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The Pediatric Infectious Disease Journal Jun 2024
PubMed: 38916926
DOI: 10.1097/INF.0000000000004466 -
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 -
BMC Microbiology May 2024We evaluated whether the sputum bacterial microbiome differs between nontuberculous mycobacteria pulmonary disease (NTM-PD) patients with stable disease not requiring... (Comparative Study)
Comparative Study
BACKGROUND
We evaluated whether the sputum bacterial microbiome differs between nontuberculous mycobacteria pulmonary disease (NTM-PD) patients with stable disease not requiring antibiotic treatment and those requiring antibiotics.
METHODS
We collected sputum samples from 21 clinically stable NTM-PD patients (stable group) and 14 NTM-PD patients needing antibiotic treatment (treatment group). We also obtained 13 follow-up samples from the stable group. We analyzed the 48 samples using 16S rRNA gene sequencing (V3-V4 region) and compared the groups.
RESULTS
In the linear discriminant analysis effect size (LEfSe) analysis, the species Porphyromonas pasteri, Haemophilus parahaemolyticus, Prevotella nanceiensis, and Gemella haemolysans were significantly more prevalent in the sputum of the stable group compared to the treatment group. No taxa showed significant differences in alpha-/beta-diversity or LEfSe between the 21 baseline and 13 follow-up sputum samples in the stable group. In the stable group, the genus Bergeyella and species Prevotella oris were less common in patients who achieved spontaneous culture conversion (n = 9) compared to those with persistent NTM positivity (n = 12) (effect size 3.04, p = 0.039 for Bergeyella; effect size 3.64, p = 0.033 for P. oris). In the treatment group, H. parainfluenzae was more common in patients with treatment success (n = 7) than in treatment-refractory patients (n = 7) (effect size 4.74, p = 0.013).
CONCLUSIONS
Our study identified distinct bacterial taxa in the sputum of NTM-PD patients based on disease status. These results suggest the presence of a microbial environment that helps maintain disease stability.
Topics: Humans; Sputum; Male; Female; Microbiota; Aged; Mycobacterium Infections, Nontuberculous; RNA, Ribosomal, 16S; Middle Aged; Anti-Bacterial Agents; Bacteria; Nontuberculous Mycobacteria; DNA, Bacterial; Lung Diseases
PubMed: 38760693
DOI: 10.1186/s12866-024-03308-2 -
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 -
Journal of Oral Microbiology 2024Tongue coating microbiota has aroused particular interest in profiling oral and digestive system cancers. However, little is known on the relationship between tongue...
BACKGROUND
Tongue coating microbiota has aroused particular interest in profiling oral and digestive system cancers. However, little is known on the relationship between tongue coating microbiome and colorectal cancer (CRC).
METHODS
Metagenomic shotgun sequencing was performed on tongue coating samples collected from 30 patients with CRC, 30 patients with colorectal polyps (CP), and 30 healthy controls (HC). We further validated the potential of the tongue coating microbiota to predict the CRC by a random forest model.
RESULTS
We found a greater species diversity in CRC samples, and the nucleoside and nucleotide biosynthesis pathway was more apparent in the CRC group. Importantly, various species across participants jointly shaped three distinguishable fur types.The tongue coating microbiome profiling data gave an area under the receiver operating characteristic curve (AUC) of 0.915 in discriminating CRC patients from control participants; species such as , and aided differentiation of CRC patients from healthy participants.
CONCLUSION
These results elucidate the use of tongue coating microbiome in CRC patients firstly, and the fur-types observed contribute to a better understanding of the microbial community in human. Furthermore, the tongue coating microbiota-based biomarkers provide a valuable reference for CRC prediction and diagnosis.
PubMed: 38686186
DOI: 10.1080/20002297.2024.2344278 -
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 -
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 -
EJVES Vascular Forum 2023First described in 1937, Q fever remains a relatively new disease, with much to be learned about its presentation and diagnosis. Due to its role in the development of...
INTRODUCTION
First described in 1937, Q fever remains a relatively new disease, with much to be learned about its presentation and diagnosis. Due to its role in the development of aortic aneurysms and vascular graft infections, its implications in the vascular domain have become increasingly reported. This is a report of two cases of vascular complications associated with oxiella burnetii infection, and the challenges in managing their unique presentations.
REPORTS
Case 1: A 70 year old man with a prosthetic aortobiiliac graft and past Q fever infection presented with acute sepsis. Abdominal computed tomography (CT) showed soft tissue thickening and stranding around the graft, and locules of gas within the vessel. Pelvic magnetic resonance imaging (MRI) revealed a chain of abscesses within the right gluteal region, of which aspirate grew and . Open explanation of the aortic graft and replacement by superficial femoral vein was performed. Tissue culture confirmed a polymicrobial infection, and PCR of the aortic wall and pre-aortic lymph node was positive for Q fever. He was treated for recrudescent Q fever infection with a good outcome and recovery. Case 2: A 73 year old man had an incidental abdominal aortic aneurysm (AAA) identified at the time of Q fever diagnosis. Following an incomplete course of doxycycline and hydroxychloroquine, the aneurysm rapidly progressed, leading to presentation with right flank pain. Fluorodeoxyglucose (FDG) positron emission tomography (PET) showed multiple foci of uptake within the aneurysm wall. Open AAA repair with a polyester graft was performed, with AAA tissue positive for Q fever on PCR. The operation was successful, with the patient continuing clearance therapy at time of writing.
DISCUSSION
Q fever infection poses serious implications for patients with vascular grafts and AAAs, and thus, should be considered in the differential diagnosis of mycotic aortic aneurysms and in aortic graft infections.
PubMed: 37389372
DOI: 10.1016/j.ejvsvf.2023.05.005 -
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 -
Revista Espanola de Quimioterapia :... Aug 2023
Topics: Humans; Prevotella; Lung Diseases; Bacteroidaceae Infections
PubMed: 37184104
DOI: 10.37201/req/001.2023