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This study aimed to investigate the intestinal microbiota in duodenal ulcer (DU) patients, effects of proton pump inhibitors,clarithromycin and amoxicillin, PCA) for Helicobacter pylori ( H . pylori ) and Bacillus subtilis and Enterococcus faecium (BSEF) on intestinal microbiota. DU patients were randomly assigned to receive either PCA (group TT) or PCA plus BSEF(group TP). The fecal microbiome was conducted using high throughput 16S rDNA gene and internal transcribed spacer sequencings. The diversity and abundance of intestinal bacteria in the DU were significantly lower than health check control (HC) group. In the TT group, the abundance and diversity of both intestinal bacteria and fungi decreased after PCA treatment, compared with those before treatment, whereas in the TP group no obvious changes were observed. In the TT group at all the time points, both the intestinal bacteria and fungi were different from those in the HC group. However, in the TP group, at 10w the bacterial flora abundance was close to that in the HC group. The results indicate that anti- H . pylori treatment induced significant decrease in the diversity of intestinal microbiota, while the combined therapy supplemented with BSEF could protect and restore the intestinal microbiota.

Managing the side effects of diarrhea, which is associated with intestinal microbial dysbiosis, is a crucial challenge in Helicobacter pylori eradication therapy. The aim of this study is to explore whether administration of a probiotic strain Enterococcus faecium 129 BIO 3B-R, a multi-antibiotic resistant lactic acid bacterium, influences the side effects of Helicobacter pylori eradication therapy in adults. Seventy-six adults undergoing this therapy were randomized to receive either Enterococcus faecium 129 BIO 3B-R or a placebo in a double-blind manner. No significant difference was observed in the incidence of diarrhea, the primary endpoint, or in any other secondary endpoints, including intestinal microbiota diversity, between two groups in the overall study population. However, in a post-hoc age-stratified analysis, participants aged 70 and older who used Enterococcus faecium 129 BIO 3B-R experienced tended to have more diarrhea during the eradication period but subsequently experienced significantly less diarrhea after eradication compared to the control group (23.1% vs. 60%). Treatment with Enterococcus faecium 129 BIO 3B-R also maintained higher α-diversity in their intestinal microbiota than those in the placebo group. Those data suggest that the administration of Enterococcus faecium 129 BIO 3B-R could potentially alleviate diarrhea and intestinal dysbiosis in over 70-year-old elderly patients undergoing Helicobacter pylori eradication.

The opportunistic pathogen Enterococcus faecium colonizes humans and a wide range of animals, endures numerous stresses, resists antibiotic treatment and stubbornly persists in clinical environments. The widespread application of antibiotics in hospitals and agriculture has contributed to the emergence of vancomycin-resistant E. faecium, which causes many hospital-acquired infections. In this Review, we explore recent discoveries about the evolutionary history, the environmental adaptation and the colonization and dissemination mechanisms of E. faecium and vancomycin-resistant E. faecium. These studies provide critical insights necessary for developing novel preventive and therapeutic approaches against vancomycin-resistant E. faecium and also reveal the intricate interrelationships between the environment, the microorganism and the host, providing knowledge that is broadly relevant to how antibiotic-resistant pathogens emerge and endure.This Review explores recent insights into the evolutionary history, the environmental adaptation and the colonization and dissemination mechanisms of Enterococcus faecium, and highlight potential novel preventative and therapeutic approaches to its infections.

Enterococcus faecium is a promising probiotic with potential antimicrobial effects. This study aimed to evaluate the probiotic and antimicrobial properties of E. faecium MBBL3, isolated from healthy cow milk, against bovine mastitis pathogens Klebsiella pneumoniae MBBL2 ( Kp MBBL2) and Escherichia coli MBBL4 ( Ec MBBL4), using comprehensive genomic and functional analyses. The genome assembly and functional annotations of MBBL3 unveiled many important probiotic traits, and comparative genomic analysis demonstrated its high degree of genetic similarity with other Enterococcus strains. MBBL3 exhibited the ability to ferment a diverse range of carbohydrates and possessed 76 genes linked to carbohydrate-active enzyme, including five key CAZy families with potential antimicrobial activity. Additionally, MBBL3 harbored genes essential for bile salt and acid tolerance, stress resistance, and surface adhesion. Furthermore, MBBL3 was found to harbor gene clusters encoding secondary metabolites with antimicrobial potentials. Safety evaluations revealed a low pathogenic potential, while in-vitro assays demonstrated antibiotic susceptibility and a reduction in the growth of Kp MBBL2 and Ec MBBL4, respectively. It's bacteriocin Enterolysin_A exhibited strong molecular interactions with virulence-associated proteins of the mastitis pathogens. Thus, the promising probiotic potential and antimicrobial activity of E. faecium MBBL3, particularly against mastitis-related pathogens coupled with its safety profile, render it a promising candidate for further investigation.

To investigate the molecular characteristics and biofilm-forming ability of 116 Enterococcus faecium ( Efm ) and 72 Enterococcus faecalis ( Efs ) isolates obtained from patients with bloodstream infections (BSI) at a Chinese hospital between July 2011 and March 2018. The presence of glycopeptide resistance genes and five virulence genes ( esp , gelE , asa1 , hyl , and cylA ) was screened using two multiplex PCR. MLST was used to assess the clonality. Crystal violet staining was used to detect biofilms. Vancomycin resistance was detected in 30.1% of Efm and 2.8% of Efs isolates, respectively. All VRE strains carried the vanA gene. The esp , gelE , asa1 , and cylA genes in 72 Efs strains were detected at 62.5%, 84.7%, 84.7%, and 69.4%, respectively. Among the 116 Efm isolates, 74.1% and 25.8% carried esp and hyl , respectively. The esp gene was significantly associated with vancomycin-resistant Efm (VREfm) compared to vancomycin-susceptible Efm (VSEfm). In total, 91.7% of Efs and 20.0% of Efm produced biofilms. Twenty-six STs were identified among the 72 Efs isolates, with ST4 (29.2%) being the predominant. In total, 116 Efm strains were grouped into 26 STs, with ST78 (46.6%) being the predominant. Both VREfm (41.7%) and VSEfm (48.8%) were dominant in ST78. There is no clear evidence suggesting that some STs are associated with vancomycin resistance or biofilm formation. Both Efm and Efs BSI isolates showed a polyclonal pattern with a dominant clone and many unique types, implying the coexistence of clonal dissemination and an influx of new clones. The horizontal transmission of resistance genes may play a more important role in VREfm prevalence than clonal expansion.

Background As an important nosocomial pathogen, Enterococcus faecium has received increasing attention in recent years. However, a large number of studies have focused on the hospital-associated isolates and ignored isolates originated from the natural environments. Results In this study, comparative genomic analysis was conducted on 161 isolates originated from human, animal, and naturally fermented dairy products. The results showed that the environment played an important role in shaping the genomes of Enterococcus faecium . The isolates from human had the largest average genome size, while the isolates from dairy products had the smallest average genome size and fewest antibiotic resistance genes. A phylogenetic tree was reconstructed based on the genomes of these isolates, which revealed new insights into the phylogenetic relationships among the dairy isolates and those from hospitals, communities, and animals. Furthermore, 202 environment-specific genes were identified, including 136 dairy-specific, 31 human blood-specific, and 35 human gastrointestinal-specific genes. Interestingly, five dairy-specific genes (namely lacF , lacA / B , lacD , lacG , and lacC ) that constituted an integrated lactose metabolism pathway existed in almost all dairy isolates. The pathway conservation demonstrated an active role of the environment in shaping the genomes of Enterococcus faecium . Conclusions This study shows that the Enterococcus faecium species has great genomic plasticity and high versatility to occupy broad ecological roles, dwelling as non-harmful dairy and animal gut commensals as well as significant nosocomial pathogens that disseminate antibiotic resistance genes.

Background The hospital-adapted A1 group of Enterococcus faecium remains an organism of significant concern in the context of drug-resistant hospital-associated infections. How this pathogen evolves and disseminates remains poorly understood. Methods A large, globally representative collection of short-read genomic data from the hospital-associated A1 group of Enterococcus faecium was assembled ( n  = 973). We analysed, using a novel analysis approach, global diversity in terms of both the dynamics of the accessory genome and homologous recombination among conserved genes. Results Two main modes of genomic evolution continue to shape E. faecium : the acquisition and loss of genes, including antimicrobial resistance genes, through mobile genetic elements including plasmids, and homologous recombination of the core genome. These events lead to new clones emerging at the local level, followed by the erosion of signals of clonality through recombination, and in some identifiable cases producing new clonal clusters. These patterns lead to new, emerging lineages which are able to spread globally over relatively short timeframes. Conclusions The ability of A1 E. faecium to continually present new combinations of genes for potential selection suggests that controlling this pathogen will remain challenging but establishing a framework for understanding genomic evolution is likely to aid in tracking the threats posed by newly emerging lineages.

Background Enterococcus faecium and Enterococcus faecalis are opportunistic pathogens that form an increasing concern for hospital-acquired infections due to their natural and acquired antimicrobial resistance (AMR). Although phage therapy has gained global interest as a response to emerging AMR, Enterococcus remains an understudied target for phage therapy. In this context, we aimed to isolate Enterococcus -specific phages and study their in vitro infection efficacy when combined into cocktails, in the presence of antibiotics and human serum and against bacterial biofilms. Results We isolated one E. faecium -phage fHoEfm07, that did not resemble any known phage genera and four E. faecalis -phages belonging to Saphexavirus (fHoEfa01 and fHoEfa06) and Efquatrovirus (fHoEfa03 and fHoEfa04) genera. The phages from the genus Saphexavirus and fHoEfm07 were suitable for therapeutic applications based on their genome characterization; however, the phages belonging to the Efquatrovirus genus contained a potential AMR-related gene. In vitro studies indicated that interactions between phages, antibiotics, and human serum depended on the specific phage-host pairing or antibiotic concentration. Moreover, only phage fHoEfa03 reduced the biofilm masses after 3 h and 24 h phage treatment. Conclusions This study provides valuable insights into the potential of Enterococcus phages in conditions mimicking phage therapy. The characterization of novel phages, assessment of their therapeutic suitability, and exploration of synergistic treatment strategies contribute to the foundational knowledge required to advance phage therapy.

Bacterial pathogens that infect patients also contaminate hospital surfaces. These contaminants impact hospital infection control and epidemiology, prompting quantitative examination of their transmission dynamics. Here we investigate spatiotemporal and phylogenetic relationships of multidrug resistant (MDR) bacteria on intensive care unit surfaces from two hospitals in the United States (US) and Pakistan collected over one year. MDR bacteria isolated from 3.3% and 86.7% of US and Pakistani surfaces, respectively, include common nosocomial pathogens, rare opportunistic pathogens, and novel taxa. Common nosocomial isolates are dominated by single lineages of different clones, are phenotypically MDR, and have high resistance gene burdens. Many resistance genes (e.g., bla NDM , bla OXA carbapenamases), are shared by multiple species and flanked by mobilization elements. We identify Acinetobacter baumannii and Enterococcus faecium co-association on multiple surfaces, and demonstrate these species establish synergistic biofilms in vitro. Our results highlight substantial MDR pathogen burdens in hospital built-environments, provide evidence for spatiotemporal-dependent transmission, and demonstrate potential mechanisms for multi-species surface persistence. The authors investigate the burden and spatiotemporal dynamics of multidrug-resistant bacteria on intensive care unit surfaces from two hospitals in the US and Pakistan over a year. They find Acinetobacter baumannii and Enterococcus faecium co-association, likely due to synergistic biofilm formation.

Antibiotic resistance among enterococci and γ-proteobacteria is an increasing problem in healthcare settings. Dense colonization of the gut by antibiotic-resistant bacteria facilitates their spread between patients and also leads to bloodstream and other systemic infections. Antibiotic-mediated destruction of the intestinal microbiota and consequent loss of colonization resistance are critical factors leading to persistence and spread of antibiotic-resistant bacteria. The mechanisms underlying microbiota-mediated colonization resistance remain incompletely defined and are likely distinct for different antibiotic-resistant bacterial species. It is unclear whether enterococci or γ-proteobacteria, upon expanding to high density in the gut, confer colonization resistance against competing bacterial species. Herein, we demonstrate that dense intestinal colonization with vancomycin-resistant Enterococcus faecium (VRE) does not reduce in vivo growth of carbapenem-resistant Klebsiella pneumoniae. Reciprocally, K. pneumoniae does not impair intestinal colonization by VRE. In contrast, transplantation of a diverse fecal microbiota eliminates both VRE and K. pneumoniae from the gut. Fluorescence in situ hybridization demonstrates that VRE and K. pneumoniae localize to the same regions in the colon but differ with respect to stimulation and invasion of the colonic mucus layer. While VRE and K. pneumoniae occupy the same three-dimensional space within the gut lumen, their independent growth and persistence in the gut suggests that they reside in distinct niches that satisfy their specific in vivo metabolic needs.