The Enterococcus: a Model of Adaptability to Its Environment

In vitro activities of licochalcone A against planktonic cells and biofilm of Enterococcus faecalis

This study aims to evaluate the in vitro antibacterial and anti-biofilm activities of licochalcone A on Enterococcus faecalis and to investigate the possible target genes of licochalcone A in E. faecalis. This study found that licochalcone A had antibacterial activities against E. faecalis, with the MIC50 and MIC90 were 25 μM. Licochalcone A (at 4 × MIC) indicated a rapid bactericidal effect on E. faecalis planktonic cells, and killed more E. faecalis planktonic cells (at least 3-log10 cfu/ml) than vancomycin, linezolid, or ampicillin at the 2, 4, and 6 h of the time-killing test. Licochalcone A (at 10 × MIC) significantly reduced the production of E. faecalis persister cells (at least 2-log10 cfu/ml) than vancomycin, linezolid, or ampicillin at the 24, 48, 72, and 96 h of the time-killing test. Licochalcone A (at 1/4 × MIC) significantly inhibited the biofilm formation of E. faecalis. The RNA levels of biofilm formation-related genes, agg, esp, and srtA, markedly decreased when the E. faecalis isolates were treated with licochalcone A at 1/4 × MIC for 6 h. To explore the possible target genes of licochalcone A in E. faecalis, the licochalcone A non-sensitive E. faecalis clones were selected in vitro by induction of wildtype strains for about 140 days under the pressure of licochalcone A, and mutations in the possible target genes were detected by whole-genome sequencing. This study found that there were 11 nucleotide mutations leading to nonsynonymous mutations of 8 amino acids, and among these amino acid mutations, there were 3 mutations located in transcriptional regulator genes (MarR family transcriptional regulator, TetR family transcriptional regulator, and MerR family transcriptional regulator). In conclusion, this study found that licochalcone A had an antibacterial effect on E. faecalis, and significantly inhibited the biofilm formation of E. faecalis at subinhibitory concentrations.

Disruption of the tagF Orthologue in the epa Locus Variable Region of Enterococcus faecalis Causes Cell Surface Changes and Suppresses an eep-Dependent Lysozyme Resistance Phenotype

The disease-producing capacity of the opportunistic pathogen Enterococcus faecalis is enhanced by the ability of the bacterium to evade killing by antimicrobial agents. Survival of E. faecalis in the presence of the human antimicrobial enzyme lysozyme is mediated in part by the site 2 metalloprotease Eep; however, a complete model of enterococcal lysozyme resistance has not been elucidated. To better understand the molecular basis for lysozyme resistance in E. faecalis, we analyzed Δeep suppressor mutants that acquire resistance to lysozyme through mutation of the gene OG1RF_11713, a predicted teichoic acid biosynthesis-encoding gene located within the variable region of the enterococcal polysaccharide antigen (epa) locus. Sequence comparisons revealed that OG1RF_11713 is most similar to the cytidine-5'-diphosphate (CDP)-glycerol:poly-(glycerolphosphate)glycerophosphotransferase TagF from Staphylococcus epidermidis. Inactivation of OG1RF_11713 in both the wild-type and Δeep genetic backgrounds was sufficient to increase the resistance of E. faecalis OG1RF to lysozyme. Minimal amounts of N-acetylgalactosamine were detectable in cell wall carbohydrate extracts of OG1RF_11713 deletion mutants, and this was associated with a reduction in negative cell surface charge. Targeted disruption of OG1RF_11713 was also associated with increased susceptibility to the antibiotic polymyxin B and membrane-targeting detergents and decreased susceptibility to the lantibiotic nisin. This work implicates OG1RF_11713 as a major determinant of cell envelope integrity and provides further validation that lysozyme resistance is intrinsically linked to the modification of enterococcal cell wall polysaccharides. IMPORTANCE Enterococcus faecalis is a leading cause of health-care-associated infections for which there are limited treatment options. E. faecalis is resistant to several antibiotics and to high concentrations of the human antimicrobial enzyme lysozyme. The molecular mechanisms that mediate lysozyme resistance in E. faecalis are complex and remain incompletely characterized. This work demonstrates that a gene located within the variable region of the enterococcal polysaccharide antigen locus of E. faecalis strain OG1RF (OG1RF_11713), which is predicted to encode a component of the teichoic acid biosynthesis machinery, is part of the lysozyme resistance circuitry and is important for enterococcal cell wall integrity. These findings suggest that OG1RF_11713 is a potential target for new therapeutic strategies to combat enterococcal infections.

Gut microbiota composition reflects disease progression, severity and outcome, and dysfunctional immune responses in patients with hypertensive intracerebral hemorrhage

OBJECTIVE

In this study, we aimed to explore the alterations in gut microbiota composition and cytokine responses related to disease progression, severity, and outcomes in patients with hypertensive intracerebral hemorrhage (ICH).

METHODS

Fecal microbiota communities of 64 patients with ICH, 46 coronary heart disease controls, and 23 healthy controls were measured by sequencing the V3-V4 region of the 16S ribosomal RNA (16S rRNA) gene. Serum concentrations of a broad spectrum of cytokines were examined by liquid chips and ELISA. Relationships between clinical phenotypes, microbiotas, and cytokine responses were analyzed in the group with ICH and stroke-associated pneumonia (SAP), the major complication of ICH.

RESULTS

In comparison with the control groups, the gut microbiota of the patients with ICH had increased microbial richness and diversity, an expanded spectrum of facultative anaerobes and opportunistic pathogens, and depletion of anaerobes. Enterococcus enrichment and Prevotella depletion were more significant in the ICH group and were associated with the severity and functional outcome of ICH. Furthermore, Enterococcus enrichment and Prevotella depletion were also noted in the SAP group in contrast to the non-SAP group. Enterococci were also promising factors in the prognosis of ICH. The onset of ICH induced massive, rapid activation of the peripheral immune system. There were 12 cytokines (Eotaxin, GM-CSF, IL-8, IL-9, IL-10, IL-12p70, IL-15, IL-23, IL-1RA, IP-10, RANTES, and TNF-α) changed significantly with prolongation of ICH, and the Th2 responses correlated with the 90-day outcomes. Cytokines TNF-α, IP-10, IL-1RA, IL-8, IL-18, and MIP-1β in SAP group significantly differed from non-SAP group. Among these cytokines, only IP-10 levels decreased in the SAP group. Enterococcus was positively associated with IL-1RA and negatively associated with IP-10, while Prevotella was inversely associated in both the ICH and SAP groups.

CONCLUSION

This study revealed that gut dysbiosis with enriched Enterococcus and depleted Prevotella increased the risk of ICH and subsequently SAP. The altered gut microbiota composition and serum cytokine profiles are potential biomarkers that reflect the inciting physiologic insult/stress involved with ICH.

Evolutionary conservation of motifs within vanA and vanB of vancomycin-resistant enterococci

Background and Aim: Global Health is threatened by the rapid emergence of multidrug-resistant bacteria. Antibiotic resistomes rapidly evolve, yet conserved motifs elucidated in our study have the potential for future drug targets for precision medicine. This study aimed to identify conserved genetic sequences and their evolutionary pathways among vancomycin-resistant Enterococcus species such as Enterococcus faecium and Enterococcus faecalis. Materials and Methods: We retrieved a total of 26 complete amino acid and nucleotide sequences of resistance determinant genes against vancomycin (vanA and vanB), streptomycin (aac-aah), and penicillin (pbp5) from the publicly available genetic sequence database, GenBank. The sequences were comprised of bacteria classified under the genera of Enterococcus, Staphylococcus, Amycolatopsis, Ruminococcus, and Clostridium. Sequences were aligned with Clustal Omega Multiple Sequence Alignment program and Percent Identity Matrices were derived. Phylogenetic analyses to elucidate evolutionary relationships between sequences were conducted with the neighbor-end joining method through the Molecular Evolutionary Genetics Analysis (MEGAX) software, developed by the Institute of Molecular Evolutionary Genetics at Pennsylvania State University. Subsequent network analyses of the resistance gene, vanB, within E. faecium were derived from ScanProsite and InterPro. Results: We observed the highest nucleotide sequence similarity of vanA regions within strains of E. faecium (100%) and E. faecalis (100%). Between Enterococcus genera, we continued to observe high sequence conservation for vanA and vanB, up to 99.9% similarity. Phylogenetic tree analyses suggest rapid acquisition of these determinants between strains within vanA and vanB, particularly between strains of Enterococcus genera, which may be indicative of horizontal gene transfer. Within E. faecium, Adenosine 5'-Triphosphate (ATP)-Grasp and D-ala-D-ala ligase (Ddl) were found as conserved domains of vanA and vanB. We additionally found that there is notable sequence conservation, up to 66.67%, between resistomes against vancomycin and streptomycin among E. faecium. Conclusion: Resistance genes against vancomycin have highly conserved sequences between strains of Enterococcus bacteria. These conserved sequences within vanA and vanB encode for ATP-Grasp and Ddl motifs, which have functional properties for maintaining cell wall integrity. High sequence conservation is also observed among resistance genes against penicillin and streptomycin, which can inform future drug targets for broader spectrum therapies.

Nano-Al2O3 particles affect gut microbiome and resistome in an in vitro simulator of the human colon microbial ecosystem

Nano-Al₂O₃ has been widely used in various consumer products and water treatment processes because of its unique physicochemical properties. The probability of human exposure to nano-Al₂O₃ increases significantly, of which oral ingestion is an important route. However, effects and underlying mechanisms of nano-Al₂O₃ on gut microbiota and resistome are still not well delineated. Here, we systematically investigated the effects of nano-Al₂O₃ on the human gut microbiome by an in vitro simulator of human colon microbial ecosystem. Results indicated that nano-Al₂O₃ interfered with the gut microbiota, and significantly suppressed the short-chain fatty acids metabolism, which might pose adverse effects on the host. More seriously, high level of nano-Al₂O₃ (50 mg/L) was more destructive to the gut flora, though the damage might be temporary. In addition, sub-inhibitory low-dose of nano-Al₂O₃ (0.1 mg/L) significantly enhanced the abundance of antibiotic resistance genes (ARGs) after 7-day exposure. This is attributed to that low concentration of nano-Al₂O₃ can promote horizontal transfer of ARGs by increasing cell membrane permeability and relative abundance of transposase (e.g. tnpA, IS613, and Tp614). Our findings confirmed the adverse effects of nano-Al₂O₃ on the human gut resistome and emphasized the necessity to assess potential risks of nanomaterials on the human gut health.

Patient-derived Enterococcus faecium with inflammatory genotypes promote colitis

BACKGROUND

Dysbiosis of gut microbiota promotes colitis in ulcerative colitis (UC). Enterococcus faecium is an important constituent of dysbiotic microbiota. However, the mechanisms underlying E. faecium-induced colitis remain unclear.

METHODS

Overall, 23 E. faecium strains isolated from human feces and 3 commercial strains were inoculated into Il10^-/- mice. Mouse colons were histologically evaluated and analyzed using real-time PCR analysis of cytokines. Genes in 26 E. faecium strains were identified by whole-genome shotgun sequencing of genomic DNA. The production of reactive oxygen species (ROS) from each strain was measured. An antioxidant, lipoic acid, was orally administered to the colitis mouse model.

RESULTS

Inoculation of E. faecium derived from patients with UC resulted in colitis in Il10^-/- mice. The genotypes of 26 strains were characterized by identifying 1893 known genes; clustering all the strains based on the genotypes showed two major groups-inflammatory and probiotic clusters. Additionally, linear discriminant analysis clarified that lipoic acid metabolism was a significantly abundant pathway in the probiotic cluster compared to the inflammatory cluster. Further, the production of ROS was greater in inflammatory than in probiotic strains. Administration of lipoic acid in E. faecium-inoculated mice ameliorated colitis.

CONCLUSIONS

Enterococcus faecium strains in the inflammatory cluster promoted colitis with higher production of ROS than the strains in the probiotic cluster.

Meta-analysis of the global prevalence of Enterococcus spp. in foods: Antibiotic resistance profile of Enterococcus faecalis and Enterococcus faecium

Aim: The objective of this study was to evaluate the prevalence and diversity of Enterococcus spp. and antibiotic-resistant Enterococcus faecalis and Enterococcus faecium isolates in different foods worldwide.

Method and Result: This study used meta-analytical methods. Besides, Web of Science (n= 705), Medline (n= 6), and Scopus (n= 1.338) were searched for studies in the years 1995-2021 using related keywords. Results showed that the pooled prevalence for Enterococcus spp. and antibiotic-resistant of E. faecalis and E. faecium isolates were found 0.41 (95% C.I. 0.34-0.47), 0.25 (95% C.I. 0.13-0.38), respectively. According to the results of the subgroup analysis, the lowest and highest prevalence of Enterococcus spp. in food types were calculated for red meat (0.56), and fermented foods (0.29). Also, as a result of subgroup analyses by country the highest prevalence of Enterococcus spp. was calculated in studies conducted in Slovakia (0.74). In contrast, the lowest prevalence was calculated in studies conducted in Georgia (0.07).

Conclusion: The meta-analyses improved our understanding of the prevalence of Enterococcus spp. and the antibiotic resistance of E. faecalis and E. faecium isolates in different foods and provided results that can be useful as input for quantitative microbiological risk evaluation modeling.

Significance and Impact of Study: We demonstrated the antibiotic resistance of E. faecalis and E. faecium in foods and gaps that could be addressed in the future. Therefore, it is believed that the results compiled herein will contribute to the epidemiological surveillance of the presence and antibiotic resistance of E. faecalis and E. faecium in foods.

In Vitro and In Vivo Studies of Oritavancin and Fosfomycin Synergism against Vancomycin-Resistant Enterococcus faecium

Therapeutic options for infections caused by vancomycin-resistant enterococci are currently suboptimal. Combination regimens where fosfomycin is used alongside existing treatments are emerging given the proven synergistic potential and PK/PD properties. In the studies presented here, we tested five vanA and five vanB clinical isolates of Enterococcus faecium using a combination of oritavancin + fosfomycin both in vitro (checkerboard, time killing) and in vivo (Galleria mellonella). The combination of oritavancin and fosfomycin increased drug susceptibility, showing a synergistic effect in 80% of isolates and an additive effect in the remaining isolates. The combination restored fosfomycin susceptibility in 85% of fosfomycin-resistant isolates. Time killing on four selected isolates demonstrated that the combination of oritavancin and fosfomycin provided a CFU/mL reduction > 2 log10 compared with the most effective drug alone and prevented the bacterial regrowth seen after 8−24 h at sub-inhibitory drug concentrations. In addition, the combination was also tested in a biofilm assay with two isolates, and a strong synergistic effect was observed in one isolate and an additive effect in the other. Finally, we demonstrated in vivo (Galleria mellonella) a higher survival rate of the larvae treated with the combination therapy compared to monotherapy (fosfomycin or oritavancin alone). Our study provides preclinical evidence to support trials combining oritavancin and fosfomycin for VRE BSI in humans, even when biofilm is involved.

Ion Exchange Biomaterials to Capture Daptomycin and Prevent Resistance Evolution in Off-Target Bacterial Populations

Daptomycin (DAP), a cyclic anionic lipopeptide antibiotic, is among the last resorts to treat multidrug-resistant Gram-positive bacterial infections, caused by vancomycin-resistant Enterococcus faecium or methicillin-resistant Staphylococcus aureus. DAP is administered intravenously, and via biliary excretion, ∼5-10% of the intravenous DAP dose arrives in the gastrointestinal (GI) tract where it drives resistance evolution in the off-target populations of E. faecium bacteria. Previously, we have shown in vivo that the oral administration of cholestyramine, an ion exchange biomaterial (IXB) sorbent, prevents DAP treatment from enriching DAP resistance in the populations of E. faecium shed from mice. Here, we investigate the biomaterial-DAP interfacial interactions to uncover the antibiotic removal mechanisms. The IXB-mediated DAP capture from aqueous media was measured in controlled pH/electrolyte solutions and in the simulated intestinal fluid (SIF) to uncover the molecular and colloidal mechanisms of DAP removal from the GI tract. Our findings show that the IXB electrostatically adsorbs the anionic antibiotic via a time-dependent diffusion-controlled process. Unsteady-state diffusion-adsorption mass balance describes the dynamics of adsorption well, and the maximum removal capacity is beyond the electric charge stoichiometric ratio because of DAP self-assembly. This study may open new opportunities for optimizing cholestyramine adjuvant therapy to prevent DAP resistance, as well as designing novel biomaterials to remove off-target antibiotics from the GI tract.

Antimicrobial Resistance, Virulence Profiles, and Public Health Significance of Enterococcus faecalis Isolated from Clinical Mastitis of Cattle in Bangladesh

This study was designed to identify Enterococcus faecalis from clinical mastitis of cattle and determine their antimicrobial resistance and virulence determinants to evaluate their potential public health significance. A total of 105 composite milk samples (80 from cattle with clinical mastitis and 25 from apparently healthy cattle) were analyzed. E. faecalis were isolated by culturing on enterococcal selective media and identified by PCR and sequencing. Antimicrobial resistance phenotype was elucidated by the disc diffusion method, and MIC was determined by broth microdilution method according to CLSI guidelines. Detection of antimicrobial resistance and virulence genes was done by PCR. E. faecalis were isolated from 11.25% (9/80) of the clinical mastitis and 4% (1/25) of the apparently healthy cattle milk samples. The disc diffusion test revealed 40% isolates as resistant to tetracycline and azithromycin, respectively. Among them, 20% (2/10) of isolates showed resistance to both tetracycline and azithromycin. Tetracycline-resistant isolates showed MIC ranging from ≥64 to >128 μg/ml and carried tetracycline-resistant genes tetK, tetL, and tetM in 25%, 25%, and 50% of the resistant isolates, respectively. On the other hand, all the isolates were sensitive to amoxicillin, ampicillin, bacitracin, chloramphenicol, gentamicin, penicillin, and vancomycin. In addition, the isolates carried at least one of the nine virulence genes screened with pil having the highest frequency, followed by fsrB, fsrC, ace, sprE, gelE, and agg genes. Positive correlations were evident between ace, fsrC, gelE, and sprE genes that are associated with the attachment and biofilm formation in E. faecalis. E. faecalis isolated in this study carried antibiotic resistance and virulence determinants which explain their competence to be potential human pathogens.

Proteomic Characterization of Virulence Factors and Related Proteins in Enterococcus Strains from Dairy and Fermented Food Products

Enterococcus species are Gram-positive bacteria that are normal gastrointestinal tract inhabitants that play a beneficial role in the dairy and meat industry. However, Enterococcus species are also the causative agents of health care-associated infections that can be found in dairy and fermented food products. Enterococcal infections are led by strains of Enterococcus faecalis and Enterococcus faecium, which are often resistant to antibiotics and biofilm formation. Enterococci virulence factors attach to host cells and are also involved in immune evasion. LC-MS/MS-based methods offer several advantages compared with other approaches because one can directly identify microbial peptides without the necessity of inferring conclusions based on other approaches such as genomics tools. The present study describes the use of liquid chromatography−electrospray ionization tandem mass spectrometry (LC−ESI−MS/MS) to perform a global shotgun proteomics characterization for opportunistic pathogenic Enterococcus from different dairy and fermented food products. This method allowed the identification of a total of 1403 nonredundant peptides, representing 1327 proteins. Furthermore, 310 of those peptides corresponded to proteins playing a direct role as virulence factors for Enterococcus pathogenicity. Virulence factors, antibiotic sensitivity, and proper identification of the enterococcal strain are required to propose an effective therapy. Data are available via ProteomeXchange with identifier PXD036435. Label-free quantification (LFQ) demonstrated that the majority of the high-abundance proteins corresponded to E. faecalis species. Therefore, the global proteomic repository obtained here can be the basis for further research into pathogenic Enterococcus species, thus facilitating the development of novel therapeutics.

Modulating Activity Evaluation of Gut Microbiota with Versatile Toluquinol

Gut microbiota have important implications for health by affecting the metabolism of diet and drugs. However, the specific microbial mediators and their mechanisms in modulating specific key intermediate metabolites from fungal origins still remain largely unclear. Toluquinol, as a key versatile precursor metabolite, is commonly distributed in many fungi, including Penicillium species and their strains for food production. The common 17 gut microbes were cultivated and fed with and without toluquinol. Metabolic analysis revealed that four strains, including the predominant Enterococcus species, could metabolize toluquinol and produce different metabolites. Chemical investigation on large-scale cultures led to isolation of four targeted metabolites and their structures were characterized with NMR, MS, and X-ray diffraction analysis, as four toluquinol derivatives (1–4) through O1/O4-acetyl and C5/C6-methylsulfonyl substitutions, respectively. The four metabolites were first synthesized in living organisms. Further experiments suggested that the rare methylsulfonyl groups in 3–4 were donated from solvent DMSO through Fenton’s reaction. Metabolite 1 displayed the strongest inhibitory effect on cancer cells A549, A2780, and G401 with IC₅₀ values at 0.224, 0.204, and 0.597 μM, respectively, while metabolite 3 displayed no effect. Our results suggest that the dominant Enterococcus species could modulate potential precursors of fungal origin and change their biological activity.

Molecular Typing Reveals Environmental Dispersion of Antibiotic-Resistant Enterococci under Anthropogenic Pressure

As a consequence of global demographic challenges, both the artificial and the natural environment are increasingly impacted by contaminants of emerging concern, such as bacterial pathogens and their antibiotic resistance genes (ARGs). The aim of this study was to determine the extent to which anthropogenic contamination contributes to the spread of antibiotic resistant enterococci in aquatic compartments and to explore genetic relationships among Enterococcus strains. Antimicrobial susceptibility testing (ampicillin, imipenem, norfloxacin, gentamycin, vancomycin, erythromycin, tetracycline, trimethoprim-sulfamethoxazole) of 574 isolates showed different rates of phenotypic resistance in bacteria from wastewaters (91.9–94.4%), hospital effluents (73.9%), surface waters (8.2–55.3%) and groundwater (35.1–59.1%). The level of multidrug resistance reached 44.6% in enterococci from hospital effluents. In all samples, except for hospital sewage, the predominant species were E. faecium and E. faecalis. In addition, E. avium, E. durans, E. gallinarum, E. aquimarinus and E. casseliflavus were identified. Enterococcus faecium strains carried the greatest variety of ARGs (bla_TEM-1, aac(6′)-Ie-aph(2″), aac(6′)-Im, vanA, vanB, ermB, mefA, tetB, tetC, tetL, tetM, sul1), while E. avium displayed the highest ARG frequency. Molecular typing using the ERIC2 primer revealed substantial genetic heterogeneity, but also clusters of enterococci from different aquatic compartments. Enterococcal migration under anthropogenic pressure leads to the dispersion of clinically relevant strains into the natural environment and water resources. In conclusion, ERIC-PCR fingerprinting in conjunction with ARG profiling is a useful tool for the molecular typing of clinical and environmental Enterococcus species. These results underline the need of safeguarding water quality as a strategy to limit the expansion and progression of the impending antibiotic-resistance crisis.

Photo-oxidative stress response and virulence traits are co-regulated in E. faecalis after antimicrobial photodynamic therapy

Knowledge of photo-oxidative stress responses in bacteria that survive antimicrobial photodynamic therapy (aPDT) is scarce. Whereas aPDT is attracting growing clinical interest, subsequent stress responses are crucial to evaluate as they may lead to the up-regulation of pathogenic traits. Here, we aimed to assess transcriptional responses to sublethal aPDT-stress and identify potential connections with virulence-related genes. Six Enterococcus faecalis strains were investigated; ATCC 29212, three dental root-canal isolates labelled UmID1, UmID2 and UmID3 and two vancomycin-resistant isolates labelled A1 and A2. TMPyP was employed as a photosensitiser. A viability dose-response curve to increasing concentrations of TMPyP was determined by culture plating. Differential expression of genes involved in oxidative stress responses (dps and hypR), general stress responses (dnaK, sigma-factor^V and relA), virulence-related genes (ace, fsrC and gelE) and vancomycin-resistance (vanA) was assessed by reverse-transcription qPCR. TMPyP-mediated aPDT inactivated all strains with comparable efficiencies. TMPyP at 0.015 μM was selected to induce sublethal photo-oxidative stress. Despite heterogeneities in gene expression between strains, transcriptional profiles revealed up-regulations of transcripts dps, hypR as well as dnaK and sigma factor^V after exposure to TMPyP alone and to light-irradiated TMPyP. Specifically, the alternative sigma factor^V reached up to 39 ± 113-fold (median ± IQR) (p = 0.0369) in strain A2. Up-regulation of the quorum sensing operon, fsr, and its downstream virulence-related gelatinase gelE were also observed in strains ATCC-29212, A1, A2 and UmID3. Finally, photo-oxidative stress induced vanA-type vancomycin-resistance gene in both carrier isolates, reaching up to 3.3 ± 17-fold in strain A2 (p = 0.015). These findings indicate that, while aPDT successfully inactivates vancomycin-resistant and naïve strains of E. faecalis, subpopulations of surviving cells respond by co-ordinately up-regulating a network of genes involved in stress survival and virulence. This includes the induction of vancomycin-resistance genes in carrier isolates. These data may provide the mechanistic basis to circumvent bacterial responses and improve future clinical protocols.

Enterococcus hirae bacteremia associated with perinephric collection and renal abscesses in a diabetic woman

Enterococcus hirae infection accounts for about 1% of all enterococcal infections. This number is likely to be underestimated because of inadequate identification. Human infection due to E. hirae is rarely reported. We present the case of a young woman with diabetes mellitus who developed symptoms of pyelonephritis and diabetic ketoacidosis. Renal computed tomography scan revealed the presence of subcapsular perinephric collection and renal abscesses. Her blood culture yielded E. hirae. Our patient was successfully treated with antimicrobials based on the susceptibility result. To our knowledge, this is the first reported case of perinephric collection and renal abscesses associated with E. hirae bacteremia.

Evolution of Chlorhexidine Susceptibility and of the EfrEF Operon among Enterococcus faecalis from Diverse Environments, Clones, and Time Spans

Chlorhexidine (CHX) is widely used to control the spread of pathogens (e.g., human/animal clinical settings, ambulatory care, food industry). Enterococcus faecalis, a major nosocomial pathogen, is broadly distributed in diverse hosts and environments facilitating its exposure to CHX over the years. Nevertheless, CHX activity against E. faecalis is understudied. Our goal was to assess CHX activity and the variability of ChlR-EfrEF proteins (associated with CHX tolerance) among 673 field isolates and 1,784 E. faecalis genomes from the PATRIC database from different sources, time spans, clonal lineages, and antibiotic-resistance profiles. The CHX MIC (MICCHX) and minimum bactericidal concentration (MBCCHX) against E. faecalis presented normal distributions (0.5 to 64 mg/L). However, more CHX-tolerant isolates were detected in the food chain and recent human infections, suggesting an adaptability of E. faecalis populations in settings where CHX is heavily used. Heterogeneity in ChlR-EfrEF sequences was identified, with isolates harboring incomplete ChlR-EfrEF proteins, particularly the EfrE identified in the ST40 clonal lineage, showing low MICCHX (≤1mg/L). Distinct ST40-E. faecalis subpopulations carrying truncated and nontruncated EfrE were detected, with the former being predominant in human isolates. This study provides a new insight about CHX susceptibility and ChlR-EfrEF variability within diverse E. faecalis populations. The MICCHX/MBCCHX of more tolerant E. faecalis (MICCHX = 8 mg/L; MBCCHX = 64 mg/L) remain lower than in-use concentrations of CHX (≥500 mg/L). However, increased CHX use, combined with concentration gradients occurring in diverse environments, potentially selecting multidrug-resistant strains with different CHX susceptibilities, signals the importance of monitoring the trends of E. faecalis CHX tolerance within a One Health approach. IMPORTANCE Chlorhexidine (CHX) is a disinfectant and antiseptic used since the 1950s and included in the World Health Organization's list of essential medicines. It has been widely applied in hospitals, the community, the food industry, animal husbandry and pets. CHX tolerance in Enterococcus faecalis, a ubiquitous bacterium and one of the leading causes of human hospital-acquired infections, remains underexplored. Our study provides novel and comprehensive insights about CHX susceptibility within the E. faecalis population structure context, revealing more CHX-tolerant subpopulations from the food chain and recent human infections. We further show a detailed analysis of the genetic diversity of the efrEF operon (previously associated with E. faecalis CHX tolerance) and its correlation with CHX phenotypes. The recent strains with a higher tolerance to CHX and the multiple sources where bacteria are exposed to this biocide alert us to the need for the continuous monitoring of E. faecalis adaptation toward CHX tolerance within a One Health approach.

Fermentation Blues: Analyzing the Microbiota of Traditional Indigo Vat Dyeing in Hunan, China

Traditional indigo dyeing through anaerobic fermentation has recently gained worldwide attention in efforts to address concerns regarding the sustainability of industrial indigo dyeing and the impact of toxic reducing agents such as sodium dithionite (Na2S2O4) on human health and the ecological environment. Intriguingly, changes in the microbiota during indigo fermentation are known to potently affect the onset of indigo reduction, and thus elucidation of the microbial community transitions could help develop methods to control the initiation of indigo reduction. Here, we investigated the microbiota associated with the traditional indigo dyeing practiced in Hunan, China. Specifically, we identified the bacterial and fungal components of the microbiota at distinct stages in the indigo fermentation process by analyzing 16S rRNA gene and internal transcribed spacer sequences. Our analyses revealed two substantial changes in the microbiota during the traditional indigo fermentation process. The first change, which was probably caused by the introduction of Chinese liquor (featuring a high alcohol concentration), resulted in decreased bacterial diversity and increased proportions of Pseudomonas, Stenotrophomonas, and Bacillaceae family members. The second change, which could be attributed to the addition of specific plant species, led to an increase in the abundance of Alkalibacterium, Amphibacillus, the obligate anaerobe Turicibacter, the facultative anaerobe Enterococcus, and ZOR0006, as well as to a decrease in the pH and redox potential values. Our results indicate that the specific plant mixture included in the procedure here could be used as an effective additive to accelerate the initiation of indigo reduction during the fermentation process. To the best of our knowledge, this is the first report revealing the fungal diversity during the indigo fermentation process and, furthermore, showing that the fungal diversity has remained in transition despite the relatively stable bacterial diversity in the proper indigo fermentation process. Although traditional indigo fermentation in China is challenging to manage, we can benefit from local knowledge of the fermentation process, and understanding the scientific bases of traditional indigo fermentation will facilitate the development of environmentally friendly procedures. IMPORTANCE Chemical reducing agents included in modern indigo dyeing to initiate indigo reduction can be harmful to both human health and the environment. Given that traditional indigo dyeing involves natural fermentation in a dye vat using natural organic additives without the use of toxic chemicals and that changes in the microbiota during traditional indigo fermentation potently affect the onset of indigo reduction, elucidation of these microbial community transitions could help develop methods to control the initiation of indigo reduction. This study on the microbiota associated with the traditional indigo dyeing practiced in Hunan, China, has identified the bacterial and fungal communities at distinct stages of the indigo fermentation process. Notably, the addition of specific plant species might yield the desired microbial communities and appropriate fermentation conditions, which could be used as an effective additive to accelerate the initiation of indigo reduction. This study has also revealed the fungal diversity during the indigo fermentation process for the first time and shown that the fungal diversity has remained in transition despite the relatively stable bacterial diversity. Thus, this work provides new insights into the traditional indigo fermentation process used in China and substantially enhances current efforts devoted to designing environmentally friendly methods for industrial indigo dyeing.

3D Printed Microfluidic Bioreactors Used for the Preferential Growth of Bacterial Biofilms through Dielectrophoresis

A realistic modelling of the way biofilms form and evolve in time requests a dynamic approach. In this study, the proposed route uses continuous-flow bioreactors under controlled flow rates and temperature in the culture medium containing bacteria or fungi. 3D printed, Polylactic acid (PLA), flow-based bioreactors with integrated copper electrodes were used to investigate the effect of dielectrophoresis on the formation and growth of Staphylococcus aureus ATCC 25923, Enterococcus faecalis ATCC 29212, Pseudomonas aeruginosa ATCC 27853, and Klebsiella pneumoniae ATCC 13883 biofilms. Bacterial suspensions of 1McF turbidity have been prepared and circulated through the bioreactors. At the same time, a 30 V potential difference was applied on the system. The effect of the non-uniform electric field induced upon the bacterial cells was determined using quantitative methods, such as an adjusted microtiter plate technique, as well as spectral domain optical coherence tomography (SD-OCT) images. The morphology and the surface quality of the biofilms were investigated using Scanning Electron Microscopy (SEM) images. The results show that the different bacterial cells present a positive dielectrophoretic behaviour, with the preferential formation of biofilms in the high field gradient region.

Dextran-shelled oxygen-loaded nanodroplets modulate macrophages killing and inflammatory response to Enterococcus faecalis

Chronic wounds are associated with inflammation, infections, and hypoxic environment. Macrophages play a crucial role in wound healing removing bacteria and secreting signal molecules to coordinate tissue repair. Recently, dextran-shelled Oxygen-Loaded NanoDroplets (OLNDs) have been proposed as new tools to counteract hypoxia in chronic wounds. Here we investigated the effects of OLNDs on Enterococcus faecalis (E. faecalis) killing and the secretion of inflammatory and angiogenic factors by murine (BMDM) and human (dTHP-1, differentiated THP-1) macrophages, in normoxia and hypoxia. Both OLNDs and Oxygen-Free NanoDroplets (OFNDs) significantly increased reactive oxygen species production by BMDM in normoxia (4.1 and 4 fold increase by 10% OLNDs and OFNDs, respectively, after 120 min) and hypoxia (3.8 and 4 fold increase by 10% OLNDs and OFNDs respectively) but not by dTHP-1. Moreover, only OLNDs induced nitric oxide secretion by BMDM in normoxia. Consequently, both nanodroplets improved E. faecalis killing by BMDM in normoxia (% of killing OLNDs = 44.2%; p < 0.01; OFNDs = 41.4%; p < 0.05) and hypoxia (% of killing OLNDs = 43.1%; p < 0.01; OFNDs = 37.7%; p < 0.05), while dTHP-1-mediated killing was not affected. The secretion of the inflammatory cytokines (TNFα, IL-6, IL-1β) induced by E. faecalis infection in dTHP-1 was reduced by both types of nanodroplets, suggesting a novel anti-inflammatory activity of the dextran shell. Instead, the increase of VEGF induced by hypoxia was reduced only by OLNDs. These data provide new knowledge on the effects of OLNDs as innovative adjuvant in chronic wounds healing promoting bacterial killing and reducing inflammation.

The enigmatic physiological roles of AhpCF, Gpx, Npr and Kat in peroxide stress response of Enterococcus faecium

In this work, the physiological roles of the primary peroxide scavenging activities of Enterococcus faecium AUS0004 strain were analysed. This healthcare-associated pathogen harbours genes encoding putative NADH peroxidase (Npr), alkyl hydroperoxide reductase (AhpCF), glutathione peroxidase (Gpx) and manganese-dependent catalase (Mn-Kat). Gene expression analyses showed that npr and kat genes are especially and significantly induced in cells treated with hydrogen peroxide (H₂O₂) and cumene hydroperoxide (CuOOH), which suggested an important function of these enzymes to protect E. faecium against peroxide stress. Mutants affected in one or several predicted anti-oxidative activities mentioned above showed that neither the peroxidases nor the catalase are implicated in the defence against peroxide challenges. However, our investigations allowed us to show that Npr is responsible for the degradation of approximately 45% of metabolically derived H₂O₂ which avoids accumulation of the peroxide to lethal concentrations.

Epidemiology, microbiological and clinical characteristics of Enterococcus species bloodstream infections: A 10-year retrospective cohort study from Qatar

Background and objective

Enterococcus species is one of the leading causes of community and healthcare-associated infections resulting in significant morbidity and mortality. In this study, we aim to evaluate the epidemiology, microbiological and clinical characteristics of Enterococcus Blood Stream Infections (BSIs) over 10 years period in a national secondary care setting.

Methods

A retrospective cohort study was conducted on verified cases of enterococcal BSIs in adults from January 2009–December 2018 from specialized care hospitals at Hamad Medical Corporation, Qatar. Epidemiological, microbiological and clinical data were reported and analyzed.

Results

A total of 263 enterococcus BSIs cases were identified, predominant were males (65%) with a median age of 63 (IQR 48–74). E. faecalis and E. faecium were predominate at 93.5% (73.38% and 20.15% respectively). Diabetes was the commonest premorbid condition (54.3%) followed by chronic kidney disease (36.5%). Central lines and genitourinary were the most common sources (18.25%, 14.83% respectively) while no identified source was reported in 45.25% of cases. Ampicillin susceptibility was 82.51% while vancomycin resistance was reported in 10.6% of isolates. Successful bacteremia clearance was achieved in 81.37% of cases at a mean of 4 days (Range 2–5 days) while metastatic complications occurred in 5.3% of cases. Univariate mortality risk analysis was associated with ICU admission, low level of consciousness, high bacteremia scores, and presence of catheters. The 30 days mortality was high at 66.54% with CKD and cancer patients at the highest mortality risks (OR 16.334 (CI 4.2–62.4) and 16 (CI 3–84) respectively.

Conclusion

Significant mortality was associated with enterococcus BSI despite low rates for ampicillin and vancomycin resistance necessitating early identification of susceptible patients to instigate suitable preventive measures.

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Enterococcus bacteremia cases were enrolled retrospectively over a decade timeframe.

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E. faecalis and E. faecium constitute the majority at 93.5%.

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Significant mortality was associated with enterococcus bloodstream infection.

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Low rates for ampicillin and vancomycin resistance.

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Enterococcus bacteremia carries high mortality in CKD and cancer patients.

Characterization and anti-biofilm activity of bacteriophages against urinary tract Enterococcus faecalis isolates

Strong biofilm-forming Enterococcus feacalis urinary tract pathogens (n = 35) were used to determine the lytic spectrum of six bacteriophages isolated from sewage samples. Only 17 Enterococcus feacalis isolates gave lytic zones with the tested bacteriophages from which five isolates were susceptible to all of them. The isolated enterococcal phages are characterized by wide range of thermal (30–90 °C) and pH (3–10) stability. They belong to order Caudovirales, from which four bacteriophages (EPA, EPB, EPD, EPF) belong to family Myoviridae and two (EPC, EPE) belong to family Siphoviridae. In addition, they have promising antibiofilm activity against the tested strong-forming biofilm E. faecalis isolates. The enterococcal phages reduced the formed and preformed biofilms to a range of 38.02–45.7% and 71.0–80.0%, respectively, as compared to the control. The same promising activities were obtained on studying the anti-adherent effect of the tested bacteriophages on the adherence of bacterial cells to the surface of urinary catheter segments. They reduced the number of adherent cells to a range of 30.8–43.8% and eradicated the pre-adherent cells to a range of 48.2–71.1%, as compared to the control. Overall, the obtained promising antibiofilm activity makes these phages good candidates for application in preventing and treating biofilm associated Enterococcus faecalis infections.

A Pilot Study: Favorable Effects of Clostridium butyricum on Intestinal Microbiota for Adjuvant Therapy of Lung Cancer

Probiotics as medications have previously been shown to change intestinal microbial characteristics, potentially influencing cancer therapy efficacy. Patients with non-squamous non-small cell lung cancer (NS-NSCLC) treated by bevacizumab plus platinum-based chemotherapy were randomized to obtain Clostridium butyricum supplement (CBS) or receive a placebo as adjuvant therapy. Clinical efficacy and safety were assessed using progression-free survival (PFS), overall survival (OS), and adverse events (AE). Intestinal microbiota was longitudinally explored between CBS and placebo groups over time. Patients who took CBS had significantly decreased bacterial richness and abundance, as well as increased the total richness of the genus Clostridium, Bifidobacterium, and Lactobacillus compared to the placebo group (p < 0.05). Beta diversity and the interactional network of intestinal microbiota were distinctly different between CBS and placebo group. However, there were no significant variations between them in terms of microbial taxonomical taxa and alpha diversity. The potential opportunistic pathogen Shewanella was still detectable after treatment in the placebo group, while no distinguishing microbial markers were found in the CBS group. In terms of clinical efficacy, the CBS group had a significantly reduced AE compare to the placebo group (p < 0.05), although no significantly longer PFS and OS. Therefore, favorable modifications in intestinal microbiota and significant improvements in drug safety make probiotics be promising adjunctive therapeutic avenues for lung cancer treatment.

Moringa oleifera Lam. Peptide Remodels Intestinal Mucosal Barrier by Inhibiting JAK-STAT Activation and Modulating Gut Microbiota in Colitis

Ulcerative colitis is a chronic inflammatory bowel disease (IBD), but progress in exploring its pathogenesis and finding effective drugs for its prevention and treatment has stalled in recent years. The seeds of Moringa oleifera Lam. are rich in proteins known to have multiple physiological activities. In our earlier work, we had isolated and purified a peptide (MOP) having the sequence KETTTIVR, from M. oleifera seeds; however, its anti-inflammatory activity and mechanism in vivo were unclear. Here we used the dextran sulfate sodium (DSS)-induced colitis model to study the anti-inflammatory activity and mechanism of this MOP. Our results are the first to show that MOP can ameliorate the pathological phenotype, inflammation, and intestinal barrier disruption in mice with colitis. Furthermore, RNA sequencing revealed that MOP inhibits the Janus kinase/signal transducer and activator of transcription (JAK-STAT) pathway activation. Next, by using 16s rRNA gene sequencing, we found that MOP can ameliorate DSS-induced gut microbiota dysbiosis. In addition, an untargeted metabolomics analysis suggested that MOP is able to modulate the level of lipid and amino acid metabolites in IBD-stricken mice. Altogether, these results indicate that MOP ameliorates colitis by remodeling intestinal mucosal barrier by inhibiting JAK-STAT pathway’s activation and regulating gut microbiota and its metabolites, thus providing a basis for further processing and design of bioactive foods from M. oleifera seeds.

Development of 4-[4-(Anilinomethyl)-3-phenyl-pyrazol-1-yl] Benzoic Acid Derivatives as Potent Anti-Staphylococci and Anti-Enterococci Agents

From a library of compounds, 11 hit antibacterial agents have been identified as potent anti-Gram-positive bacterial agents. These pyrazole derivatives are active against two groups of pathogens, staphylococci and enterococci, with minimum inhibitory concentration (MIC) values as low as 0.78 μg/mL. These potent compounds showed bactericidal action, and some were effective at inhibiting and eradicating Staphylococcus aureus and Enterococcus faecalis biofilms. Real-time biofilm inhibition by the potent compounds was studied, by using Bioscreen C. These lead compounds were also very potent against S. aureus persisters as compared to controls, gentamycin and vancomycin. In multiple passage studies, bacteria developed little resistance to these compounds (no more than 2 × MIC). The plausible mode of action of the lead compounds is the permeabilization of the cell membrane determined by flow cytometry and protein leakage assays. With the detailed antimicrobial studies, both in planktonic and biofilm contexts, some of these potent compounds have the potential for further antimicrobial drug development.

Bacteriophage-Resistant Mutant of Enterococcus faecalis Is Impaired in Biofilm Formation

Enterococcus faecalis is a common gram-positive non-spore-forming bacterium in nature and is found in the upper respiratory tract, intestine, and mouth of healthy people. E. faecalis is also one of the common pathogens causing nosocomial infections and is resistant to several antibiotics commonly used in practice. Thus, treating drug-resistant E. faecalis with antibiotics is challenging, and new approaches are needed. In this study, we isolated a bacteriophage named EFap02 that targets E. faecalis strain EFa02 from sewage at Southwest Hospital. Phage EFap02 belongs to the Siphoviridae family with a long tail of approximately 210 nm, and EFap02 can tolerate a strong acid and alkali environment and high temperature. Its receptor was identified as the capsular polysaccharide. Phage-resistant mutants had loss-of-function mutations in glycosyltransferase (gtr2), which is responsible for capsular polysaccharide biosynthesis, and this caused the loss of capsular polysaccharide and interruption of phage adsorption. Although phage-resistant mutants against EFap02 can be selected, such mutants are impaired in biofilm formation due to the loss of capsular polysaccharide, which compromises its virulence. Therefore, this study provided a detailed description of the E. faecalis EFap02 phage with the potential for treating E. faecalis infection.

Enterococcus Virulence and Resistant Traits Associated with Its Permanence in the Hospital Environment

Enterococcus are opportunistic pathogens that have been gaining importance in the clinical setting, especially in terms of hospital-acquired infections. This problem has mainly been associated with the fact that these bacteria are able to present intrinsic and extrinsic resistance to different classes of antibiotics, with a great deal of importance being attributed to vancomycin-resistant enterococci. However, other aspects, such as the expression of different virulence factors including biofilm-forming ability, and its capacity of trading genetic information, makes this bacterial genus more capable of surviving harsh environmental conditions. All these characteristics, associated with some reports of decreased susceptibility to some biocides, all described in this literary review, allow enterococci to present a longer survival ability in the hospital environment, consequently giving them more opportunities to disseminate in these settings and be responsible for difficult-to-treat infections.

Efficacy of teicoplanin in bloodstream infections caused by Enterococcus faecium: post-hoc analysis of a nationwide surveillance

OBJECTIVES

Vancomycin and teicoplanin are glycopeptides with activity against Enterococcus faecium. However, studies on the clinical efficacy of teicoplanin are limited. The present study was aimed to compare the therapeutic efficacy of teicoplanin and vancomycin in E. faecium bacteremia.

METHODS

Patients with bloodstream infections were identified prospectively from July 2015 to December 2016 in 14 hospitals as part of a multicenter nationwide surveillance. Patients with E. faecium monomicrobial bacteremia were selected. Teicoplanin and vancomycin groups included patients who were treated with either agent for ≥48 h. The primary outcome was 30-day all-cause in-hospital mortality. The Cox proportional hazards model with inverse probability weighting was used to account for the imbalance in baseline characteristics between the two groups.

RESULTS

Among 97 patients with E. faecium bacteremia, 33 (34%) were treated with teicoplanin and 64 (66%) with vancomycin. There were no significant differences in 30-day in-hospital mortality (18.2% vs. 26.6%, P=0.358), 7-day mortality (6.1% vs. 15.6%, P=0.212). Further, multivariable analysis confirmed that the use of teicoplanin was not significantly associated with mortality (adjusted odds ratio, 0.72; 95% confidence interval, 0.28-1.86; P=0.494).

CONCLUSION

No significant differences in the clinical outcomes. These findings suggest teicoplanin as a useful alternative to vancomycin.

Dissemination of Quinupristin-Dalfopristin and Linezolid resistance genes among hospital environmental and healthy volunteer fecal isolates of Enterococcus faecalis and Enterococcus faecium

BACKGROUND

Streptogramins and linezolid are important in the treatment of infections caused by vancomycin-resistant enterococci.

PURPOSE

Then, we aimed to evaluate the resistance rates against these drugs and the prevalence of genes involved in hospital environmental and fecal normal-flora isolates of Enterococcus faecalis and Enterococcus faecium.

METHODS AND RESULTS

The strains were isolated from the stool samples and hospital environments by culturing on M-Enterococcus (ME) agar, and identified by phenotypic and genotypic microbiological tests. The disk agar diffusion method was used to identify the antimicrobial susceptibility pattern of the isolates. The genomic DNA extraction was done by the alkaline lysis method, and the PCR test was used to detect the resistance genes. A total of 145 enterococci isolates were taken, from which 84 (57.9%) isolates were detected as E. faecalis and 61 (42.06%) isolates were E. faecium. Moreover, 70 (83.33), 4 (4.76%), 1 (1.19%), and 40 (47.61%) isolates of E. faecalis and 20 (32.78%), 1 (1.63%), 4 (6.55%), and 26 (42.62%) E. faecium isolates were resistant against quinupristin-dalfopristin, linezolid, vancomycin, and erythromycin, respectively. Also, 112 (77.24%), 50 (34.48%), 39 (26.89%), 27 (18.62%), 19 (13.1%), 4 (2.75%), and 1 (0.68%) isolates were contained LsaA, vatD, vgbB, vatE, cfr, lsaE and optrA genes, respectively. None of the isolates carried the vgbA gene.

CONCLUSIONS

High-level streptogramin resistance rate and high prevalence of resistance genes in enterococci isolated from the stool of healthy persons and the hospital environment indicates the importance of possible transmission of resistance genes from these isolates to clinical ones.

Gut Microbiota Imbalance in Metastatic Colorectal Patients Treated With EGFRI and Long-Term Antibiotic Therapy for Cutaneous Toxicity: A Pilot Study

Patients with metastatic colorectal cancer (mCRC) frequently experience epidermal growth factor inhibitors (EGFRI)-induced skin side effects. Antibiotic treatment with doxycycline is often required in order to manage the skin and mucosal toxicity. Since these patients already have significant gut dysbiosis, the long-term antibiotic treatment may destabilize their gut microbiome.

Objectives

The assessment of intestinal dysbiosis in patients undergoing treatment with EGFRI, who require antibiotic treatment with doxycycline in order to manage adverse skin effects.

Methods

We conducted a prospective pilot study between 2020 and 2021 involving 10 patients with mCRC. These patients were undergoing treatment with EGFRI and required either short-term or long-term treatment with doxycycline in order to manage skin toxicity.

Results

The patients with mCRC who were treated with doxycycline for 8 weeks showed overexpression of Escherichia coli, Candida, and Geotrichum species compared to the patients who only received doxycycline treatment for two weeks.

Conclusions

The elevated levels of Escherichia coli and Candida species in the patients who received doxycycline for eight weeks compared to the patients who received the treatment for two weeks could provide a starting point for the development of a standardized guideline regarding the use of pre-active or reactive antibiotic treatment. We also highlight the importance of analyzing the intestinal microbiome of these patients. The identification of overexpressed species, as well as the deficiency of certain protective species, could guide the administration of probiotics to cover and repair the affected intestinal flora.

Descriptive Analysis of Circulating Antimicrobial Resistance Genes in Vancomycin-Resistant Enterococcus (VRE) during the COVID-19 Pandemic

COVID-19 offers ideal premises for bacteria to develop antimicrobial resistance. In this study, we evaluated the presence of several antimicrobial resistance genes (ARG) in vancomycin-resistant Enterococcus (VRE) isolated from rectal swabs from patients at a hospital in Cluj-Napoca, Romania. Rectal swabs were cultivated on CHROMID^® VRE (bioMérieux, Marcy—l’ Étoile, France) and positive isolates were identified using MALDI-TOF Mass Spectrometry (Bruker Daltonics, Bremen, Germany) and further analyzed using the PCR technique for the presence of the following ARGs: van A, van B, tet(M), tet(L), ermB, msrA, mefA, aac(6′)-Im, aph(2)-Ib, ant(4′)-Ia, sul1, sul2, sul3, and NDM1. We isolated and identified 68 isolates of Enterococcus faecium and 11 isolates of Enterococcus faecalis. The molecular analysis showed 66 isolates positive for the vanA gene and eight positive for vanB. The most frequent association of ARG in VRE was vanA-tet(M)-ermB. There was no statistically significant difference between Enterococcus faecium and Enterococcus faecalis regarding ARGs. Our work proves that during the COVID-19 pandemic, highly resistant isolates of Enterococcus were present in patients in the intensive care unit; thus, better healthcare policies should be implemented for the management and control of these highly resistant isolates in the future.

Antibiofilm activity of phytochemicals against Enterococcus faecalis: A literature review

Enterococcus faecalis is a leading causative pathogen of recalcitrant infections affecting heart valves, urinary tract, surgical wounds and dental root canals. Its robust biofilm formation, production of virulence factors and antibiotic resistance contribute significantly to its pathogenicity in persistent infections. The decreased effectiveness of most of antibiotics in preventing and/or eradicating E. faecalis biofilms mandates the discovery of alternative novel antibiofilm agents. Phytochemicals are potential sources of antibiofilm agents due to their antivirulence activity, diversity of chemical structure and multiple mechanisms of action. In this review, we describe the phenotypic and genetic attributes that contribute to antimicrobial tolerance of E. faecalis biofilms. We illuminate the benefits of implementing the phytochemicals to tackle microbial pathogens. Finally, we report the antibiofilm activity of phytochemicals against E. faecalis, and explain their mechanisms of action. These compounds belong to different chemical classes such as terpenes, phenylpropenes, flavonoids, curcuminoids and alkaloids. They demonstrate the ability to inhibit the formation of and/or eradicate E. faecalis biofilms. However, the exact mechanisms of action of most of these compounds are not fully understood. Therefore, the future studies should elucidate the underlying mechanisms in detail.

Exploring the impact of biochar on antibiotics and antibiotics resistance genes in pig manure aerobic composting through untargeted metabolomics and metagenomics

This study investigated the effect of biochar on antibiotics and antibiotic resistance genes (ARGs) during aerobic composting of pig manure. First, the composition and content of antibiotics in the manure were determined qualitatively and quantitatively. Biochar promoted the degradation of these antibiotics (oxytetracycline, chlortetracycline, and tetracycline). The relative abundance (RA) of antibiotic-resistant bacteria carrying ARGs accounted for about 29.32% of the total bacteria. Firmicutes and Actinomycetes were dominant phylum-level bacteria at the early and late stages of composting, respectively. Biochar decreased the total RA of ARGs by 16.83%±4.10%. tetW and tetL, closely related to tetracycline resistance, were significantly diminished during aerobic composting, and biochar was able to promote this removal. Biochar enhanced RAs of Mycobacterium tuberculosis kasA mutant. RAs of ARGs related to antibiotic efflux pumps, such as baeS and arlS, remained at a high level. Conclusively, biochar promotes degradation of antibiotics and removal of ARGs.

Cordyceps Improves Obesity and its Related Inflammation via Modulation of Enterococcus cecorum Abundance and Bile Acid Metabolism

Dysbiotic gut microbiota has been identified as a primary mediator of inherent inflammation that underlies the pathogenesis of obesity. Cordyceps comprises the larval body and the stroma of Cordyceps sinensis (BerK.) Sacc. parasiting on Hepialidae larvae of moths (H. pialusoberthur) with potent metabolic regulation functions. The underlying anti-obesity mechanisms, however, remain largely unknown. Here, we demonstrate that the water extract of Cordyceps attenuates glucose and lipid metabolism disorders and its associated inflammation in high-fat diet (HFD)-fed mice. 16S rRNA gene sequencing and microbiomic analysis showed that Cordyceps reduced the amounts of Enterococcus cecorum, a bile-salt hydrolase-producing microbe to regulate the metabolism of bile acids in the gut. Importantly, E. cecorum transplantation or liver-specific knockdown of farnesoid X receptor (FXR), a bile acid receptor, diminished the protective effect of Cordyceps against HFD-induced obesity. Together, our results shed light on the mechanisms that underlie the glucose- and lipid-lowering effects of Cordyceps and suggest that targeting intestinalE. cecorum or hepatic FXR are potential anti-obesity and anti-inflammation therapeutic avenues.

Antimicrobial Biocides Susceptibility and Tolerance-Associated Genes in Enterococcus faecalis and Enterococcus faecium Isolates Collected from Human and Environmental Sources

Enterococci are among the most common causes of nosocomial infections worldwide. Antimicrobial biocides are extensively used to control the growth of microorganisms on different surfaces. The purpose of this study was to determine the susceptibility of Enterococcus faecalis and Enterococcus faecium isolates collected in Iran to biocide agents, formaldehyde (FOR), benzalkonium chloride (BZC), triclosan (TRE), and chlorhexidine digluconate (CHDG). Additionally, the frequency of biocide tolerance-associated (BTA) genes, qacA/B, qacED1, emeA, sigV and gasp65 were investigated. In this study, 222 isolates of E. faecalis and 425 isolates of E. faecium from clinical and non-clinical sources were investigated. Minimum inhibitory concentration (MIC) of biocide agents was determined using agar dilution method. Biocides epidemiological cutoff values (ECOFFs) were determined using 95% rule. BTA genes were identified using PCR testing. ECOFFs for CHDG, BZC, TRE and FOR were 8 µg/mL, 16 µg/mL, 32 µg/mL and 512 µg/mL for both species, respectively. MIC values showed that the distribution of isolates with high level of tolerance to antimicrobial biocides was clearly different, depending on ecological niches. The BTA genes, qacA/B, qacED1, emeA, sigV and gasp65 were detected in 19.4% (43), 19.8% (44), 42.8% (95), 89.6% (199) and 70.2% (156) of E. faecalis and 10.3% (44), 17.2% (73), 27.8% (118), 42.2% (188) and 82.8% (352) of E. faecium isolates, respectively. Based on the distribution pattern of BTA genes 14 and 18 different profiles were identified for E. faecalis and E. faecium isolates respectively. Generally, the isolates carrying at least a single BTA gene showed higher MIC₉₀ against all biocides compared to isolates with no BTA genes. However, there were no clear association between MIC₉₀ values and carrying particular BTA genes profile. The results of this study showed that CHDG was the most effective biocide against E. faecalis and E. faecium isolates. The data presented in current study can be used to define the biocides resistance breakpoints.

Small Things Matter: The 11.6-kDa TraB Protein is Crucial for Antibiotic Resistance Transfer Among Enterococci

Conjugative transfer is the most important means for spreading antibiotic resistance genes. It is used by Gram-positive and Gram-negative bacteria, and archaea as well. Conjugative transfer is mediated by molecular membrane-spanning nanomachines, so called Type 4 Secretion Systems (T4SS). The T4SS of the broad-host-range inc18-plasmid pIP501 is organized in a single operon encoding 15 putative transfer proteins. pIP501 was originally isolated from a clinical Streptococcus agalactiae strain but is mainly found in Enterococci. In this study, we demonstrate that the small transmembrane protein TraB is essential for pIP501 transfer. Complementation of a markerless pIP501∆traB knockout by traB lacking its secretion signal sequence did not fully restore conjugative transfer. Pull-downs with Strep-tagged TraB demonstrated interactions of TraB with the putative mating pair formation proteins, TraF, TraH, TraK, TraM, and with the lytic transglycosylase TraG. As TraB is the only putative mating pair formation complex protein containing a secretion signal sequence, we speculate on its role as T4SS recruitment factor. Moreover, structural features of TraB and TraB orthologs are presented, making an essential role of TraB-like proteins in antibiotic resistance transfer among Firmicutes likely.

Litter Management Strategies and Their Impact on the Environmental and Respiratory Microbiome Might Influence Health in Poultry

Aerial and respiratory tract-associated bacterial diversity has been scarcely studied in broiler production systems. This study examined the relationship between the environmental air and birds’ respiratory microbiome, considering a longitudinal sampling. Total viable bacteria and coliforms in the air were quantified, and the 16S rRNA gene was sequenced from tracheal and air samples obtained through a novelty protocol. Air results showed a decrease in coliforms over time. However, at week 3, we reported an increase in coliforms (from 143 to 474 CFUc/m3) associated with litter management. Additionally, 16S rRNA gene results indicated a distinctive air microbial community, associated primarily with Bacillota phylum particularly of the Bacilli class (>58%), under all conditions. Tracheal results indicated a predominance of Escherichia coli/Shigella at the beginning of the productive cycle, shifting toward the middle and end of the cycle to Gallibacterium. However, at week 3, the dominance of Escherichia coli/Shigella (>99.5%) associated with litter aeration by tumbling stood out. Tracheal and air samples displayed a statistically different community structure, but shared differentially abundant features through time: Enterococcus, Gallibacterium, and Romboutsia ilealis. These results indicate the impact of production management protocols on the birds’ respiratory system that should be considered a breakpoint in poultry farm health.

The Cationic Antimicrobial Peptide Activity of Lysozyme Reduces Viable Enterococcus faecalis Cells in Biofilms

Enterococcus faecalis, a leading cause of health care-associated infections, forms biofilms and is resistant to many antimicrobial agents. Planktonic-phase E. faecalis is resistant to high concentrations of the enzyme lysozyme, which catalyzes the hydrolysis of N-acetylmuramic acid and N-acetylglucosamine linkages in peptidoglycan and is also a cationic antimicrobial peptide (CAMP). E. faecalis lysozyme resistance in planktonic cells is stimulated upon activation of the extracytoplasmic function sigma factor SigV via cleavage of the anti-sigma factor RsiV by the transmembrane protease Eep. Planktonically grown E. faecalis lacking eep is more sensitive than wild-type strains to growth inhibition by lysozyme. This study was initiated to determine whether E. faecalis OG1RFΔeep biofilms would be protected from lysozyme. Serendipitously, we discovered that exposure of both E. faecalis OG1RF and OG1RFΔeep biofilms to chicken egg white lysozyme resulted in decreases in biofilm cell viability of 3.7 and 3.8 log₁₀ CFU/mL, respectively. Treatment of biofilms of both strains with recombinant purified human lysozyme was associated with reductions in cell viability of >99.9% for both strains. Lysozyme-treated OG1RF and OG1RFΔeep biofilms contained a higher percentage of dead cells by Live/Dead staining and were associated with more extracellular DNA. Heat-inactivated human lysozyme, which was devoid of muramidase activity, as well as the lysozyme-derived CAMP LP9 and the CAMP polymyxin B, decreased biofilm cell viability. These results are consistent with a model in which the CAMP activity, rather than the muramidase activity, of lysozyme causes lysis of E. faecalis biofilm cells despite them having an intact lysozyme resistance-inducing signaling pathway. Finally, lysozyme was also effective in reducing viable biofilm cells of several other E. faecalis strains, including the vancomycin-resistant strain V583 and multidrug-resistant strain MMH594. This study demonstrates the potential for lysozyme to be developed as a novel antibiofilm therapeutic.

Environmental, Microbiological, and Immunological Features of Bacterial Biofilms Associated with Implanted Medical Devices

The spread of biofilms on medical implants represents one of the principal triggers of persistent and chronic infections in clinical settings, and it has been the subject of many studies in the past few years, with most of them focused on prosthetic joint infections. We review here recent works on biofilm formation and microbial colonization on a large variety of indwelling devices, ranging from heart valves and pacemakers to urological and breast implants and from biliary stents and endoscopic tubes to contact lenses and neurosurgical implants. We focus on bacterial abundance and distribution across different devices and body sites and on the role of environmental features, such as the presence of fluid flow and properties of the implant surface, as well as on the interplay between bacterial colonization and the response of the human immune system.

Small RNAs beyond Model Organisms: Have We Only Scratched the Surface?

Small RNAs (sRNAs) are essential regulators in the adaptation of bacteria to environmental changes and act by binding targeted mRNAs through base complementarity. Approximately 550 distinct families of sRNAs have been identified since their initial characterization in the 1980s, accelerated by the emergence of RNA-sequencing. Small RNAs are found in a wide range of bacterial phyla, but they are more prominent in highly researched model organisms compared to the rest of the sequenced bacteria. Indeed, Escherichia coli and Salmonella enterica contain the highest number of sRNAs, with 98 and 118, respectively, with Enterobacteriaceae encoding 145 distinct sRNAs, while other bacteria families have only seven sRNAs on average. Although the past years brought major advances in research on sRNAs, we have perhaps only scratched the surface, even more so considering RNA annotations trail behind gene annotations. A distinctive trend can be observed for genes, whereby their number increases with genome size, but this is not observable for RNAs, although they would be expected to follow the same trend. In this perspective, we aimed at establishing a more accurate representation of the occurrence of sRNAs in bacteria, emphasizing the potential for novel sRNA discoveries.

Comparative Analysis of the Fecal Microbiota of Relict Gull (Larus relictus) in Mu Us Desert (Hao Tongcha Nur) and Bojiang Haizi in Inner Mongolia, China

The gut microbiota contributes to host health by improving digestive efficiency and maintaining homeostasis. The relict gull (Larus relictus), a national first-class protected bird in China, is listed as vulnerable in the International Union for Conservation of Nature Red List. Here, 16S rRNA gene sequencing was performed to characterize and compare the community composition and diversity of the gut microbiota sampled from relict gulls in two breeding sites. In total, 418 operational taxonomic units (OUTs) were obtained and classified into 15 phyla and 228 genera. Alpha diversity analysis revealed no significant differences in community diversity among the two breeding sites. Beta diversity analyses showed that the microbial communities at the two sites were different. Six dominant phyla and fourteen dominant genera were identified. The most abundant bacterial genera had a significant relationship with the diet and living environment, and some bacterial genera were found to adapt to the plateau environment in which relict gulls live, which enables the relict gulls to use local resources effectively to accumulate energy. Simultaneously, a variety of highly abundant pathogenic bacteria were found, suggesting that these gulls may spread diseases among the local gull population. Certain measures should be taken to protect this species and to prevent the spread of diseases.

Isolation and identification of mucin-degrading bacteria originated from human feces and their potential probiotic efficacy according to host-microbiome enterotype

AIM

Mucin-degrading bacteria are known to be beneficial for gut health. We aimed to isolate human-derived mucin-degrading bacteria and identify potential probiotic characteristics and their effects on the bacterial community and short-chain fatty acid (SCFA) production according to three different enterotypes of the host.

METHODS AND RESULTS

Bacteria with mucin decomposition ability from human feces were isolated and identified by 16S rRNA sequencing and MALDI-TOF. Heat resistance, acid resistance, antibiotic resistance, and antibacterial activity were analyzed in the selected bacteria. Their adhesion capability to the Caco-2 cell was determined by scanning electron microscopy. Their ability to alter the bacterial community and SCFA production of the isolated bacteria was investigated in three enterotypes. The three isolated strains were Bifidobacterium(B.) animalis SPM01 (CP001606.1, 99%), B. longum SPM02 (NR_043437.1, 99%), and Limosilactobacillus(L.) reuteri SPM03 (CP000705.1, 99%) deposited in Korean Collection for Type Culture (KCTC-18958P). Among them, B. animalis exhibited the highest mucin degrading ability. They exhibited strong resistance to acidic conditions, moderate resistance to heat, and the ability to adhere tightly to Caco-2 cells. Three isolated mucin-degrading bacteria incubation increased Lactobacillus in the fecal bacteria from Bacteroides and Prevotella enterotypes. However, only L. reuteri elevated Lactobacillus in the fecal bacteria from the Ruminococcus enterotype. B. longum and B. animalis increased the α-diversity in the Ruminococcus enterotype, while their incubation with other intestinal types decreased the α-diversity. B. animalis and L. reuteri increased the butyric acid level in fecal bacteria from the Prevotella enterotype, and L. reuteri elevated the acetic acid level in those from the Ruminococcus enterotype. However, the overall SCFA changes were minimal.

CONCLUSIONS

The isolated mucin-degrading bacteria act as probiotics and modulate gut microbiota and SCFA production differently according to the host's enterotypes.

SIGNIFICANCE AND IMPACT OF STUDY

Probiotics need to be personalized according to the enterotypes in clinical application.

Enterococcus faecalis and Candida albicans dual-species biofilm: establishment of an in vitro protocol and characterization

Enterococcus faecalis is the most important agent of persistent apical periodontitis, and recently, Candida albicans has also been implicated in periapical infections. This study aimed to optimize an in vitro E. faecalis and C. albicans dual-species biofilm protocol for endodontic research. Different physicochemical conditions for biofilm formation were tested. Susceptibility assays to antimicrobials, biochemical composition and an ultra-morphological structure analyses were performed. Reproducible dual-species biofilms were established in BHI medium at 35 °C, for 48 h and in a microaerophilic atmosphere. An increase in biomass and chitin content was detected after vancomycin treatment. Structural analysis revealed that the dual-species biofilm was formed by both microorganisms adhered to the substrate. The proposed protocol could be useful for the study of interkingdom relationships and help to find new strategies against periapical infections.

Identification of Protein Drug Targets of Biofilm Formation and Quorum Sensing in Multidrug Resistant Enterococcus faecalis

Abstract:

Enterococcus faecalis (E. faecalis) is an opportunistic multidrug-resistant (MDR) pathogen found in the guts of humans and farmed animals. Due to the occurrence of (MDR) strain there is an urgent need to look for an alternative treatment approach. E. faecalis is a Gram-positive bacterium, which is among the most prevalent multidrug resistant hospital pathogens. Its ability to develop quorum sensing (QS) mediated biofilm formation further exacerbates the pathogenicity and triggers lifethreatening infections. Therefore, developing a suitable remedy for curing E. faecalis mediated enterococcal infections is an arduous task. Several putative virulence factors and proteins are involved in the development of biofilms in E. faecalis. Such proteins often play important roles in virulence, disease, and colonization by pathogens. The elucidation of the structure-function relationship of such protein drug targets and the interacting compounds could provide an attractive paradigm towards developing structure-based drugs against E. faecalis. This review provides a comprehensive overview of the current status, enigmas that warrant further studies, and the prospects toward alleviating the antibiotic resistance in E. faecalis. Specifically, the role of biofilm and quorum sensing (QS) in the emergence of MDR strains had been elaborated along with the importance of the protein drug targets involved in both the processes.

Penicillin-resistant, ampicillin-susceptible Enterococcus faecalis isolates are uncommon in non-clinical sources

This study aimed to investigate whether penicillin-resistant, ampicillin-susceptible E. faecalis (PRASEF) isolates are disseminated in non-clinical sources, and to compare the molecular characteristics and antimicrobial resistance (AMR) profile of clinical and non-clinical E. faecalis isolates. Non-clinical samples (n = 280) were collected and 101 E. faecalis isolates were recovered from food (n = 18), faeces of healthy animals (n = 24), water (n = 28) and sewage (n = 31). PRASEF (n = 68) and penicillin-susceptible, ampicillin-susceptible E. faecalis (n = 77) isolates of clinical origin were also evaluated. A significant variety of AMR profiles was observed among non-clinical isolates according to the source. No food isolate exhibited a multidrug resistance (MDR) phenotype different from those of isolates from animal faeces (50.0%) and sewage (38.7%). Overall, the MDR phenotype was more frequent among clinical (56.6%) than non-clinical isolates (22.8%) (p < 0.01). Non-clinical PRASEF isolates (n = 3) were only recovered from hospital sewage. Note that representative clinical and non-clinical PRASEF isolates were grouped in pulsotype A, and belonged to CC9 (clonal complex). In conclusion, E. faecalis isolates exhibiting the unusual penicillin-resistant but ampicillin-susceptible phenotype appeared to be restricted to the hospital environment. Our findings highlight the ability of PRASEF isolates to survive in sewage, which could enable these hospital-adapted lineages to spread to new ecological niches.

Sex Difference of Effect of Sophora flavescens on Gut Microbiota in Rats

Objective

By observing the sex difference of the gut microbiota in rats and the influence of Sophora flavescens (S. flavescens) on the gut microbiota in rats of different genders, it is hoped that it can provide reference materials for the rational use of S. flavescens in clinical practice.

Method

Taking samples of the jejunum (containing intestinal contents) and feces of 8-week-old rats, and detecting the composition of gut microbiota of females and males by 16S rRNA sequencing technology; At the same time, 8-week-old rats were gavaged with different doses of S. flavescens decoction, and the duodenum, jejunum, ileum, and colon (including the intestinal contents) samples were collected at 1, 2, and 3 weeks, using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) technology and real-time fluorescent quantitative PCR (qRT-PCR) technology to observe the changes in the structure and the quantitative changes of 4 major intestinal dominant bacteria Enterococcus, Bacteriodes, Lactobacillus, and Clostridium in each intestinal segment, respectively.

Result

(1) The gut microbiota of normal rats without administration also had obvious gender differences; (2) S. flavescens significantly affects the composition of gut microbiota, and in different intestinal segments, this effect was different between genders under different dosages and different continuous administration times.

Conclusion

The effect of S. flavescens on the gut microbiota of rats had gender differences.

Investigating antibiotic resistance in enterococci in Gabonese livestock

Background and Aim:

The emergence of antibiotic resistance is a major problem worldwide. Antibiotics are often used to prevent or treat infections in livestock. This study aimed to investigate antibiotic resistance in enterococci in Gabonese livestock.

Materials and Methods:

We collected 174 animal samples (46 laying hens, 24 swine, 62 cattle, and 42 sheep) from farms in four provinces of Gabon. Bacterial strains belonging to the genus Enterococcus were obtained using selective media and polymerase chain reaction targeting the tuf gene. Antibiotic susceptibility was determined by the disk diffusion method on Mueller-Hinton agar.

Results:

Enterococci were present in 160 of the samples (97%), distributed as follows: laying hens (100%, 41/41), swine (100%, 22/22), small ruminants (88%, 37/42), and cattle (100%, 60/60). Resistance to cephalothin/cephalexin, streptomycin, and rifampicin (RIF) was high, and resistance to vancomycin (VAN), erythromycin, and tetracycline was moderate. A high diversity of resistance was found in Haut-Ogooué and Estuaire provinces. Laying hens and swine showed moderate levels of resistance to ciprofloxacin and penicillin, while sheep and cattle had high levels of resistance to RIF. All species showed a high level of resistance to VAN. We found various patterns of multiple resistances in the isolates, and the multiple resistance indexes ranged from 0.2 to 0.8.

Conclusion:

This study shows that livestock in Gabon can be considered potential reservoirs of resistance.