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PloS One 2011The complexity of the human microbiome makes it difficult to reveal organizational principles of the community and even more challenging to generate testable hypotheses....
The complexity of the human microbiome makes it difficult to reveal organizational principles of the community and even more challenging to generate testable hypotheses. It has been suggested that in the gut microbiome species such as Bacteroides thetaiotaomicron are keystone in maintaining the stability and functional adaptability of the microbial community. In this study, we investigate the interspecies associations in a complex microbial biofilm applying systems biology principles. Using correlation network analysis we identified bacterial modules that represent important microbial associations within the oral community. We used dental plaque as a model community because of its high diversity and the well known species-species interactions that are common in the oral biofilm. We analyzed samples from healthy individuals as well as from patients with periodontitis, a polymicrobial disease. Using results obtained by checkerboard hybridization on cultivable bacteria we identified modules that correlated well with microbial complexes previously described. Furthermore, we extended our analysis using the Human Oral Microbe Identification Microarray (HOMIM), which includes a large number of bacterial species, among them uncultivated organisms present in the mouth. Two distinct microbial communities appeared in healthy individuals while there was one major type in disease. Bacterial modules in all communities did not overlap, indicating that bacteria were able to effectively re-associate with new partners depending on the environmental conditions. We then identified hubs that could act as keystone species in the bacterial modules. Based on those results we then cultured a not-yet-cultivated microorganism, Tannerella sp. OT286 (clone BU063). After two rounds of enrichment by a selected helper (Prevotella oris OT311) we obtained colonies of Tannerella sp. OT286 growing on blood agar plates. This system-level approach would open the possibility of manipulating microbial communities in a targeted fashion as well as associating certain bacterial modules to clinical traits (e.g.: obesity, Crohn's disease, periodontal disease, etc).
Topics: Algorithms; Bacteroides; Bayes Theorem; Biofilms; DNA; Dental Plaque; Hot Temperature; Humans; Metagenome; Models, Biological; Models, Genetic; Models, Theoretical; Nucleic Acid Hybridization; Oligonucleotide Array Sequence Analysis; Periodontitis; Principal Component Analysis; Systems Biology
PubMed: 22163302
DOI: 10.1371/journal.pone.0028438 -
The American Journal of Case Reports Nov 2021BACKGROUND Bacterial pericarditis can present a diagnostic challenge due to the difficulty of obtaining tissue for bacterial identification. This report is of a...
BACKGROUND Bacterial pericarditis can present a diagnostic challenge due to the difficulty of obtaining tissue for bacterial identification. This report is of a 34-year-old man who presented with fever and cough. Diagnosis was initially delayed without a tissue sample, but the patient was later found to have polymicrobial bacterial pericarditis. CASE REPORT A 34-year-old man from the Democratic Republic of Congo presented to the emergency room with cough, fever, and night sweats. He was admitted and found to have pericardial thickening and fluid collection with calcifications. A tissue sample was not obtained for diagnosis, and he was discharged on RIPE (rifampin, isoniazid, pyrazinamide, and ethambutol) and steroids for presumed tuberculosis pericarditis. He worsened clinically and was readmitted to the hospital with evolving pericardial effusion with air present, in addition to new pleural effusion and parenchymal consolidation. He subsequently underwent thoracotomy and pericardial biopsy. Tissue cultures and sequence-based bacterial analysis eventually revealed the presence of Prevotella oris and Fusobacterium nucleatum. He improved dramatically with appropriate antibiotic therapy. CONCLUSIONS This report demonstrates the importance of undergoing further diagnostic work-up for bacterial pericarditis, especially in resource-rich settings. Although tuberculosis pericarditis should remain high on the differential, it is imperative not to anchor on that diagnosis. Instead, when feasible and safe, tissue biopsy should be obtained and sent for organism identification. AFB smears and cultures, Xpert MTB/RIF, and sequence-based bacterial analysis have all been used for identification. Delay in diagnosis can lead to progression of disease and unnecessary incorrect therapies.
Topics: Adult; Humans; Male; Pericardial Effusion; Pericarditis; Pericarditis, Tuberculous; Prevotella
PubMed: 34782592
DOI: 10.12659/AJCR.933684 -
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 -
Journal of Endodontics Aug 2016The purpose of this study was to combine multiple displacement amplification and checkerboard DNA-DNA hybridization to qualitatively and quantitatively evaluate the...
INTRODUCTION
The purpose of this study was to combine multiple displacement amplification and checkerboard DNA-DNA hybridization to qualitatively and quantitatively evaluate the microbiota present in infections refractory to endodontic treatment.
METHODS
The subjects of this study were 40 patients presenting with periapical lesions refractory to endodontic treatment. Samples were taken by scraping or filing root canal walls with a #10 K-type hand file. Sample DNA was amplified by multiple displacement amplification, and the levels of 107 bacterial taxa were analyzed by checkerboard DNA-DNA hybridization. The taxa were divided into 3 distinct microbial populations depending on their mean proportion in samples (% DNA probe counts ± standard error of the mean) as follows: dominant (≥3.0%), subdominant (>1.6%-3.0%), and residual (≤1.6%) populations. The significance of differences was determined using the Mann-Whitney test.
RESULTS
The taxa present with the highest mean proportions (constituting the dominant population) were Corynebacterium diphtheriae (8.03 ± 0.98), Porphyromonas gingivalis (5.42 ± 2.09), Streptococcus sobrinus (5.33 ± 0.69), and Stenotrophomonas maltophilia (4.72 ± 1.73). Among the subdominant population were Eubacterium saphenum (3.85 ± 1.06), Helicobacter pylori (3.16 ± 0.62), Dialister pneumosintes (3.12 ± 1.1), Clostridium difficile (2.74 ± 0.41), Enterobacter agglomerans (2.64 ± 0.54), Salmonella enterica (2.51 ± 0.52), Mobiluncus mulieris (2.44 ± 0.6), and Klebsiella oxytoca (2.32 ± 0.66). In the population of bacteria present at the lowest mean proportions (the residual population), Bacteroides ureolyticus (0.04 ± 0.01), Haemophilus influenzae (0.04 ± 0.02), and Prevotella oris (0.01 ± 0.01) were found at the lowest mean proportions. Enterococcus faecalis was detected in the residual population (0.52 ± 0.26).
CONCLUSIONS
The microbial climax community in teeth refractory to endodontic treatment not only harbors medically important species but also contains distinct microbial consortia present with different population levels.
Topics: Bacteria; DNA Probes; DNA, Bacterial; Dental Pulp Cavity; Dental Pulp Necrosis; Humans; Microbiota; Nucleic Acid Hybridization; Periapical Diseases; Root Canal Therapy
PubMed: 27377440
DOI: 10.1016/j.joen.2016.05.014 -
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 -
Clinical Infectious Diseases : An... Jun 1995We conducted a retrospective study to update the bacteriology of 46 cases of anaerobic empyema that were originally studied between 1976 and 1993 at the Wadsworth...
We conducted a retrospective study to update the bacteriology of 46 cases of anaerobic empyema that were originally studied between 1976 and 1993 at the Wadsworth Anaerobic Bacteriology Clinical Research Laboratory (Los Angeles). Anaerobic bacteriologic studies were completed for all 46 pleural fluid specimens, and aerobic bacteriologic studies were completed for 41 of these specimens. Thirty-seven clinical charts were available for review. A total of 161 anaerobic isolates (3.5 per patient) representing 64 species or groups were recovered. The most common isolates were as follows: Fusobacterium nucleatum (19); Prevotella oris-buccae group (13, 9 of which were P. oris); Bacteroides fragilis group (11, 4 of which were B. fragilis); pigmented Prevotella species (17, 8 of which were in the Prevotella intermedia-nigrescens group); Peptostreptococcus species (17, 9 of which were Peptostreptococcus micros); Eubacterium species (7); Lactobacillus species (8); Actinomyces species (7); and Clostridium species (7). Nineteen if the cases were of purely anaerobic etiology; of these, eight were caused by a single organism: F. nucleatum (five cases); B. fragilis (two cases); and Prevotella mangus (one case). Of the 45 aerobic isolates (1.1 per patient), viridans streptococci were most common (21 isolates), followed by group D nonenterococcal streptococcus (four isolates). Only nine gram-negative rods (six enteric and three nonenteric organisms) and one Staphylococcus aureus isolate were recovered. The susceptibility to penicillin of 64 isolates was examined with the use of the spiral gradient method; 21 (33%) of these isolates were beta-lactamase positive (MICs ranged from 1.1 to > or = 54 micrograms/mL vs < or = 0.27 micrograms/mL for beta-lactamase-negative strains).
Topics: Adult; Aged; Aged, 80 and over; Bacteria, Aerobic; Bacteria, Anaerobic; Bacterial Infections; Empyema; Humans; Male; Microbial Sensitivity Tests; Middle Aged; Retrospective Studies
PubMed: 7548560
DOI: 10.1093/clinids/20.supplement_2.s224 -
Journal of Endodontics Jul 2011The characterization of microbial communities infecting the endodontic system in each clinical condition may help on the establishment of a correct prognosis and...
INTRODUCTION
The characterization of microbial communities infecting the endodontic system in each clinical condition may help on the establishment of a correct prognosis and distinct strategies of treatment. The purpose of this study was to determine the bacterial diversity in primary endodontic infections by 16S ribosomal-RNA (rRNA) sequence analysis.
METHODS
Samples from root canals of untreated asymptomatic teeth (n = 12) exhibiting periapical lesions were obtained, 16S rRNA bacterial genomic libraries were constructed and sequenced, and bacterial diversity was estimated.
RESULTS
A total of 489 clones were analyzed (mean, 40.7 ± 8.0 clones per sample). Seventy phylotypes were identified of which six were novel phylotypes belonging to the family Ruminococcaceae. The mean number of taxa per canal was 10.0, ranging from 3 to 21 per sample; 65.7% of the cloned sequences represented phylotypes for which no cultivated isolates have been reported. The most prevalent taxa were Atopobium rimae (50.0%), Dialister invisus, Prevotella oris, Pseudoramibacter alactolyticus, and Tannerella forsythia (33.3%).
CONCLUSIONS
Although several key species predominate in endodontic samples of asymptomatic cases with periapical lesions, the primary endodontic infection is characterized by a wide bacterial diversity, which is mostly represented by members of the phylum Firmicutes belonging to the class Clostridia followed by the phylum Bacteroidetes.
Topics: Adolescent; Adult; Bacteria; Bacteroidetes; Clostridium; Dental Pulp Cavity; Genomic Library; Humans; Microbial Consortia; Middle Aged; Periapical Diseases; RNA, Bacterial; RNA, Ribosomal, 16S; Ruminococcus; Sequence Analysis, RNA; Young Adult
PubMed: 21689545
DOI: 10.1016/j.joen.2011.04.007 -
Antimicrobial Agents and Chemotherapy Nov 1999The activities of gemifloxacin (SB 265805, LB20304) and comparator agents were determined by an agar dilution method against 419 clinical strains of less-commonly... (Comparative Study)
Comparative Study
The activities of gemifloxacin (SB 265805, LB20304) and comparator agents were determined by an agar dilution method against 419 clinical strains of less-commonly identified species of anaerobes. Gemifloxacin was generally more active than trovafloxacin against gram-positive strains by one to two dilutions. Peptostreptococci (Peptostreptococcus asaccharolyticus, Peptostreptococcus magnus, Peptostreptococcus micros, and Peptostreptococcus prevotii) and Porphyromonas spp. (Porphyromonas asaccharolytica, Porphyromonas canoris, Porphyromonas gingivalis, and Porphyromonas macacae) were all susceptible to =0.25 microgram of gemifloxacin per ml. The MICs of gemifloxacin at which 90% of the following strains were inhibited (MIC(90)s) were =2 microgram/ml: Actinomyces israelii, Actinomyces odontolyticus, Clostridium innocuum, Clostridium clostridioforme, Anaerobiospirillum spp., Bacteroides tectum, Bacteroides ureolyticus, Bacteroides gracilis (now Campylobacter gracilis), Prevotella intermedia, Prevotella heparinolytica, and the Prevotella oris-buccae group. Fusobacterium naviforme and Fusobacterium necrophorum were also susceptible to =2 microgram of gemifloxacin per ml, while Fusobacterium varium strains exhibited a bimodal pattern; the other Fusobacterium species, such as Fusobacterium ulcerans and Fusobacterium russii, as well as Veillonella spp., the Prevotella melaninogenica group, Prevotella bivia, Clostridium difficile, and Bilophila wadsworthia were relatively resistant to gemifloxacin (MIC(90)s, >/=4 microgram/ml).
Topics: Anti-Infective Agents; Bacteria, Anaerobic; Bacterial Infections; Colony Count, Microbial; Fluoroquinolones; Gemifloxacin; Humans; Microbial Sensitivity Tests; Naphthyridines
PubMed: 10543754
DOI: 10.1128/AAC.43.11.2726 -
Journal of Thoracic Disease Oct 2019Culture-independent methods such as quantitative polymerase chain reaction (qPCR) are more sensitive for detecting pathogens than conventional culture. This study aimed...
Potential clinical utility of multiple target quantitative polymerase chain reaction (qPCR) array to detect microbial pathogens in patients with chronic obstructive pulmonary disease (COPD).
BACKGROUND
Culture-independent methods such as quantitative polymerase chain reaction (qPCR) are more sensitive for detecting pathogens than conventional culture. This study aimed to test the clinical potential of a multiple target qPCR array in identifying sputum pathogens, compared to traditional culture.
METHODS
Forty chronic obstructive pulmonary disease (COPD) patients provided spontaneous sputum and blood samples during an exacerbation event (n=25 patients) and in stable state (n=15 patients). Sputum was processed and analysed by microscopy, culture and sensitivity testing (MCS) to identify living microbial isolates, and multiple target qPCR (44 targets for bacterial and fungal pathogens and antibiotic resistance genes), and 16S rRNA gene sequencing.
RESULTS
Six microbial isolates (5 bacterial, 1 fungal) were cultured from 20 exacerbation and 10 stable patient sputum samples. Four of these microbial isolates had their presence in patient sputum confirmed by qPCR. All bacterial targets detected by qPCR were further confirmed by 16S rRNA gene sequencing at a genus level. qPCR identified significantly more bacterial pathogens than culture (P<0.001). The most prevalent bacterial species identified by qPCR were (72% of patients), (40%), (32%) and (17%). Microbial species diversity and richness were not significantly different between samples obtained from exacerbating and clinically stable cases. 16S rRNA gene sequencing identified (P=0.022, FDR =0.043 AUC =0.72) as a significantly different bacterial OTU (operational taxonomic units) in exacerbation sputum samples compared to stable state samples.
CONCLUSIONS
Multiple target qPCR was more sensitive for detection of sputum pathogens in COPD patients than conventional culture. 16S rRNA gene sequencing confirmed the identity at a genus level of all bacterial targets detected by qPCR, as well as identifying bacterial OTUs that could potentially be used to distinguish between exacerbation and stable COPD disease states. Multiple target qPCR pathogen detection in the sputum of COPD patients warrants further investigation to determine how it may influence COPD clinical management.
PubMed: 31737352
DOI: 10.21037/jtd.2019.10.39 -
Operative Dentistry 2003Self-etching primers are now considered the new generation of dentin bonding systems that modify and incorporate the bacteria-containing smear layer into their bonding... (Comparative Study)
Comparative Study
Self-etching primers are now considered the new generation of dentin bonding systems that modify and incorporate the bacteria-containing smear layer into their bonding mechanism. The antibacterial effects of the self-etching primers Clearfil SE Bond, Mac Bond, Imperva FL Bond, One-Up BondF and Prompt L-Pop were evaluated using the bacteria Streptococcus mutans ATCC25175, Peptostreptococcus anaerobius, Peptostreptococcus prevotii, Peptostreptococcus asaccharolyticus, Lactobacillus acidophilus, Lactobacillus catenaforme, Lactobacillus jensenii, Actinomyces odontolyticus, Porphyromonas endodontalis, Clostridium ramosum, Prevotella oris, Prevotella denticola and Fusobacterium nucleatum, with a disk diffusion method. A single-bottle total-etch dentin adhesive (Excite) was used for comparisons and chlorhexidine (0.2%) was used as the positive control. After incubation, zones of inhibited bacterial growth were observed. One-Up BondF, Prompt L-Pop and Excite showed growth inhibition for all bacterial strains. The bonding agents of Clearfil SE Bond, Mac Bond and Imperva FL Bond were unable to inhibit the growth of Lactobacillus jensenii and Actinomyces odontolyticus, while the primers of these systems produced inhibition halos to all tested microorganisms greater than that of chlorhexidine.
Topics: Actinomyces; Alkanes; Anti-Infective Agents, Local; Chlorhexidine; Clostridium; Dentin-Bonding Agents; Fusobacterium nucleatum; Gram-Negative Bacteria; Gram-Positive Bacteria; Humans; Lactobacillus; Lactobacillus acidophilus; Maleates; Materials Testing; Methacrylates; Peptostreptococcus; Porphyromonas; Prevotella; Resin Cements; Statistics, Nonparametric; Streptococcus mutans
PubMed: 12670069
DOI: No ID Found