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The Science of the Total Environment Jun 2024Identification of methods for the standardized assessment of bacterial pathogens and antimicrobial resistance (AMR) in environmental water can improve the quality of... (Review)
Review
An analysis of culture-based methods used for the detection and isolation of Salmonella spp., Escherichia coli, and Enterococcus spp. from surface water: A systematic review.
Identification of methods for the standardized assessment of bacterial pathogens and antimicrobial resistance (AMR) in environmental water can improve the quality of monitoring and data collected, support global surveillance efforts, and enhance the understanding of environmental water sources. We conducted a systematic review to assemble and synthesize available literature that identified methods for assessment of prevalence and abundance of bacterial fecal indicators and pathogens in water for the purposes of monitoring bacterial pathogens and AMR. After screening for quality, 175 unique publications were identified from 15 databases, and data were extracted for analysis. This review identifies the most common and robust methods, and media used to isolate target organisms from surface water sources, summarizes methodological trends, and recognizes knowledge gaps. The information presented in this review will be useful when establishing standardized methods for monitoring bacterial pathogens and AMR in water in the United States and globally.
Topics: Water Microbiology; Enterococcus; Salmonella; Environmental Monitoring; Escherichia coli
PubMed: 38575025
DOI: 10.1016/j.scitotenv.2024.172190 -
The Journal of Hospital Infection Nov 2023Vancomycin-resistant enterococci (VRE) cause many infections in the healthcare context. Knowledge regarding the epidemiology and burden of VRE infections, however,... (Meta-Analysis)
Meta-Analysis Review
Vancomycin-resistant enterococci (VRE) cause many infections in the healthcare context. Knowledge regarding the epidemiology and burden of VRE infections, however, remains fragmented. We aimed to summarize recent studies on VRE epidemiology and outcomes in hospitals, long-term-care facilities (LTCFs) and nursing homes worldwide based on current epidemiological reports. We searched MEDLINE/PubMed, the Cochrane Library, and Web of Science for observational studies, which reported on VRE faecium and faecalis infections in in-patients published between January 2014 and December 2020. Outcomes were incidence, infection rate, mortality, length of stay (LOS), and healthcare costs. We conducted a meta-analysis on mortality (PROSPERO registration number: CRD42020146389). Of 681 identified publications, 57 studies were included in the analysis. Overall quality of evidence was moderate to low. VRE incidence was rarely and heterogeneously reported. VRE infection rate differed highly (1-55%). The meta-analysis showed a higher mortality for VRE faecium bloodstream infections (BSIs) compared with VSE faecium BSIs (risk ratio, RR 1.46; 95% confidence interval (CI) 1.17-1.82). No difference was observed when comparing VRE faecium vs VRE faecalis BSI (RR 1.00, 95% CI 0.52-1.93). LOS was higher in BSIs caused by E. faecium vs E. faecalis. Only three studies reported healthcare costs. In contrast to previous findings, our meta-analysis of included studies indicates that vancomycin resistance independent of VRE species may be associated with a higher mortality. We identified a lack of standardization in reporting outcomes, information regarding healthcare costs, and state-of-the-art microbiological species identification methodology, which may inform the set-up and reporting of future studies.
Topics: Humans; Vancomycin; Anti-Bacterial Agents; Enterococcus faecalis; Enterococcus faecium; Gram-Positive Bacterial Infections; Vancomycin-Resistant Enterococci; Sepsis
PubMed: 37734679
DOI: 10.1016/j.jhin.2023.09.008 -
Antimicrobial Resistance and Infection... Aug 2023Vancomycin-resistant Enterococci (VRE) infections are recurrently reported in different parts of India in the last two decades. However, an up-to-date, countrywide... (Meta-Analysis)
Meta-Analysis
BACKGROUND
Vancomycin-resistant Enterococci (VRE) infections are recurrently reported in different parts of India in the last two decades. However, an up-to-date, countrywide information concerning the prevalence and the rate of VRE in India is limited and hence this study aimed to estimate the pooled prevalence of VRE in India.
METHODS
A literature search was performed using various databases. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines were followed throughout. Cross-sectional studies reporting the prevalence of VRE in India from human samples whereby at least two Enterococci were isolated between 1 January 2000 and 31 December 2022 were sought for inclusion. Data were extracted and analysed using Microsoft Excel and Comprehensive Meta-analysis version 4, respectively.
RESULTS
Nineteen studies were included in the analyses. A collective total of 3683 Enterococci isolates were examined, of which 368 were VRE strains. The pooled prevalence of VRE in India was calculated at 12.4% (95% CI: 8.6-17.5; Q = 189.69; I = 90.51%; p = < 0.001). E. faecalis was the most frequently isolated species (1450 [39.37%]) followed by E. faecium (724 [19.66%]). Amongst the VRE strains, E. faecium was the most prevalent (214 [58.15%]) followed by E. faecalis (134 [36.41%]). An upsurge in the rate of VRE infections was observed in India over time: VRE prevalence was estimated at 4.8% between 2000 and 2010 and 14.1% between 2011 and 2020.
CONCLUSION
This study presents the most up-to-date information on the rate of VRE infections in India. Though lower than the findings for some less developed countries, VRE prevalence in India is notable and on the rise.
Topics: Humans; Vancomycin-Resistant Enterococci; Cross-Sectional Studies; Prevalence; India; Databases, Factual
PubMed: 37605268
DOI: 10.1186/s13756-023-01287-z -
Medicine Aug 2023Previous some systematic reviews reported that probiotics may benefit the prevention of NEC in preterm infants. But dissimilar bacterial strains and taxa used in... (Meta-Analysis)
Meta-Analysis
OBJECTIVE
Previous some systematic reviews reported that probiotics may benefit the prevention of NEC in preterm infants. But dissimilar bacterial strains and taxa used in included studies possibly result in bias. There is not a rounded systematic review which has estimated the benefit and safety of Enterococcus faecium to prevent NEC in preterm infants to date before we conducted.
METHODS
This systematic review of randomized controlled trials and retrospective studies analyzing the benefit of Enterococcus faecium to prevent NEC in preterm infants was performed using PubMed, Web of Science, Cochrane Library, EMBASE, Wanfang data and China National Knowledge Infrastructure databases from inception to April 14, 2023. The search terms were "preterm" AND "necrotizing enterocolitis" AND "Enterococcus faecium OR probiotics." Studies reporting NEC involving preterm infants who were given Enterococcus faecium were included in this systematic review. A sensitivity analysis was conducted to assess the stability of results. A funnel plot was generated to identify publication bias. Two authors appraised studies quality and extracted data independently. This work has been reported according with preferred reporting items for systematic reviews and meta-analyses and assessing the methodological quality of systematic reviews. Statistical analysis was conducted using Review Manager 5.3 software. Risk ratio (RR) with 95% confidence intervals (CI) was calculated and analyzed.
RESULTS
Seven studies (N = 1487 participants) were included in this systematic review, and 6 randomized, controlled trials (N = 1237 participants) were included in the meta-analysis. Comparing with the control groups, the Enterococcus faecium groups had a significant decline in the incidence of NEC Bell stage II or higher (RR: 0.3138, 95% CI: 0.1983-0.4965; P < .00001; 6 studies, n = 1237) and infection (RR: 0.4818, 95% CI: 0.2950-0.7869; P = .004; 3 studies, n = 710).
CONCLUSIONS
Enterococcus faecium is effective and safe in preventing NEC (Bell stage II or higher) in preterm infants. But all studies included came from China. The dosages and durations of taking Enterococcus faecium were various.
Topics: Infant; Infant, Newborn; Humans; Infant, Premature; Enterococcus faecium; Retrospective Studies; Infections; Incidence; Enterocolitis, Necrotizing
PubMed: 37565851
DOI: 10.1097/MD.0000000000034787 -
Brazilian Oral Research 2023The aim of this study was to evaluate the prevalence of Enterococcus species in the mouth of adults with periodontal health and periodontitis. A systematic search was...
The aim of this study was to evaluate the prevalence of Enterococcus species in the mouth of adults with periodontal health and periodontitis. A systematic search was made in databases in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines. The search for articles was conducted in Medline/PubMed, Latin American and Caribbean Health Sciences Literature Database (LILACS), Cochrane Library, Scopus, Embase, Web of Science databases and in the System of Information on Grey Literature in Europe (SINGLE) and included articles published in English up to April 25th, 2021. Observational studies in humans with and without periodontitis were evaluated to identify the prevalence of Enterococcus species. Articles that met the inclusion criteria were analyzed and classified to determine the quality rating in good, fair, and poor. A new detailed checklist for quality assessment was developed based on the information required for applicable data extraction in reviews. The study design, sample size, demographic data, periodontal clinical parameters, microbial analysis method, biological sample, prevalence of Enterococcus spp., and correlations with periodontal clinical parameters were assessed. After screening and full-text reading, 8 articles met the inclusion criteria. All selected studies showed a significantly higher prevalence of Enterococcus spp. in patients with periodontitis compared with periodontally healthy patients. Thus, the present systematic review suggests that the prevalence of Enterococcus faecalis in the mouth of periodontitis individuals is higher than that of periodontally healthy individuals.
Topics: Humans; Adult; Enterococcus; Prevalence; Periodontitis; Enterococcus faecalis
PubMed: 37531510
DOI: 10.1590/1807-3107bor-2023.vol37.0019 -
Neurology International Jun 2023(1) Background: Parkinson's disease (PD) is a relatively common and complex pathology, and some of its mechanisms remain to be elucidated. Change in host microbiota is... (Review)
Review
(1) Background: Parkinson's disease (PD) is a relatively common and complex pathology, and some of its mechanisms remain to be elucidated. Change in host microbiota is related to the pathophysiology of numerous diseases. This systematic review aims to gather existing data on the occidental hemisphere, compare it, and search for any significant association between Parkinson's disease and gut microbiota dysbiosis. (2) Methods: Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA) and Meta-analyses Of Observational Studies in Epidemiology (MOOSE) protocols were used for this systematic review. PubMed was used as the database search engine. Of the 166 studies found, only 10 were used, as they met our inclusion criteria: case-control studies, studies that assessed the correlation of PD and gut microbiome, studies that took place in occidental regions, and studies that were performed on humans and were written in English. The Newcastle-Ottawa Scale was used as the assessment tool for overall risk of bias in this systematic review. (3) Results: The studies analyzed were divided into three geographic areas: Region 1: United States of America and Canada; Region 2: Germany, Ireland, and Finland; and Region 3: Italy; based on geographical similarities among these populations. The following statistically significant results were described in PD patients, compared with non-PD controls. In the first region, a significant increase in the following bacteria was seen: 1. Phylum: Actinobacteriota and its Genus: ; 2. Phylum: Verrucomicrobiota and its Genus: ; 3. Genus: , , , and of the Phylum: Firmicutes; 4. Family: of Phylum: Firmicutes; 5. Phylum: Bacteroidetes and its Genus: ; 6. Phylum: Proteobacteria. A significant decrease was described in the Family: and its Genus: , , and , which belong to the Phylum: Firmicutes. In the second region, a raised number of: 1. Phylum: Verrucomicrobiota, its Genus: , and its Species: ; 2. Family: of the Phylum: Verrucomicrobiota; 3. Genus: and of the Phylum: Firmicutes; 4. Family: of the Phylum: Firmicutes; 5. Family: of the Phylum: Bacteroidetes; 6. Genus: of the Phylum: Actinobacteriota; 7. Species: of the Phylum: Thermodesulfobacteriota, was identified. Only one Genus: of the Phylum: Bacteroidetes was decreased. In the third and last region, an augmented number of these bacteria were found: 1. Phylum: Verrucomicrobiota and its Genus: ; 2. Family: and of the Phylum: Actinobacteriota; 3. Phylum: Firmicutes and its Family: and ; 4. Family: and its Genus: , of the Phylum: Firmicutes; 5. Genus: and , of the Phylum: Firmicutes; 6. Phylum: Proteobacteria, its Family: , and the Genus: , , , and ; 7. Genus: of the Phylum: Bacteroidetes. In contrast, a significant decrease in 1. Phylum: Firmicutes, its Family: , and its Genus: and 2. Genus: of the Phylum: Firmicutes, was described. (4) Conclusion: A significant gut dysbiosis, involving multiple bacterial taxa, was found in PD patients compared to healthy people in the occidental regions. However, more studies are needed to find the precise pathophysiologic involvement of other groups of pathogens, such as fungi and parasites, in the development and progression of PD.
PubMed: 37368331
DOI: 10.3390/neurolint15020047 -
BioMed Research International 2022. has been implicated in infections of treated root canals. Current irrigants and intracanal medicaments cannot eliminate completely from the root canal. Silver... (Review)
Review
. has been implicated in infections of treated root canals. Current irrigants and intracanal medicaments cannot eliminate completely from the root canal. Silver diamine fluoride (SDF) prevents caries by promoting remineralization and exerting an antibacterial effect. Studies suggest that SDF may possess antibacterial properties against . The purpose of this review is to systematically and critically analyze the literature, focusing on the use of SDF as an intracanal medicament or irrigant, when compared to other antibacterial agents. . The focused question was "Is the antibacterial effect of SDF against better than other intracanal medicaments and irrigants?" Using the keywords ((silver diamine fluoride) AND ()) AND ((sodium hypochlorite) OR (NaOCl) OR (chlorhexidine) OR (calcium hydroxide) OR (Ca(OH))), an electronic search was conducted on the following databases: PubMed/MEDLINE, ISI Web of Science, Scopus, EMBASE, and Google Scholar. The clinical trial registers ClinicalTrials.gov and CONTROL were also searched using the same keywords. General characteristics and outcomes were extracted, and quality of the studies was assessed using the Preferred Reporting Items for Laboratory studies in Endodontology (PRILE) guidelines. . Six articles (five studies and one study) were included in this systematic review. In the majority of the studies, SDF had equal or better antibacterial efficacy against compared to calcium hydroxide, sodium hypochlorite, and chlorhexidine. However, the majority of the studies did not fulfill several items in the PRILE criteria and had numerous sources of bias. . Within the limitations of the systematic review and the studies reviewed, SDF may be effective against and therefore could be used as an intracanal medicament and/or irrigant to prevent reinfections of the root canals and improve the outcomes of endodontic treatment. However, animal and clinical studies should be carried out to determine the efficacy of SDF in endodontics. . The protocol for this review was registered on PROSPERO. Registration number: CRD42021224741.
Topics: Animals; Chlorhexidine; Enterococcus faecalis; Sodium Hypochlorite; Calcium Hydroxide; Anti-Infective Agents; Anti-Bacterial Agents; Dental Pulp Cavity
PubMed: 36567909
DOI: 10.1155/2022/6544292 -
Euro Surveillance : Bulletin Europeen... Nov 2021BackgroundHospital-acquired infections (HAI) caused by spp., especially vancomycin-resistant (VRE), are of rising concern.AimWe summarised data on incidence, mortality... (Meta-Analysis)
Meta-Analysis
BackgroundHospital-acquired infections (HAI) caused by spp., especially vancomycin-resistant (VRE), are of rising concern.AimWe summarised data on incidence, mortality and proportion of HAI caused by enterococci in the World Health Organization European Region.MethodsWe searched Medline and Embase for articles published between 1 January 2010 and 4 February 2020. Random-effects meta-analyses were performed to obtain pooled estimates.ResultsWe included 75 studies. spp. and VRE accounted for 10.9% (95% confidence interval (CI): 8.7-13.4; range: 6.1-17.5) and 1.1% (95% CI: 0.21-2.7; range: 0.39-2.0) of all pathogens isolated from patients with HAI. Hospital wide, the pooled incidence of HAI caused by spp. ranged between 0.7 and 24.8 cases per 1,000 patients (pooled estimate: 6.9; 95% CI: 0.76-19.0). In intensive care units (ICU), pooled incidence of HAI caused by spp. and VRE was 9.6 (95% CI: 6.3-13.5; range: 0.39-36.0) and 2.6 (95% CI: 0.53-5.8; range: 0-9.7). Hospital wide, the pooled vancomycin resistance proportion among spp. HAI isolates was 7.3% (95% CI: 1.5-16.3; range: 2.6-11.5). In ICU, this proportion was 11.5% (95% CI: 4.7-20.1; range: 0-40.0). Among patients with hospital-acquired bloodstream infections with spp., pooled all-cause mortality was 21.9% (95% CI: 15.7-28.9; range: 14.3-32.3); whereas all-cause mortality attributable to VRE was 33.5% (95% CI: 13.0-57.3; range: 14.3-41.3).ConclusionsInfections caused by spp. are frequently identified among hospital patients and associated with high mortality.
Topics: Anti-Bacterial Agents; Cross Infection; Gram-Positive Bacterial Infections; Hospitals; Humans; Vancomycin; Vancomycin-Resistant Enterococci; World Health Organization
PubMed: 34763754
DOI: 10.2807/1560-7917.ES.2021.26.45.2001628 -
PLoS Neglected Tropical Diseases Nov 2021Vancomycin-resistant enterococci infection is a worrying worldwide clinical problem. To evaluate the accuracy of GeneXpert vanA/vanB in the diagnosis of VRE, we... (Meta-Analysis)
Meta-Analysis
PURPOSE
Vancomycin-resistant enterococci infection is a worrying worldwide clinical problem. To evaluate the accuracy of GeneXpert vanA/vanB in the diagnosis of VRE, we conducted a systematic review in the study.
METHODS
Experimental data were extracted from publications until May 03 2021 related to the diagnostic accuracy of GeneXpert vanA/vanB for VRE in PubMed, Embase, Web of Science and the Cochrane Library. The accuracy of GeneXpert vanA/vanB for VRE was evaluated using summary receiver to operate characteristic curve, pooled sensitivity, pooled specificity, positive likelihood ratio, negative likelihood ratio, and diagnostic odds ratio.
RESULTS
8 publications were divided into 3 groups according to two golden standard references, vanA and vanB group, vanA group, vanB group, including 6 researches, 5 researches and 5 researches, respectively. The pooled sensitivity and specificity of group vanA and vanB were 0.96 (95% CI, 0.93-0.98) and 0.90 (95% CI, 0.88-0.91) respectively. The DOR was 440.77 (95% CI, 37.92-5123.55). The pooled sensitivity and specificity of group vanA were 0.86 (95% CI, 0.81-0.90) and 0.99 (95% CI, 0.99-0.99) respectively, and those of group vanB were 0.85 (95% CI, 0.63-0.97) and 0.82 (95% CI, 0.80-0.83) respectively.
CONCLUSION
GeneXpert vanA/vanB can diagnose VRE with high-accuracy and shows greater accuracy in diagnosing vanA.
Topics: Anti-Bacterial Agents; Bacterial Proteins; Carbon-Oxygen Ligases; Gram-Positive Bacterial Infections; Humans; Sensitivity and Specificity; Vancomycin; Vancomycin-Resistant Enterococci
PubMed: 34748586
DOI: 10.1371/journal.pntd.0009869 -
Frontiers in Public Health 2021spp. have arisen as important nosocomial pathogens and are ubiquitous in the gastrointestinal tracts of animals and the environment. They carry many intrinsic and...
spp. have arisen as important nosocomial pathogens and are ubiquitous in the gastrointestinal tracts of animals and the environment. They carry many intrinsic and acquired antimicrobial resistance genes. Because of this, surveillance of spp. has become important with whole genome sequencing emerging as the preferred method for the characterization of enterococci. A scoping review was designed to determine how the use of whole genome sequencing in the surveillance of spp. adds to our knowledge of antimicrobial resistance in spp. Scoping review design was guided by the PRISMA extension and checklist and JBI Reviewer's Guide for scoping reviews. A total of 72 articles were included in the review. Of the 72 articles included, 48.6% did not state an association with a surveillance program and 87.5% of articles identified . The majority of articles included isolates from human clinical or screening samples. Significant findings from the articles included novel sequence types, the increasing prevalence of vancomycin-resistant enterococci in hospitals, and the importance of surveillance or screening for enterococci. The ability of enterococci to adapt and persist within a wide range of environments was also a key finding. These studies emphasize the importance of ongoing surveillance of enterococci from a One Health perspective. More studies are needed to compare the whole genome sequences of human enterococcal isolates to those from food animals, food products, the environment, and companion animals.
Topics: Animals; Enterococcus faecium; Gram-Positive Bacterial Infections; Humans; Microbial Sensitivity Tests; Vancomycin-Resistant Enterococci; Whole Genome Sequencing
PubMed: 34178909
DOI: 10.3389/fpubh.2021.599285