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Anaerobe Aug 2019Clostridioides difficile is considered one of the main etiological agents of bacterial diarrhea associated with the use of antibiotics. It is an important nosocomial...
Clostridioides difficile is considered one of the main etiological agents of bacterial diarrhea associated with the use of antibiotics. It is an important nosocomial pathogen and the main cause of morbidity and mortality. In recent years, infections associated with C. difficile have led to numerous investigations. It is well known that C. difficile associated diarrhea (CDAD) is favored by the suppression or imbalance of the intestinal microbiome during or after antibiotic therapy. Other risk factors are, for instance, advanced age, long periods of hospitalization, chemotherapy, and other gastrointestinal infections. In the 2000's, the number of CDAD cases largely increased due to the emergence of the epidemic clone named BI/NAP1 ribotype 027, responsible for causing several outbreaks in developed countries, such as Canada, the United States, and the United Kingdom. The presence of the epidemic clone has been reported in Asia, Latin America and Australia, however, infections associated with C. difficile (CDI) in these geographic regions are usually caused by other ribotypes. In Brazil, for instance, epidemiological data on the incidence of CDI are still limited, especially regarding the spread of C. difficile within hospital units, the spectrum of toxigenic genes and the antimicrobial resistance profile. Some studies have demonstrated the importance of notifying cases related to CDI and taking special care measures in order to minimize the spread of epidemic strains in Brazil. Finally, epidemiological analysis of the prevalent and/or exclusive ribotypes circulating in Brazil can contribute to understand and to correlate characteristics associated with the biology of this pathogen with other globally circulating ribotypes. This review aimed to summarize all published work related to the isolation of C. difficile from human patients in Brazil, being the main focus, the methodologies used for identification of prevalent ribotypes, the antimicrobial susceptibility profile, and the diseases associated with the acquisition of CDI.
Topics: Adolescent; Adult; Aged; Aged, 80 and over; Anti-Bacterial Agents; Brazil; Child; Child, Preschool; Clostridioides difficile; Clostridium Infections; Diarrhea; Female; Hospitalization; Humans; Incidence; Infant; Male; Middle Aged; Ribotyping; Risk Factors; Young Adult
PubMed: 30851427
DOI: 10.1016/j.anaerobe.2019.03.002 -
Acta Dermato-venereologica Jan 2019The immune mechanisms involved in atopic dermatitis (AD) are complex and little is known about the possible role of the gut microbiota in the aetiopathogenesis of AD. A...
The immune mechanisms involved in atopic dermatitis (AD) are complex and little is known about the possible role of the gut microbiota in the aetiopathogenesis of AD. A systematic review of the literature was performed according to PRISMA guidelines, and included 44 of 2,199 studies (26 observational and 18 interventional studies). Detection of gut microbiota was performed by either 16s rRNA PCR, or by culture. Observational studies were diverse regarding the age of study participants and the bacterial species investigated. Overall, the results were conflicting with regard to diversity of the gut microbiota, specific bacterial colonization, and subsequent risk of AD. Nearly half of the included interventional studies showed that an altered gut microbial colonization due to use of probiotics had a positive effect on the severity of AD. The remaining studies did not show an effect of probiotics on the severity of AD despite an alteration in the gut microbial composition. The role of the gut microbiome for the onset and severity of pre-existing AD remains controversial.
Topics: Bacteria; Dermatitis, Atopic; Gastrointestinal Microbiome; Gastrointestinal Tract; Host-Pathogen Interactions; Humans; Probiotics; Ribotyping; Risk Factors; Severity of Illness Index
PubMed: 30085318
DOI: 10.2340/00015555-3008 -
Journal of Plastic, Reconstructive &... Jan 2019We present a case of skin allograft survival in a patient who previously received a bone marrow transplant from the same HLA-matched donor. DNA fingerprinting of skin...
BACKGROUND
We present a case of skin allograft survival in a patient who previously received a bone marrow transplant from the same HLA-matched donor. DNA fingerprinting of skin biopsies showed mixed cellularity originating from the donor and recipient (68% and 32% donor DNA in the allograft skin and the native recipient's skin, respectively). Histologic sections demonstrated both grade 3/4 rejection and graft-versus-host-disease. We have conducted a systematic review in search for other cases of donor skin allograft survival after a bone marrow or hematopoietic stem cell transplantation.
METHODS
All reported cases in English, Spanish, French, and German were captured using the electronic databases. Bibliographies of relevant articles were manually searched.
RESULTS
Nineteen patients (12 females) who received skin allografts from their bone marrow or hematopoietic stem cell donors were identified. Average age was 27.2 years (range: 5 months to 64 years). Skin allografts were used to treat graft-versus-host-disease, Herlitz junctional epidermolysis bullosa, and to test tolerance before a kidney transplantation from the same donor. Eight cases were not receiving immunosuppressive therapy. Allografts survived in all patients. In three patients, skin punch biopsies were taken, and these biopsies demonstrated mixed donor and recipient cellularity. The pathology result is specified in two more cases, with no signs of rejection.
CONCLUSIONS
The same donor skin allografts may be a safe option to treat severe cutaneous conditions in recipients of a bone marrow/hematopoietic stem cell transplantation. However, future studies are needed to confirm these results.
Topics: Adolescent; Adult; Allografts; Bone Marrow Transplantation; Child; Child, Preschool; Escherichia coli Infections; Fasciitis, Necrotizing; Fatal Outcome; Female; Graft Survival; Graft vs Host Disease; Humans; Infant; Living Donors; Male; Middle Aged; Skin Transplantation; Transplant Donor Site; Transplantation, Homologous; Wound Healing; Young Adult
PubMed: 29983364
DOI: 10.1016/j.bjps.2018.05.018 -
Forensic Science International Nov 2017Molecular analyses in a post-mortem setting are becoming increasingly common, particularly in cases of sudden unexplained death, with the aim of identifying genetic... (Review)
Review
Molecular analyses in a post-mortem setting are becoming increasingly common, particularly in cases of sudden unexplained death, with the aim of identifying genetic mutations which may be responsible for causing death. In retrospective investigations, the access to suitable autopsy biological samples may be limited, and often formalin fixed paraffin embedded (FFPE) tissue is the only sample available. The preservation of tissue in formalin is known to damage DNA through crosslinking activity. This results in the extraction of severely fragmented DNA of variable yields, which subsequently reduces the ability to perform downstream molecular analyses. Numerous studies have investigated possible improvements to various aspects of the DNA extraction and amplification procedures from FFPE tissue and this review aims to collate these optimization steps in a cohesive manner. A systematic review was performed of three major databases, which identified 111 articles meeting the inclusion criteria. Five main areas for optimization and improvements were identified in the workflow: (1) tissue type, (2) fixation process, (3) post-fixation, (4) DNA extraction procedure and (5) amplification. It was found that some factors identified, for example tissue type and fixation process, could not be controlled by the researcher when conducting retrospective analyses. For this reason, optimization should be performed in other areas, within the financial means of the laboratories, and in accordance with the purposes of the investigation. Implementation of one or more of the optimization measures described here is anticipated to assist in the extraction of higher quality DNA. Despite the challenges posed by FFPE tissue, it remains a valuable source of DNA in retrospective molecular forensic investigations.
Topics: DNA; DNA Fingerprinting; Fixatives; Forensic Medicine; Formaldehyde; Humans; Paraffin Embedding; Polymerase Chain Reaction; Preservation, Biological
PubMed: 29078160
DOI: 10.1016/j.forsciint.2017.09.020 -
Nutrients Aug 2017The mechanisms behind the efficacy of exclusive enteral nutrition (EEN) in Crohn's disease (CD) remain poorly understood, despite the high rate of treatment response.... (Review)
Review
The mechanisms behind the efficacy of exclusive enteral nutrition (EEN) in Crohn's disease (CD) remain poorly understood, despite the high rate of treatment response. Evidence accumulated in the last 20 years suggests that a positive shift of the disrupted microbiota is one of the treatment effects. The purpose of this study was to critically review and summarize data reporting the microbiological effects of EEN in patients with CD. Fourteen studies were considered in the review, overall involving 216 CD patients on EEN. The studies were heterogeneous in methods of microbiota analysis and exclusion criteria. The most frequently reported effect of EEN was a reduction in microbiota diversity, reversible when patients returned to a normal diet. The effect of EEN on specific bacteria was very variable in the different studies, partially due to methodological limitations of the mentioned studies. The EEN seem to induce some metabolomic changes, which are different in long-term responder patients compared to patients that relapse earlier. Bacterial changes can be relevant to explaining the efficacy of EEN; however, microbiological data obtained from rigorously performed studies and derived from last generation techniques are largely inconsistent.
Topics: Bacteria; Crohn Disease; Enteral Nutrition; Gastrointestinal Microbiome; Humans; Intestines; Ribotyping; Treatment Outcome
PubMed: 28777338
DOI: 10.3390/nu9080832 -
BMC Research Notes Nov 2014Over the past ten years, there has been an explosion of microbiome research. Many software packages for analyzing microbial sequences such as the 16S gene from 454... (Review)
Review
BACKGROUND
Over the past ten years, there has been an explosion of microbiome research. Many software packages for analyzing microbial sequences such as the 16S gene from 454 sequencers and Illumina platforms are available. But for a new researcher, it is difficult to know which package to choose. We present a systematic review of packages for the analysis of molecular sequences used to describe and compare microbial communities. This review gives students and researchers information to help choose the best analytic pipeline for their project. To the best of our knowledge, this is the first review of such software.
FINDINGS
Seven software packages met our inclusion criteria of being cost free and publically available, offering analysis functions from platform sequencing to results presentation, and included documentation and data security. We installed and executed each of the software packages and describe the installation, documentation, features, and functions of each.
CONCLUSIONS
For the user, pipeline choices may be limited because some packages only run on select operating systems. Users should be aware of the availability of features and functions of each package. Of utmost importance is that the user must be aware of the default settings and underlying assumptions of each function. All packages are lacking sufficient methods for longitudinal analysis.Researchers can do well using any one of these seven packages. However, two packages are outstanding; mothur and QIIME, due not only to the comprehensive suite of functions and procedures incorporated into the pipelines but also because of the accompanying documentation.
Topics: Animals; DNA Contamination; Humans; Sequence Analysis, DNA; Software
PubMed: 25421430
DOI: 10.1186/1756-0500-7-830 -
PloS One 2014We conducted a systematic review of the Medline database (U.S. National Library of Medicine, National Institutes of Health, Bethesda, MD, U.S.A) to determine if... (Meta-Analysis)
Meta-Analysis Review
We conducted a systematic review of the Medline database (U.S. National Library of Medicine, National Institutes of Health, Bethesda, MD, U.S.A) to determine if consistent molecular vaginal microbiota (VMB) composition patterns can be discerned after a decade of molecular testing, and to evaluate demographic, behavioral and clinical determinants of VMB compositions. Studies were eligible when published between 1 January 2008 and 15 November 2013, and if at least one molecular technique (sequencing, PCR, DNA fingerprinting, or DNA hybridization) was used to characterize the VMB. Sixty three eligible studies were identified. These studies have now conclusively shown that lactobacilli-dominated VMB are associated with a healthy vaginal micro-environment and that bacterial vaginosis (BV) is best described as a polybacterial dysbiosis. The extent of dysbiosis correlates well with Nugent score and vaginal pH but not with the other Amsel criteria. Lactobacillus crispatus is more beneficial than L. iners. Longitudinal studies have shown that a L. crispatus-dominated VMB is more likely to shift to a L. iners-dominated or mixed lactobacilli VMB than to full dysbiosis. Data on VMB determinants are scarce and inconsistent, but dysbiosis is consistently associated with HIV, human papillomavirus (HPV), and Trichomonas vaginalis infection. In contrast, vaginal colonization with Candida spp. is more common in women with a lactobacilli-dominated VMB than in women with dysbiosis. Cervicovaginal mucosal immune responses to molecular VMB compositions have not yet been properly characterized. Molecular techniques have now become more affordable, and we make a case for incorporating them into larger epidemiological studies to address knowledge gaps in etiology and pathogenesis of dysbiosis, associations of different dysbiotic states with clinical outcomes, and to evaluate interventions aimed at restoring and maintaining a lactobacilli-dominated VMB.
Topics: Adolescent; Adult; Cluster Analysis; Female; Humans; Microbial Consortia; Microbiota; Pregnancy; Vagina; Vaginosis, Bacterial
PubMed: 25148517
DOI: 10.1371/journal.pone.0105998 -
Water Research Nov 2014Globally, denitrification is commonly employed in biological nitrogen removal processes to enhance water quality. However, substantial knowledge gaps remain concerning... (Review)
Review
Globally, denitrification is commonly employed in biological nitrogen removal processes to enhance water quality. However, substantial knowledge gaps remain concerning the overall community structure, population dynamics and metabolism of different organic carbon sources. This systematic review provides a summary of current findings pertaining to the microbial ecology of denitrification in biological wastewater treatment processes. DNA fingerprinting-based analysis has revealed a high level of microbial diversity in denitrification reactors and highlighted the impacts of carbon sources in determining overall denitrifying community composition. Stable isotope probing, fluorescence in situ hybridization, microarrays and meta-omics further link community structure with function by identifying the functional populations and their gene regulatory patterns at the transcriptional and translational levels. This review stresses the need to integrate microbial ecology information into conventional denitrification design and operation at full-scale. Some emerging questions, from physiological mechanisms to practical solutions, for example, eliminating nitrous oxide emissions and supplementing more sustainable carbon sources than methanol, are also discussed. A combination of high-throughput approaches is next in line for thorough assessment of wastewater denitrifying community structure and function. Though denitrification is used as an example here, this synergy between microbial ecology and process engineering is applicable to other biological wastewater treatment processes.
Topics: Bacteria; DNA, Bacterial; Denitrification; Environmental Microbiology; In Situ Hybridization, Fluorescence; Nitrogen; Sewage; Waste Disposal, Fluid
PubMed: 25078442
DOI: 10.1016/j.watres.2014.06.042 -
BMC Infectious Diseases Jun 2010Invasive meningococcal disease (IMD), is a widely distributed, complex human disease affecting all age categories. The causative agent, Neisseria meningitidis, is spread... (Review)
Review
BACKGROUND
Invasive meningococcal disease (IMD), is a widely distributed, complex human disease affecting all age categories. The causative agent, Neisseria meningitidis, is spread through aerosol respiratory droplets. 13 different serogroups have been identified, each with varying epidemiological features including prevalence, virulence, immunogenicity, geographical and temporal distribution. Although preventative measures are available for several of the serogroups, meningococcal disease caused by serogroup B is of particular interest due to the challenge it presents concerning vaccine development.
METHODS
A systematic review of peer reviewed studies and reports, the collection of data from national and international health resources, along with the analysis of the Multi Locus Sequence Typing database was carried out aimed at collecting information concerning serogroup B IMD and the epidemiology attached to it.
RESULTS
A continuous output of related and novel STs occurring worldwide in terms of the hypervirulent clonal complexes was observed both in published studies and the MLST database in this case using the eburst software, which highlights the genetically diverse nature of serogroup B strains.
CONCLUSIONS
With the recent dominance of serogroup B IMD seen in many countries, along with the presence of antibiotic resistance, vaccine development needs to target areas of the bacterium which tackle this widespread and heterogeneous aspect of meningococcal meningitis disease.
Topics: Adolescent; Adult; Aged; Aged, 80 and over; Bacterial Typing Techniques; Child; Child, Preschool; Cluster Analysis; DNA Fingerprinting; Drug Resistance, Bacterial; Genotype; Humans; Infant; Infant, Newborn; Meningitis, Meningococcal; Middle Aged; Neisseria meningitidis, Serogroup B; Young Adult
PubMed: 20565757
DOI: 10.1186/1471-2334-10-175 -
Tropical Medicine & International... Aug 2009The proportion of tuberculosis cases in a population that are clustered (i.e. share identical strains of Mycobacterium tuberculosis) reflects ongoing M. tuberculosis... (Meta-Analysis)
Meta-Analysis Review
OBJECTIVES
The proportion of tuberculosis cases in a population that are clustered (i.e. share identical strains of Mycobacterium tuberculosis) reflects ongoing M. tuberculosis transmission. It varies markedly, but it is unclear how much of this variation reflects measurable differences in study design, setting and the patient population. We aimed to assess the relative impact of these factors and develop a tool to improve interpretation of the proportion clustered from an individual study.
METHODS
We systematically reviewed all population-based TB clustering studies that used IS6110 RFLP as their main DNA fingerprinting technique. Meta-regression was used to see how much of the variation in the proportion clustered between studies could be explained by variables describing study design, setting and population. We compared expected clustering, based on study design and setting, with that observed.
RESULTS
Forty-six studies were included. Just four factors related to study design and setting-study duration, sampling fraction, handling of low band strains and tuberculosis incidence-explained 28% of the variation in the proportion clustered. Additionally including average patient age and proportion foreign born explained 60% of the variation in clustering for industrialized countries. Comparison of expected and observed proportions showed that for some studies the expected proportion clustered differed strongly from that observed.
CONCLUSIONS
We were able to account for much of the variation in the proportion clustered. The comparison of expected and observed clustering allows for a more valid comparison of studies and provides a tool for identifying outliers that warrant further investigation.
Topics: Adult; Aged; Analysis of Variance; DNA Fingerprinting; DNA, Bacterial; Epidemiologic Studies; Female; Humans; Male; Middle Aged; Mycobacterium tuberculosis; Tuberculosis
PubMed: 19702595
DOI: 10.1111/j.1365-3156.2009.02316.x