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Clinical Microbiology and Infection :... Jun 2019Studying hospital outbreaks by using molecular tools, i.e. synthesizing the molecular epidemiology data to its appropriate clinical-epidemiologic context, is crucial in...
BACKGROUND
Studying hospital outbreaks by using molecular tools, i.e. synthesizing the molecular epidemiology data to its appropriate clinical-epidemiologic context, is crucial in order to identify infection source, infer transmission dynamics, appropriately allocate prevention resources and implement control measures. Whole-genome sequencing (WGS) of pathogens has become the reference standard, as it is becoming more accessible and affordable. Consequently, sequencing of the full pathogen genome via WGS and major progress in fit-for-purpose genomic data analysis tools and interpretation is revolutionizing the field of outbreak investigations in hospitals. Metagenomics is an additional evolving field that might become commonly used in the future for outbreak investigations. Nevertheless, practitioners are frequently limited in terms of WGS or metagenomics, especially for local outbreak analyses, as a result of costs or logistical considerations, reduced or lack of locally available resources and/or expertise. As a result, traditional approaches, including pulsed-field gel electrophoresis, repetitive-element palindromic PCR and multilocus sequence typing, along with other typing methods, are still widely used.
AIMS
To provide practitioners with evidenced-based action plans for usage of the various typing techniques in order to investigate the molecular epidemiology of nosocomial outbreaks, of clinically significant pathogens in acute-care hospitals.
SOURCES
PubMed search with relevant keywords along with personal collection of relevant publications.
CONTENT
Representative case scenarios and critical review of the relevant scientific literature.
IMPLICATIONS
The review provides practical action plans to manage molecular epidemiologic investigations of outbreaks caused by clinically significant nosocomial pathogens, while prioritizing the use and timely integration of the various methodologies.
Topics: Cross Infection; Disease Outbreaks; Disease Transmission, Infectious; Humans; Molecular Epidemiology; Molecular Typing
PubMed: 30287413
DOI: 10.1016/j.cmi.2018.09.017 -
European Review For Medical and... Sep 2018In recent years metagenomic analysis has become more accessible for the characterization of biological specimens. There has been an important increase of studies using...
OBJECTIVE
In recent years metagenomic analysis has become more accessible for the characterization of biological specimens. There has been an important increase of studies using this technique for subgingival human samples. To date, there are no updated systematic reviews on the relationship between oral microbiota and periodontal disease. The aim of the present systematic review was to update data about studies concerning the influences of changes in oral microbiota composition on the periodontal status in human subjects.
MATERIALS AND METHODS
An electronic search was conducted in four databases (MEDLINE, Scopus, CENTRAL and Web of Science) for articles published in English from January 2014 to April 2018. In vitro or animal studies, case reports, case series, retrospective studies, review articles, abstracts and discussions were excluded. Also, studies that evaluated less than 5 microbial species, only viruses or already known periodontal pathogens were excluded. Two independent researches selected the studies and extracted the data. The quality of evidence was assessed as high, moderate or low for each microorganism.
RESULTS
Eight studies and three additional publications recovered from the bibliography search of the selected articles were included in the review. The Bacteria domain was the main detected among the others and it included 53 species. The review confirmed the presence of recognized periodontal pathogens such as the members of the red complex but also identified, with high weight of evidence, the presence of new pathogens.
CONCLUSIONS
The results of this systematic review support high evidence for the association of 3 new species/genera with the etiology of periodontitis. Future investigations on the actual role of these new pathogens in the onset and progression of the disease are needed.
Topics: Humans; Microbiota; Mouth; Periodontal Diseases
PubMed: 30280756
DOI: 10.26355/eurrev_201809_15903 -
The Cochrane Database of Systematic... May 2018Necrotizing soft tissue infections (NSTIs) are severe and rapidly spreading soft tissue infections of the subcutaneous tissue, fascia, or muscle, which are mostly caused... (Review)
Review
BACKGROUND
Necrotizing soft tissue infections (NSTIs) are severe and rapidly spreading soft tissue infections of the subcutaneous tissue, fascia, or muscle, which are mostly caused by bacteria. Associated rates of mortality and morbidity are high, with the former estimated at around 23%, and disability, sequelae, and limb loss occurring in 15% of patients. Standard management includes intravenous empiric antimicrobial therapy, early surgical debridement of necrotic tissues, intensive care support, and adjuvant therapies such as intravenous immunoglobulin (IVIG).
OBJECTIVES
To assess the effects of medical and surgical treatments for necrotizing soft tissue infections (NSTIs) in adults in hospital settings.
SEARCH METHODS
We searched the following databases up to April 2018: the Cochrane Skin Group Specialised Register, CENTRAL, MEDLINE, Embase, and LILACS. We also searched five trials registers, pharmaceutical company trial results databases, and the US Food and Drug Administration and the European Medicines Agency websites. We checked the reference lists of included studies and reviews for further references to relevant randomised controlled trials (RCTs).
SELECTION CRITERIA
RCTs conducted in hospital settings, that evaluated any medical or surgical treatment for adults with NSTI were eligible for inclusion. Eligible medical treatments included 1) comparisons between different antimicrobials or with placebo; 2) adjuvant therapies such as intravenous immunoglobulin (IGIV) therapy compared with placebo; no treatment; or other adjuvant therapies. Eligible surgical treatments included surgical debridement compared with amputation, immediate versus delayed intervention, or comparisons of number of interventions.RCTs of hyperbaric oxygen (HBO) therapy for NSTI were ineligible because HBO is the focus of another Cochrane Review.
DATA COLLECTION AND ANALYSIS
We used standard methodological procedures expected by Cochrane. The primary outcome measures were 1) mortality within 30 days, and 2) proportion of participants who experience a serious adverse event. Secondary outcomes were 1) survival time, and 2) assessment of long-term morbidity. We used GRADE to assess the quality of the evidence for each outcome.
MAIN RESULTS
We included three trials randomising 197 participants (62% men) who had a mean age of 55 years. One trial compared two antibiotic treatments, and two trials compared adjuvant therapies with placebo. In all trials, participants concomitantly received standard interventions, such as intravenous empiric antimicrobial therapy, surgical debridement of necrotic tissues, intensive care support, and adjuvant therapies. All trials were at risk of attrition bias and one trial was not blinded.Moxifloxacin versus amoxicillin-clavulanate One trial included 54 participants who had a NSTI; it compared a third-generation quinolone, moxifloxacin, at a dose of 400 mg given once daily, against a penicillin, amoxicillin-clavulanate, at a dose of 3 g given three times daily for at least three days, followed by 1.5 g three times daily. Duration of treatment varied from 7 to 21 days. We are uncertain of the effects of these treatments on mortality within 30 days (risk ratio (RR) 3.00, 95% confidence interval (CI) 0.39 to 23.07) and serious adverse events at 28 days (RR 0.63, 95% CI 0.30 to 1.31) because the quality of the evidence is very low.AB103 versus placebo One trial of 43 randomised participants compared two doses, 0.5 mg/kg and 0.25 mg/kg, of an adjuvant drug, a CD28 antagonist receptor (AB103), with placebo. Treatment was given via infusion pump for 10 minutes before, after, or during surgery within six hours after the diagnosis of NSTI. We are uncertain of the effects of AB103 on mortality rate within 30 days (RR of 0.34, 95% CI 0.05 to 2.16) and serious adverse events measured at 28 days (RR 1.49, 95% CI 0.52 to 4.27) because the quality of the evidence is very low.Intravenous immunoglobulin (IVIG) versus placebo One trial of 100 randomised participants assessed IVIG as an adjuvant drug, given at a dose of 25 g/day, compared with placebo, given for three consecutive days. There may be no clear difference between IVIG and placebo in terms of mortality within 30 days (RR 1.17, 95% CI 0.42 to 3.23) (low-certainty evidence), nor serious adverse events experienced in the intensive care unit (ICU) (RR 0.73 CI 95% 0.32 to 1.65) (low-certainty evidence).Serious adverse events were only described in one RCT (the IVIG versus placebo trial) and included acute kidney injury, allergic reactions, aseptic meningitis syndrome, haemolytic anaemia, thrombi, and transmissible agents.Only one trial reported assessment of long-term morbidity, but the outcome was not defined in the way we prespecified in our protocol. The trial used the Short Form Health Survey (SF36). Data on survival time were provided upon request for the trials comparing amoxicillin-clavulanate versus moxifloxacin and IVIG versus placebo. However, even with data provided, it was not possible to perform survival analysis.
AUTHORS' CONCLUSIONS
We found very little evidence on the effects of medical and surgical treatments for NSTI. We cannot draw conclusions regarding the relative effects of any of the interventions on 30-day mortality or serious adverse events due to the very low quality of the evidence.The quality of the evidence is limited by the very small number of trials, the small sample sizes, and the risks of bias in the included trials. It is important for future trials to clearly define their inclusion criteria, which will help with the applicability of future trial results to a real-life population.Management of NSTI participants (critically-ill participants) is complex, involving multiple interventions; thus, observational studies and prospective registries might be a better foundation for future research, which should assess empiric antimicrobial therapy, as well as surgical debridement, along with the placebo-controlled comparison of adjuvant therapy. Key outcomes to assess include mortality (in the acute phase of the condition) and long-term functional outcomes, e.g. quality of life (in the chronic phase).
Topics: Adult; Amoxicillin-Potassium Clavulanate Combination; Anti-Bacterial Agents; CD28 Antigens; Critical Care; Debridement; Female; Fluoroquinolones; Humans; Immunoglobulins, Intravenous; Male; Middle Aged; Moxifloxacin; Randomized Controlled Trials as Topic; Soft Tissue Infections
PubMed: 29851032
DOI: 10.1002/14651858.CD011680.pub2 -
International Journal of Endocrinology 2018Gut microbiome has been identified in the past decade as an important factor involved in obesity, but the magnitude of its contribution to obesity and its related... (Review)
Review
Gut microbiome has been identified in the past decade as an important factor involved in obesity, but the magnitude of its contribution to obesity and its related comorbidities is still uncertain. Among the vast quantity of factors attributed to obesity, environmental, dietary, lifestyle, genetic, and others, the microbiome has aroused curiosity, and the scientific community has published many original articles. Most of the studies related to microbiome and obesity have been reported based on the associations between microbiota and obesity, and the in-depth study of the mechanisms related has been studied mainly in rodents and exceptionally in humans. Due to the quantity and diverse information published, the need of reviews is mandatory to recapitulate the relevant achievements. In this systematic review, we provide an overview of the current evidence on the association between intestinal microbiota and obesity. Additionally, we analyze the effects of an extreme weight loss intervention such as bariatric surgery on gut microbiota. The review is divided into 2 sections: first, the association of obesity and related metabolic disorders with different gut microbiome profiles, including metagenomics studies, and second, changes on gut microbiome after an extreme weight loss intervention such as bariatric surgery.
PubMed: 29849617
DOI: 10.1155/2018/4095789 -
Microbiome Mar 2017Necrotizing enterocolitis (NEC) is a catastrophic disease of preterm infants, and microbial dysbiosis has been implicated in its pathogenesis. Studies evaluating the... (Meta-Analysis)
Meta-Analysis Review
BACKGROUND
Necrotizing enterocolitis (NEC) is a catastrophic disease of preterm infants, and microbial dysbiosis has been implicated in its pathogenesis. Studies evaluating the microbiome in NEC and preterm infants lack power and have reported inconsistent results.
METHODS AND RESULTS
Our objectives were to perform a systematic review and meta-analyses of stool microbiome profiles in preterm infants to discern and describe microbial dysbiosis prior to the onset of NEC and to explore heterogeneity among studies. We searched MEDLINE, PubMed, CINAHL, and conference abstracts from the proceedings of Pediatric Academic Societies and reference lists of relevant identified articles in April 2016. Studies comparing the intestinal microbiome in preterm infants who developed NEC to those of controls, using culture-independent molecular techniques and reported α and β-diversity metrics, and microbial profiles were included. In addition, 16S ribosomal ribonucleic acid (rRNA) sequence data with clinical meta-data were requested from the authors of included studies or searched in public data repositories. We reprocessed the 16S rRNA sequence data through a uniform analysis pipeline, which were then synthesized by meta-analysis. We included 14 studies in this review, and data from eight studies were available for quantitative synthesis (106 NEC cases, 278 controls, 2944 samples). The age of NEC onset was at a mean ± SD of 30.1 ± 2.4 weeks post-conception (n = 61). Fecal microbiome from preterm infants with NEC had increased relative abundances of Proteobacteria and decreased relative abundances of Firmicutes and Bacteroidetes prior to NEC onset. Alpha- or beta-diversity indices in preterm infants with NEC were not consistently different from controls, but we found differences in taxonomic profiles related to antibiotic exposure, formula feeding, and mode of delivery. Exploring heterogeneity revealed differences in microbial profiles by study and the target region of the 16S rRNA gene (V1-V3 or V3-V5).
CONCLUSIONS
Microbial dysbiosis preceding NEC in preterm infants is characterized by increased relative abundances of Proteobacteria and decreased relative abundances of Firmicutes and Bacteroidetes. Microbiome optimization may provide a novel strategy for preventing NEC.
Topics: Bacteria; Bacteroides; Dysbiosis; Enterocolitis, Necrotizing; Feces; Firmicutes; Gastrointestinal Microbiome; Humans; Infant, Newborn; Infant, Premature; Infant, Premature, Diseases; Intestines; Proteobacteria; RNA, Ribosomal, 16S
PubMed: 28274256
DOI: 10.1186/s40168-017-0248-8 -
Journal of Oral & Maxillofacial Research 2016To describe the microbial profiles of peri-implant diseases and the main detection methods. (Review)
Review
OBJECTIVES
To describe the microbial profiles of peri-implant diseases and the main detection methods.
MATERIAL AND METHODS
A literature search was performed in MEDLINE via PubMed database to identify studies on microbial composition of peri-implant surfaces in humans published in the last 5 years. Studies had to have clear implant status definition for health, peri-implant mucositis and/or peri-implantitis and specifically study microbial composition of the peri-implant sulcus.
RESULTS
A total of 194 studies were screened and 47 included. Peri-implant sites are reported to be different microbial ecosystems compared to periodontal sites. However, differences between periodontal and peri-implant health and disease are not consistent across all studies, possibly due to the bias introduced by the microbial detection technique. New methods non species-oriented are being used to find 'unexpected' microbiota not previously described in these scenarios.
CONCLUSIONS
Microbial profile of peri-implant diseases usually includes classic periodontopathogens. However, correlation between studies is difficult, particularly because of the use of different detection methods. New metagenomic techniques should be promoted for future studies to avoid detection bias.
PubMed: 27833735
DOI: 10.5037/jomr.2016.7310 -
Genome Medicine May 2016The effects of probiotic supplementation on fecal microbiota composition in healthy adults have not been well established. We aimed to provide a systematic review of the... (Review)
Review
BACKGROUND
The effects of probiotic supplementation on fecal microbiota composition in healthy adults have not been well established. We aimed to provide a systematic review of the potential evidence for an effect of probiotic supplementation on the composition of human fecal microbiota as assessed by high-throughput molecular approaches in randomized controlled trials (RCTs) of healthy adults.
METHODS
The survey of peer-reviewed papers was performed on 17 August 2015 by a literature search through PubMed, SCOPUS, and ISI Web of Science. Additional papers were identified by checking references of relevant papers. Search terms included healthy adult, probiotic, bifidobacterium, lactobacillus, gut microbiota, fecal microbiota, intestinal microbiota, intervention, and (clinical) trial. RCTs of solely probiotic supplementation and placebo in healthy adults that examined alteration in composition of overall fecal microbiota structure assessed by shotgun metagenomic sequencing, 16S ribosomal RNA sequencing, or phylogenetic microarray methods were included. Independent collection and quality assessment of studies were performed by two authors using predefined criteria including methodological quality assessment of reports of the clinical trials based on revised tools from PRISMA/Cochrane and by the Jadad score.
RESULTS
Seven RCTs investigating the effect of probiotic supplementation on fecal microbiota in healthy adults were identified and included in the present systematic review. The quality of the studies was assessed as medium to high. Still, no effects were observed on the fecal microbiota composition in terms of α-diversity, richness, or evenness in any of the included studies when compared to placebo. Only one study found that probiotic supplementation significantly modified the overall structure of the fecal bacterial community in terms of β-diversity when compared to placebo.
CONCLUSIONS
This systematic review of the pertinent literature demonstrates a lack of evidence for an impact of probiotics on fecal microbiota composition in healthy adults. Future studies would benefit from pre-specifying the primary outcome and transparently reporting the results including effect sizes, confidence intervals, and P values as well as providing a clear distinction of between-group and within-group comparisons.
Topics: Adult; Bacteria; Feces; Healthy Volunteers; Humans; Microbiota; Phylogeny; Probiotics; Randomized Controlled Trials as Topic
PubMed: 27159972
DOI: 10.1186/s13073-016-0300-5 -
Alimentary Pharmacology & Therapeutics Nov 2015The human intestinal microbiota is a key regulator of host metabolic and immune functions and alterations in the microbiome ('dysbiosis') have been implicated in several... (Review)
Review
BACKGROUND
The human intestinal microbiota is a key regulator of host metabolic and immune functions and alterations in the microbiome ('dysbiosis') have been implicated in several human diseases. Because of the anatomical links between the intestines and the liver, dysbiosis may also disrupt hepatic function and thereby contribute to the pathogenesis of nonalcoholic fatty liver disease (NAFLD).
AIM
To perform a comprehensive review of the medical literature investigating associations between intestinal dysbiosis and NAFLD, with a particular emphasis on studies that characterise the microbiome in NAFLD.
METHODS
We conducted a search of PubMed, Embase, and Web of Science using multiple search terms including: 'NAFLD, NASH, fatty liver, steatohepatitis' combined with 'metagenome, microbiom*, microbiota*, fecal flora, intestinal flora, gut bacteria'. Results were manually reviewed and studies selected based on relevance to intestinal microbiota and NAFLD. We also included studies that addressed potential mechanistic models of pathways linking the dysbiosis to NAFLD.
RESULTS
Nine studies (five human and four animal models) were identified in our search that assessed associations between specific intestinal microbiota composition and NAFLD. We reviewed and summarised the results of additional investigations that more broadly addressed the mechanisms by which the microbiome may impact NAFLD pathogenesis.
CONCLUSIONS
Investigations in humans and animals demonstrate associations between intestinal dysbiosis and NAFLD; however, causality has not been proven and mechanistic links require further delineation. As the field of microbiome research matures in techniques and study design, more detailed insights into NAFLD pathogenesis and its associations with the intestinal microbiota will be elucidated.
Topics: Animals; Dysbiosis; Humans; Intestines; Metagenome; Microbiota; Models, Animal; Non-alcoholic Fatty Liver Disease
PubMed: 26304302
DOI: 10.1111/apt.13376 -
PeerJ 2015Associations between microorganisms occur extensively throughout Earth's oceans. Understanding how microbial communities are assembled and how the presence or absence of...
Associations between microorganisms occur extensively throughout Earth's oceans. Understanding how microbial communities are assembled and how the presence or absence of species is related to that of others are central goals of microbial ecology. Here, we investigate co-occurrence associations between marine prokaryotes by combining 180 new and publicly available metagenomic datasets from different oceans in a large-scale meta-analysis. A co-occurrence network was created by calculating correlation scores between the abundances of microorganisms in metagenomes. A total of 1,906 correlations amongst 297 organisms were detected, segregating them into 11 major groups that occupy distinct ecological niches. Additionally, by analyzing the oceanographic parameters measured for a selected number of sampling sites, we characterized the influence of environmental variables over each of these 11 groups. Clustering organisms into groups of taxa that have similar ecology, allowed the detection of several significant correlations that could not be observed for the taxa individually.
PubMed: 26157601
DOI: 10.7717/peerj.1008 -
Annals of Nutrition & Metabolism 2012Probiotics are live microorganisms that provide health benefits to the host when ingested in adequate amounts. The strains most frequently used as probiotics include... (Review)
Review
Probiotics are live microorganisms that provide health benefits to the host when ingested in adequate amounts. The strains most frequently used as probiotics include lactic acid bacteria and bifidobacteria. Probiotics have demonstrated significant potential as therapeutic options for a variety of diseases, but the mechanisms responsible for these effects have not been fully elucidated yet. Several important mechanisms underlying the antagonistic effects of probiotics on various microorganisms include the following: modification of the gut microbiota, competitive adherence to the mucosa and epithelium, strengthening of the gut epithelial barrier and modulation of the immune system to convey an advantage to the host. Accumulating evidence demonstrates that probiotics communicate with the host by pattern recognition receptors, such as toll-like receptors and nucleotide-binding oligomerization domain-containing protein-like receptors, which modulate key signaling pathways, such as nuclear factor-ĸB and mitogen-activated protein kinase, to enhance or suppress activation and influence downstream pathways. This recognition is crucial for eliciting measured antimicrobial responses with minimal inflammatory tissue damage. A clear understanding of these mechanisms will allow for appropriate probiotic strain selection for specific applications and may uncover novel probiotic functions. The goal of this systematic review was to explore probiotic modes of action focusing on how gut microbes influence the host.
Topics: Animals; Anti-Infective Agents; Bacterial Adhesion; Bifidobacterium; Gastrointestinal Tract; Humans; Immune System; Intestinal Mucosa; Lactobacillaceae; Metagenome; Mitogen-Activated Protein Kinases; Models, Animal; NF-kappa B; Probiotics; Signal Transduction
PubMed: 23037511
DOI: 10.1159/000342079