CRP) and calcitoninogen (PCT) but negatively correlated with the percentage of lymphocytes (Lymph%) (P < 0.05). On the other hand, was positively correlated with the percentage of neutrophils (Neut%) and glycated hemoglobin (GLU) (P < 0.05), and was positively correlated with CRP (P < 0.05).
Topics: Eubacterium; Humans; Mediastinitis; Streptococcus
PubMed: 35755831
DOI: 10.3389/fcimb.2022.873161 -
BMC Infectious Diseases Sep 2023Brain abscesses caused by Prevotella oris are rarely reported. Here, we described a case of a brain infection caused by Prevotella oris that was detected by metagenomic... (Review)
Review
BACKGROUND
Brain abscesses caused by Prevotella oris are rarely reported. Here, we described a case of a brain infection caused by Prevotella oris that was detected by metagenomic next-generation sequencing (mNGS).
CASE PRESENTATION
A 63-year-old man with no medical history reported headache in the right frontotemporal region, fever, and intermittent diplopia. Magnetic resonance imaging (MRI) revealed abnormal signals and enhancement changes in the superior sellar region. mNGS testing showed that cerebrospinal fluid collected from the spine was positive for Prevotella oris. After receiving a combined treatment of antibiotic therapy, the patient recovered well.
CONCLUSION
We reviewed the relevant literature and summarized the characteristics and prognosis of this type of bacterial infection to provide ideas for clinicians to diagnose and treat this disease.
Topics: Male; Humans; Middle Aged; Brain Abscess; Prevotella; Brain; Combined Modality Therapy
PubMed: 37759232
DOI: 10.1186/s12879-023-08306-9 -
International Endodontic Journal Jul 2024To evaluate the root canal microbiome composition and bacterial functional capability in cases of primary and secondary apical periodontitis utilizing whole-metagenome...
AIM
To evaluate the root canal microbiome composition and bacterial functional capability in cases of primary and secondary apical periodontitis utilizing whole-metagenome shotgun sequencing.
METHODOLOGY
Twenty-two samples from patients with primary root canal infections, and 18 samples obtained from previously treated teeth currently diagnosed with apical periodontitis were analysed with whole-metagenome shotgun sequencing at a depth of 20 M reads. Taxonomic and functional gene annotations were made using MetaPhlAn3 and HUMAnN3 software. The Shannon and Chao1 indices were utilized to measure alpha diversity. Differences in community composition were evaluated utilizing analysis of similarity (ANOSIM) using Bray-Curtis dissimilarities. The Wilcoxon rank sum test was used to compare differences in taxa and functional genes.
RESULTS
Microbial community variations within a community were significantly lower in secondary relative to primary infections (alpha diversity p = .001). Community composition was significantly different in primary versus secondary infection (R = .11, p = .005). The predominant taxa observed among samples (>2.5%) were Pseudopropionibacterium propionicum, Prevotella oris, Eubacterium infirmum, Tannerella forsythia, Atopobium rimae, Peptostreptococcus stomatis, Bacteroidetes bacterium oral taxon 272, Parvimonas micra, Olsenella profusa, Streptococcus anginosus, Lactobacillus rhamnosus, Porphyromonas endodontalis, Pseudoramibacter alactolyticus, Fusobacterium nucleatum, Eubacterium brachy and Solobacterium moorei. The Wilcoxon rank test revealed no significant differences in relative abundances of functional genes in both groups. Genes with greater relative abundances (top 25) were associated with genetic, signalling and cellular processes including the iron and peptide/nickel transport system. Numerous genes encoding toxins were identified: exfoliative toxin, haemolysins, thiol-activated cytolysin, phospholipase C, cAMP factor, sialidase, and hyaluronic glucosaminidase.
CONCLUSIONS
Despite taxonomic differences between primary and secondary apical periodontitis, the functional capability of the microbiomes was similar.
Topics: Humans; Microbiota; Dental Pulp Cavity; Periapical Periodontitis; Metagenome; Adult; Female; Male; Middle Aged; Bacteria
PubMed: 36861850
DOI: 10.1111/iej.13911 -
European Journal of Ophthalmology Nov 2022To study the metagenomics of the microbes isolated from the canaliculus of patients with infective canaliculitis.
PURPOSE
To study the metagenomics of the microbes isolated from the canaliculus of patients with infective canaliculitis.
METHODS
A prospective study was performed on five consecutive canalicular samples obtained for the metagenomic analysis from the patients with infective canaliculitis who underwent non-incisional canalicular curettage at a tertiary care Dacryology service. The canalicular concretions were collected intraoperatively soon after a canalicular curettage and immediately transported on ice to the laboratory. Following DNA extraction and library preparation, a whole shotgun metagenome sequencing was performed on the Illumina™ platform. The downstream processing and bioinformatics of the samples were performed using multiple software packaged in SqueezeMeta™ pipeline or MG-RAST™ pipeline.
RESULTS
The taxonomic hit distribution across the samples showed that bacteria were the most common isolates (mean-80.5%), followed by viruses (mean-0.74%), and archaea (0.01%). The five major phyla identified across the samples of infective canaliculitis were, Fusobacteria, Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes. The prevalent organisms include and amongst few others. was noted in all the samples, though it was not the most abundant. The microbial gene mapping and protein prediction demonstrated proteins with known functions to range from 69.91% to 87.09% across the samples. The functional subsystem profiling demonstrated genes associated with carbohydrate, amino acid, and co-enzyme transport and metabolism, cell wall or cell membrane biogenesis, energy production and conversion, transcription, translation, and cellular communications.
CONCLUSION
This is the first whole metagenome sequencing of infective canaliculitis. Infected canaliculi harbor diverse microbial communities, including bacteria, viruses, and archaea. Functional analysis has provided newer insights into the ecosystem dynamics and strategies of microbial communities.
Topics: Amino Acids; Bacteria; Canaliculitis; Carbohydrates; DNA; Ecosystem; Humans; Ice; Prospective Studies
PubMed: 35354326
DOI: 10.1177/11206721221091646 -
Turkish Journal of Medical Sciences 2023Dental caries is a frequently occurring and multifactorial chronic disease in children resulting from the interaction of cariogenic bacteria and host susceptibility. The...
BACKGROUND/AIM
Dental caries is a frequently occurring and multifactorial chronic disease in children resulting from the interaction of cariogenic bacteria and host susceptibility. The aim of this study was to elucidate the impacts of primary immunodeficiency disorders (PIDs) on microbiota of dental caries in children by 16S rRNA gene-based metagenomic analysis.
MATERIALS AND METHODS
Enrolled in this study were 15 children with primary PID with caries (PID group) and 15 healthy children with caries as a control (CG). The DMFT index, saliva flow rate, and buffering capacity of each participant were assessed before the metagenomic analyses were conducted. For taxonomic profiling, the reads were obtained by high-throughput sequencing of the V3-V4 hypervariable region of 16S rRNA.
RESULTS
The DMFT score, saliva flow rate, and buffering capacity of the groups were similar. The flow rate and buffering capacity had no correlation with the number of species with 95% confidence. The metagenomic analysis resulted in the identification of 2440 bacterial species in all of the samples. Among the 50 most prevalent species present at ≥1% relative abundance, and were differentially more abundant in the PID group. The PID group and CG showed similar species richness and evenness, but 4 of the 5 samples with the highest Shannon-Weiner and Inverse Simpson indices belonged to the PID group. The Spearman test results for correlation of the species in the PID subgroups showed that had a positively correlated relationship with both and genera incertae sedis.
CONCLUSION
This study provided insight into the caries microbiota of children with immunodeficiency diseases. Differentially abundant species, novel bacterial associations, and unique bacterial species were disclosed in the PID samples, indicating the role of the immune system in altering the caries microbiota. The prominent bacterial species and associations in the PID group should be suspected in regard to their link with present or future diseases.
Topics: Humans; Dental Caries; Child; RNA, Ribosomal, 16S; Female; Male; Metagenomics; Microbiota; Primary Immunodeficiency Diseases; Child, Preschool; Saliva; Case-Control Studies
PubMed: 38813004
DOI: 10.55730/1300-0144.5719 -
Frontiers in Microbiology 2021Previous studies have focused on the rumen microbiome and enteric methane (CH) emissions in dairy cows, yet little is known about steers, especially steers of dairy...
Previous studies have focused on the rumen microbiome and enteric methane (CH) emissions in dairy cows, yet little is known about steers, especially steers of dairy breeds. In the present study, we comparatively examined the rumen microbiota, fermentation characteristics, and CH emissions from six non-cannulated Holstein (710.33 ± 43.02 kg) and six Jersey (559.67 ± 32.72 kg) steers. The steers were fed the same total mixed ration (TMR) for 30 days. After 25 days of adaptation to the diet, CH emissions were measured using GreenFeed for three consecutive days, and rumen fluid samples were collected on last day using stomach tubing before feeding (0 h) and 6 h after feeding. CH production (g/d/animal), CH yield (g/kg DMI), and CH intensity (g/kg BW) were higher in the Jersey steers than in the Holstein steers. The lowest pH value was recorded at 6 h after feeding. The Jersey steers had lower rumen pH and a higher concentration of ammonia-nitrogen (NH-N). The Jersey steers had a numerically higher molar proportion of acetate than the Holstein steers, but the opposite was true for that of propionate. Metataxonomic analysis of the rumen microbiota showed that the two breeds had similar species richness, Shannon, and inverse Simpson diversity indexes. Principal coordinates analysis showed that the overall rumen microbiota was different between the two breeds. Both breeds were dominated by , and its highest relative abundance was observed 6 h after feeding. The genera , , and the species , and were more abundant in Holstein steers while the genera , , and the species , and in the Jersey steers. The Jersey steers were dominated by while the Holstein steers by . The overall results suggest that sampling hour has little influence on the rumen microbiota; however, breeds of steers can affect the assemblage of the rumen microbiota and different mitigation strategies may be needed to effectively manipulate the rumen microbiota and mitigate enteric CH emissions from these steers.
PubMed: 33868186
DOI: 10.3389/fmicb.2021.601061 -
International Journal of Molecular... Sep 2022A common symptom in Alzheimer's disease (AD) is cognitive decline, of which the potential pathogenesis remains unclear. In order to understand the mechanism of gut...
A common symptom in Alzheimer's disease (AD) is cognitive decline, of which the potential pathogenesis remains unclear. In order to understand the mechanism of gut microbiota in AD, it is necessary to clarify the relationship between gut microbiota and metabolites. Behavioral tests, pathological examination, metagenomics, and metabolomics were applied to analyze the difference of gut microbiota and metabolome between APP/PS1 (PAP) mice with cognitive decline and age-matched controls, and their possible correlations. Our results showed that PAP mice and health mice had different structures of the bacterial communities in the gut. The abundances and diversities of the bacterial communities in health mice were higher than in PAP mice by metagenomics analysis. The abundances of , , and were significantly increased in PAP mice, while the abundances of , , and were greatly reduced. Furthermore, PAP mice possessed peculiar metabolic phenotypes in stool, serum, and hippocampus relative to WT mice, as is demonstrated by alterations in neurotransmitters metabolism, lipid metabolism, aromatic amino acids metabolism, energy metabolism, vitamin digestion and absorption, and bile metabolism. Microbiota-host metabolic correlation analysis suggests that abnormal metabolism in stool, serum, and hippocampus of PAP mice may be modulated by the gut microbiota, especially , , and . Therefore, abnormal metabolism activity is associated with gut microbiota in Alzheimer's disease mice. Our results imply that modifying host metabolism through targeting gut microbiota may be a novel and viable strategy for the prevention and treatment of AD in the future.
Topics: Alzheimer Disease; Amino Acids, Aromatic; Animals; Bacteria; Gastrointestinal Microbiome; Metabolome; Mice; Neurotransmitter Agents; Vitamins
PubMed: 36232865
DOI: 10.3390/ijms231911560