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Nefrologia 2024Diabetes, dyslipidemia, older age, gender, urinary tract infections, and recent antibiotic intake have been associated with a decrease in the urobiome richness and other...
INTRODUCTION AND OBJECTIVES
Diabetes, dyslipidemia, older age, gender, urinary tract infections, and recent antibiotic intake have been associated with a decrease in the urobiome richness and other fluctuations in this microbiome. Gut and blood microbiome have been reported to be altered in patients with chronic kidney disease (CKD), and specifically in peritoneal dialysis (PD) patients. Still, there are currently no studies describing the urogenital microbiome in CKD-PD patients. In this study we characterized the urobiome profile in 46 PD patients and analyzed its clinical and inflammatory parameters.
MATERIALS AND METHODS
Mid-stream urine, fecal and blood samples were collected from 46 patients undergoing PD at Centro Hospitalar Universitário de São João (CHUSJ) in Porto, Portugal. Exclusion criteria were age under 18 years old, inability to give informed consent, history of infection in the last three months, and antibiotic intake in the last three months. The microbiome communities were analyzed by amplification and sequencing of the V3-V4 region of the bacterial 16S rRNA gene. Correlations with the patients' clinical data and inflammatory profile were performed.
RESULTS
CKD-PD patients presented a unique urobiome profile dominated by Bacillota, Actinomycetota and Pseudomonadota and characterized by a lower Shannon diversity than fecal and blood microbiome. The taxonomic profiles of urogenital samples were organized in multiple subtypes dominated by populations of Lactobacillus, Staphylococcus, Streptococcus, Gardnerella, Prevotella, Escherichia-Shigella, being similar to other non-PD-CKD patients. Gender, sCD14, residual diuresis and history of peritonitis were significantly associated to variations in the urobiome. Although not reaching statistical significance, diabetes and the time on PD also showed association with particular taxonomic groups. Depletion of Gardnerella, Staphylococcus, Corynebacterium, Lactobacillus or Dermabacter populations correlated with CKD-PD patients with history of diabetes, history of peritonitis and altered levels of sCD14.
CONCLUSIONS
Our results highlight urogenital microbiome as a potential partner and/or marker in the overall health state of CKD-PD patients.
Topics: Humans; Female; Male; Peritoneal Dialysis; Middle Aged; Microbiota; Renal Insufficiency, Chronic; Aged; Urogenital System; Adult; Feces
PubMed: 38697697
DOI: 10.1016/j.nefroe.2024.04.004 -
BMC Microbiology Jan 2024Reliable species identification of cultured isolates is essential in clinical bacteriology. We established a new study algorithm named NOVA - Novel Organism Verification...
Novel Organism Verification and Analysis (NOVA) study: identification of 35 clinical isolates representing potentially novel bacterial taxa using a pipeline based on whole genome sequencing.
BACKGROUND
Reliable species identification of cultured isolates is essential in clinical bacteriology. We established a new study algorithm named NOVA - Novel Organism Verification and Analysis to systematically analyze bacterial isolates that cannot be characterized by conventional identification procedures MALDI-TOF MS and partial 16 S rRNA gene sequencing using Whole Genome Sequencing (WGS).
RESULTS
We identified a total of 35 bacterial strains that represent potentially novel species. Corynebacterium sp. (n = 6) and Schaalia sp. (n = 5) were the predominant genera. Two strains each were identified within the genera Anaerococcus, Clostridium, Desulfovibrio, and Peptoniphilus, and one new species was detected within Citrobacter, Dermabacter, Helcococcus, Lancefieldella, Neisseria, Ochrobactrum (Brucella), Paenibacillus, Pantoea, Porphyromonas, Pseudoclavibacter, Pseudomonas, Psychrobacter, Pusillimonas, Rothia, Sneathia, and Tessaracoccus. Twenty-seven of 35 strains were isolated from deep tissue specimens or blood cultures. Seven out of 35 isolated strains identified were clinically relevant. In addition, 26 bacterial strains that could only be identified at the species level using WGS analysis, were mainly organisms that have been identified/classified very recently.
CONCLUSION
Our new algorithm proved to be a powerful tool for detection and identification of novel bacterial organisms. Publicly available clinical and genomic data may help to better understand their clinical and ecological role. Our identification of 35 novel strains, 7 of which appear to be clinically relevant, shows the wide range of undescribed pathogens yet to define.
Topics: Bacteria; Whole Genome Sequencing; Corynebacterium; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; RNA, Ribosomal, 16S; Bacterial Typing Techniques
PubMed: 38178003
DOI: 10.1186/s12866-023-03163-7 -
Frontiers in Cellular and Infection... 2023To explore the changes of bacterial flora in anophthalmic patients wearing ocular prosthesis (OP) and the microbiome diversity in conditions of different OP materials.
PURPOSE
To explore the changes of bacterial flora in anophthalmic patients wearing ocular prosthesis (OP) and the microbiome diversity in conditions of different OP materials.
METHODS
A cross-sectional clinical study was conducted, involving 19 OP patients and 23 healthy subjects. Samples were collected from the upper, lower palpebral, caruncle, and fornix conjunctiva. 16S rRNA sequencing was applied to identify the bacterial flora in the samples. The eye comfort of each OP patient was determined by a questionnaire. In addition, demographics information of each participant was also collected.
RESULTS
The diversity and richness of ocular flora in OP patients were significantly higher than that in healthy subjects. The results of flora species analysis also indicated that in OP patients, pathogenic microorganisms such as and increased significantly, while the resident flora of and decreased significantly. Within the self-comparison of OP patients, compared with Polymethyl Methacrylate (PMMA), prosthetic material of glass will lead to the increased colonization of opportunistic pathogens such as and , while gender and age have no significant impact on ocular flora.
CONCLUSIONS
The ocular flora of OP patients was significantly different from that of healthy people. Abundant colonization of pathogenic microorganisms may have an important potential relationship with eye discomfort and eye diseases of OP patients. PMMA, as an artificial eye material, demonstrated potential advantages in reducing the colonization of opportunistic pathogens.
Topics: Humans; Eye, Artificial; Lacrimal Apparatus; Polymethyl Methacrylate; Cross-Sectional Studies; RNA, Ribosomal, 16S; Anophthalmos; Bacteria; Microbiota
PubMed: 36960044
DOI: 10.3389/fcimb.2023.1117673 -
Frontiers in Microbiology 2022Antimicrobial chemicals are used as preservatives in cosmetics, pharmaceuticals, and food to prevent the growth of bacteria and fungi in the products. Unintentional...
Antimicrobial chemicals are used as preservatives in cosmetics, pharmaceuticals, and food to prevent the growth of bacteria and fungi in the products. Unintentional exposure in humans to such chemicals is well documented, but whether they also interfere with human oral microbiome composition is largely unexplored. In this study, we explored whether the oral bacterial composition is affected by exposure to antibacterial and environmental chemicals. Gingival fluid, urine, and interview data were collected from 477 adults (18-47 years) from the RHINESSA study in Bergen, Norway. Urine biomarkers of triclosan, triclocarban, parabens, benzophenone-3, bisphenols, and 2,4- and 2,5-dichlorophenols (DCPs) were quantified (by mass spectrometry). Microbiome analysis was based on 16S amplicon sequencing. Diversity and differential abundance analyses were performed to identify how microbial communities may change when comparing groups of different chemical exposure. We identified that high urine levels (>75th percentile) of propyl parabens were associated with a lower abundance of bacteria genera , and , as compared with low propylparaben levels (<25 percentile). High exposure to ethylparaben was associated with a higher abundance of . High urine levels of bisphenol A were associated with a lower abundance of and exposure to another environmental chemical, 2,4-DCP, was associated with a lower abundance of , and . High exposure to antibacterial and environmental chemicals was associated with an altered composition of gingiva bacteria; mostly commensal bacteria in the oral cavity. Our results highlight a need for a better understanding of how antimicrobial chemical exposure influences the human microbiome.
PubMed: 35572708
DOI: 10.3389/fmicb.2022.790496 -
Frontiers in Cellular and Infection... 2022Chronic infections play an important role in the progress of lung disease in patients suffering from cystic fibrosis (CF). Recent studies indicate that polymicrobial...
Chronic infections play an important role in the progress of lung disease in patients suffering from cystic fibrosis (CF). Recent studies indicate that polymicrobial microbiome profiles in the airway are associated with less inflammation. Thus, the hypothesis was raised that certain commensal bacteria might protect the host from inflammation. We therefore performed a screening study with commensals isolated from CF airway microbiome samples to identify potential beneficial commensals. We isolated more than 80 aerobic or facultative anaerobic commensal strains, including strains from genera , , , , , and . Through a screening experiment of co-infection in human epithelial cell lines, we identified multiple commensal strains, especially strains belonging to , that reduced triggered inflammatory responses. The results were confirmed by co-infection experiments in precision cut lung slices (PCLS) from mice. The underlying mechanisms of the complex host-pathogen-commensal crosstalk were investigated from both the host and the bacterial sides with a focus on . Transcriptome changes in the host in response to co-infection and mono-infection were evaluated, and the results indicated that several signalling pathways mediating inflammatory responses were downregulated by co-infection with compared to mono-infection, such as neutrophil extracellular trap formation. The genomic differences among strains with and without protective effects were investigated by whole genome sequencing, revealing genes only present in the strains showing protective effects. In summary, through both and studies, we could identify a variety of commensal strains that may reduce host inflammatory responses induced by infection. These findings support the hypothesis that CF airway commensals may protect the host from inflammation.
Topics: Animals; Cystic Fibrosis; Humans; Inflammation; Lung; Mice; Microbiota; Pseudomonas Infections; Pseudomonas aeruginosa
PubMed: 35174108
DOI: 10.3389/fcimb.2022.824101 -
Diagnostic Microbiology and Infectious... Oct 2020We investigated the clinical relevance of Dermabacter hominis isolated from samples of 108 patients. Polymicrobial growth was evident in 88% of specimens. Isolation of...
We investigated the clinical relevance of Dermabacter hominis isolated from samples of 108 patients. Polymicrobial growth was evident in 88% of specimens. Isolation of D. hominis was of definitive or possible significance in only 14% of patients. Vancomycin remains the drug of choice given a penicillin resistance rate of 84%.
Topics: Actinobacteria; Actinomycetales; Actinomycetales Infections; Adult; Aged; Aged, 80 and over; Anti-Bacterial Agents; Bacterial Typing Techniques; DNA, Bacterial; Drug Resistance, Bacterial; Female; Humans; Male; Middle Aged; Penicillins; Retrospective Studies; Vancomycin
PubMed: 32683204
DOI: 10.1016/j.diagmicrobio.2020.115118 -
Revista Do Instituto de Medicina... 2020Myiasis represents a group of neglected tropical diseases caused by the infestation of vertebrate tissues by dipterous larvae. We herein report an imported case of...
Myiasis represents a group of neglected tropical diseases caused by the infestation of vertebrate tissues by dipterous larvae. We herein report an imported case of foruncular myasis caused by Dermatobia hominis in Mexico City. The species was confirmed by DNA sequencing and phylogenetic reconstruction analysis.
Topics: Actinobacteria; Adult; Animals; Diptera; Humans; Larva; Mexico; Myiasis; Phylogeny; Sequence Analysis, DNA; Skin Diseases, Parasitic; Travel
PubMed: 32667394
DOI: 10.1590/s1678-9946202062047 -
Annals of Medicine and Surgery (2012) Dec 2018Strains of the genus is a recently established species, recognized as relatively rare opportunistic human pathogen, and is infrequently isolated from clinical...
INTRODUCTION
Strains of the genus is a recently established species, recognized as relatively rare opportunistic human pathogen, and is infrequently isolated from clinical specimens, including blood cultures, abscesses, wounds, bone, eye, and skin.
PRESENTATION OF CASE
We present a 78-year old female with chronic symmetrical peripheral gangrene and hand infection. The patient underwent surgical debridement with amputation on gangrene with infection of both fingers. At 2 weeks postoperatively, pus discharge was newly observed and the patient underwent reoperation. In the subsequent reinfection, unknown organism has been repeatedly identified, may be the most likely causative agent. On the basis of phenotypic and genotypic distinctness and DNA-DNA hybridization results, new strain should be placed in the genus as representing a novel species, for which the name sp. nov. is proposed.
DISCUSSION
We judged the novel species as the causative bacteria. Because of, a novel species called was repeatedly identified more than common bacteria. It can be considered as a postoperative nosocomial infection or opportunistic infection. It is not clear how the infection of occurred.
CONCLUSION
This is the first reported case of a human infection. We were able to treat patients without any complications by operative treatment and administering appropriate antimicrobial agents according to antibiotics susceptibility test.
PubMed: 30402221
DOI: 10.1016/j.amsu.2018.10.008 -
New Microbes and New Infections Nov 2018We report the core features of strain 1a5R-CH16 sp. nov., strain 2a1I-BL09 sp. nov., strain 1a7I-CH12an sp. nov. and strain 1a6R-CH11an sp. nov. In 2016, these...
We report the core features of strain 1a5R-CH16 sp. nov., strain 2a1I-BL09 sp. nov., strain 1a7I-CH12an sp. nov. and strain 1a6R-CH11an sp. nov. In 2016, these isolates were cultured from porcine nasal swabs taken from healthy pigs from farms in the region around Münster, Germany.
PubMed: 30364690
DOI: 10.1016/j.nmni.2018.09.005 -
Frontiers in Microbiology 2018Two strains, VM2412 and VR2415, were isolated from the feces of an Andean condor () living in Seoul Grand Park, Gyeonggi-do, South Korea. Cells of both strains were...
Two strains, VM2412 and VR2415, were isolated from the feces of an Andean condor () living in Seoul Grand Park, Gyeonggi-do, South Korea. Cells of both strains were observed to be Gram-stain positive, non-motile, aerobic, catalase positive and oxidase negative. Growth was found to occur at 10-30°C, showing optimum growth at 30°C. The strains could tolerate up to 15% (w/v) NaCl concentration and grow at pH 6-9. The strains shared 99.3% 16S rRNA gene sequence similarity to each other but were identified as two distinct species based on 89.0-89.2% ANIb, 90.3% ANIm, 89.7% OrthoANI and 38.0% dDDH values calculated using whole genome sequences. Among species with validly published names, DCY80 shared high 16S rRNA gene sequence similarities with strains VM2412 (98.7%) and VR2415 (98.4%) and close genetic relatedness with strains VM2412 (83.3-83.5% ANIb, 87.0% ANIm, 84.3% OrthoANI and 27.8% dDDH) and VR2415 (82.8-83.2% ANIb, 86.7% ANIm, 83.9% OrthoANI and 27.2% dDDH). The major fatty acid of the two strains was identified as anteiso-C and the polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, presumptively phosphatidylethanolamine and three unidentified glycolipids. Strain VR2415 also produced an unidentified phospholipid. The cell walls of the two strains contained -diaminopimelic acid as diagnostic diamino acid and the whole cell sugars were ribose, glucose, and galactose. The strains contained MK-7 as their predominant menaquinone. The genomes of strains VM2412, VR2415, and DCY80 were sequenced in this study. The genomic G+C contents of strains VM2412 and VR2415 were determined to be 70.8 and 70.4 mol%, respectively. A genome-based phylogenetic tree constructed using an up-to-date bacterial core gene set (UBCG) showed that the strains formed a clade with members of the genus , supporting their taxonomic classification into the genus . Based on phenotypic and genotypic analyses in this study, strains VM2412 and VR2415 are considered to represent two novel species of the genus and the names sp. nov. and sp. nov. are proposed for strains VM2412 (=KCTC 39996 = JCM 32142) and VR2415 (=KCTC 39997 = JCM 32143), respectively.
PubMed: 30131788
DOI: 10.3389/fmicb.2018.01809