Enterococci: Between Emerging Pathogens and Potential Probiotics

Chemical migration, digestive behaviors and effect on gut microbiota of PLA and PBAT oligomers

As biodegradable food contact materials (FCMs), polylactic acid (PLA) and poly(butylene adipate-co-terephthalate) (PBAT) may release oligomers into food and raise potential health concerns. This study investigated the migration characteristics and digestive behaviors of oligomers by combining migration experiments, an in vitro digestion model, and high-resolution mass spectrometry. Moreover, the effects of the migrants from both materials on gut microbiota were evaluated following in vitro colonic fermentation for 48 h. The results indicated that 51 PLA oligomers and 45 PBAT oligomers were released into food simulants, with the migration increasing with ethanol concentration. Cyclic oligomers exhibited higher migration than linear oligomers. During digestion, PLA oligomers were almost completely degraded, whereas PBAT oligomers increased, additionally, cyclic oligomers were more susceptible to degradation. Migrants from both materials exhibited cytotoxicity effect on Caco-2 cells, disrupted the gut microbiota homeostasis, affecting multiple metabolic pathways. Especially, the migrants from PBAT inhibited the production of acetic, butyric, and isobutyric acids, while reducing the degradation of propionic acid. Overall, PBAT may pose a greater hazard than PLA. In conclusion, based on a new perspective of "lifecycle", this systematic study will contribute to a deeper understanding of the safety of PLA and PBAT when utilized as FCMs.

Antagonistic Effects of Lactic Acid Bacteria Isolated from Ethiopian Traditional Fermented Foods and Beverages Against Foodborne Pathogens

Lactic acid bacteria (LAB) found in Ethiopian traditional fermented foods and beverages have potential antagonistic effects against foodborne pathogens due to their capacity to produce various antimicrobial metabolites. This study evaluated the antagonistic activity of LAB isolated from Ethiopian traditional fermented foods and beverages against foodborne pathogens and characterized their antimicrobial substances. A total of 180 traditional fermented foods and beverages were collected, and the antagonistic activities of LAB were evaluated against selected foodborne pathogens. The effects of pH, temperature, enzymes, and food additives on the antagonistic effects of cell-free supernatant produced by LAB were investigated. LAB identification and characterization were conducted using an integrated phenotypic approach and MALDI TOF MS spectrum analysis, and data were analyzed using one-way ANOVA and Tukey post hoc analysis. A total of 956 LAB were isolated, of which seventeen (17 LAB) isolates of Pediococcus pentosaceus (Pc. pentosaceus (n = 7)), Pediococcus acidilactici (Pc. acidilactici (n = 2)), Enterococcus faecium (Ec. faecium (n = 6)), and Lactococcus lactis (Lc. lactis (n = 2)) were screened for antagonistic activity based on their ability to produce bacteriocins, probiotic activity, and preservative potential. Pc. pentosaceus JULABB16, Pc. pentosaceus JULABB01, and Ec. faecium JULABBr39 showed strong antagonistic activity against all pathogens, with mean inhibition zone diameters ranging from 23.50 to 35.50 mm. Lc. lactis, Pc. pentosaceus, Pc. acidilactici, and Ec. faecium produced bioactive metabolites that were sensitive to proteolytic enzymes and capable of withstanding high temperatures (80-100 °C) and acid concentrations (pH 2-10). The CFS produced by Lc. lactis, Pc. pentosaceus, Pc. acidilactici, and Ec. faecium showed the most impending antagonistic activity against all pathogens. The bioactive substances produced by LAB isolates had promising effects against food spoilage and pathogenic bacteria, making them potential natural food preservatives.

Prevalence and antimicrobial resistance of gram-positive pathogens in Lebanon: The need for surveillance and stewardship

Background

Resistance in Gram-positive organisms, including methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus (VRE), poses a significant healthcare challenge globally. However, data on these organisms in Lebanon remain limited. This retrospective study aimed to assess the prevalence and antimicrobial resistance patterns of Staphylococcus aureus (S. aureus), coagulase-negative Staphylococci (CoNS), and Enterococcus spp. in clinical infections at the Lebanese Hospital Geitaoui - UMC from 2017 to 2023.

Methods

A total of 2676 isolates were collected from urine, blood, respiratory specimens, and other infection sites. Bacterial identification was performed following WHO clinical bacteriology procedures, utilizing gram staining, catalase and coagulase tests, and biochemical assays. Antimicrobial susceptibility testing was conducted using the Kirby-Bauer disk diffusion method and minimum inhibitory concentration (MIC) analysis, interpreted according to Clinical and Laboratory Standards Institute (CLSI) guidelines. Statistical analyses were performed using SPSS® version 24, with significance set at p < 0.05.

Results

CoNS were the most prevalent (42.83 %), followed by Enterococcus spp. (28.81 %) and S. aureus (28.36 %). Blood cultures had the highest isolation rates (29.04 %), predominantly CoNS (76.45 %). Enterococcus spp. dominated urinary tract infections (85.01 %), while S. aureus was prevalent in wound/surgical site infections (59.23 %). Gender-specific trends showed CoNS and S. aureus more in males, while Enterococcus spp. infections were more common in females.

Conclusion

This study provides valuable insights into the prevalence and resistance patterns of Gram-positive pathogens in a Lebanese hospital setting. The findings highlight the need for continuous surveillance and stringent antibiotic stewardship to combat antimicrobial resistance effectively.

Genome analysis reveals a biased distribution of virulence and antibiotic resistance genes in the genus Enterococcus and an abundance of safe species

Enterococci are lactic acid bacteria (LAB) that, as their name implies, often are found in the gastrointestinal tract of animals. Like many other gut-dwelling LAB, for example, various lactobacilli, they are frequently found in other niches as well, including plants and fermented foods from all over the world. In fermented foods, they contribute to flavor and other organoleptic properties, help extend shelf life, and some even possess probiotic properties. There are many positive attributes of enterococci; however, they have been overshadowed by the occurrence of antibiotic-resistant and virulent strains, often reported for the two species, Enterococcus faecalis and Enterococcus faecium. More than 40,000 whole-genome sequences covering 64 Enterococcus type species are currently available in the National Center for Biotechnology Information repository. Closer inspection of these sequences revealed that most represent the two gut-dwelling species E. faecalis and E. faecium. The remaining 62 species, many of which have been isolated from plants, are thus quite underrepresented. Of the latter species, we found that most carried no potential virulence and antibiotic resistance genes, an observation that is aligned with these species predominately occupying other niches. Thus, the culprits found in the Enterococcus genus mainly belong to E. faecalis, and a biased characterization has resulted in the opinion that enterococci do not belong in food. Since enterococci possess many industrially desirable traits and frequently are found in other niches besides the gut of animals, we suggest that their use as food fermentation microorganisms is reconsidered.IMPORTANCEWe have retrieved a large number of Enterococcus genome sequences from the National Center for Biotechnology Information repository and have scrutinized these for the presence of virulence and antibiotic resistance genes. Our results show that such genes are prevalently found in the two species Enterococcus faecalis and Enterococcus faecium. Most other species do not harbor any virulence and antibiotic resistance genes and display great potential for use as food fermentation microorganisms or as probiotics. The study contributes to the current debate on enterococci and goes against the mainstream perception of enterococci as potentially dangerous microorganisms that should not be associated with food and health.

Sequencing and genome-scale virulome reconstruction of Enterococcus faecalis clinical isolates delineate genes involved in gelatinase activity and biofilm formation

INTRODUCTION

Enterococci are a leading cause of nosocomial infections with a wide array of virulence factors. Clinically isolated enterococci vary in gelatinase activity and biofilm-forming ability, yet the genetic basis for this variation is not fully understood.

AIM

This study aimed to identify genetic factors associated with the discrepancy in biofilm formation and gelatinase activity.

METHODS

Biofilm formation was quantified by the crystal violet assay and the gelatinase activity was determined on gelatin agar plates. The genomes of 33 clinical Enterococcus faecalis isolates were sequenced by Illumina HiSeq and annotated by the Rapid Annotations using Subsystems Technology tool kit (RASTtk) and tools within the Bacterial Viral Bioinfromatic Resource Center (BV-BRC). Virulence factors and prophages were predicted, and genotype-phenotype associations were statistically assessed.

RESULTS

All isolates formed biofilms with different intensities, with the majority (65 %) forming moderate to strong biofilms. Gelatinase activity was detected in 39 % of isolates. The hyaluronic acid precursor gene (EF0818), adhesion protein gene (prgB/asc10), manganese uptake gene (psaA), enterococcal surface protein gene (esp), and the complete capsule locus (cps) were significantly positively correlated with biofilm intensity (p < 0.05), while the quorum sensing genes, fsrA and fsrB, collagen adhesion gene (ace), and capsule gene, cpsF, were significantly positively correlated with gelatinase activity (p < 0.05). Prophage content was positively associated with biofilm formation.

CONCLUSION

Whole-genome sequencing identified genes and prophages linked to biofilm formation and gelatinase activity in E. faecalis. Future studies will experimentally confirm the role of identified genes in virulence and their possible anti-virulence intervention potential.

Occurrence and assessment of antibiotic resistance and virulence of Enterococcus spp. strains isolated from fecal samples of wild animals

About 60% of the etiological agents of human infections are of animal origin, and the microorganisms causing them can be isolated not only from farmed and domestic animals, but also from wildlife. Enterococcus spp. may exhibit intrinsic or acquired resistance to many antibiotic groups, posing significant therapeutic challenges. The aim of this study was to identify and assess the antibiotic resistance and virulence genes of Enterococcus strains isolated from fecal samples of wild animals. The 118 strains were obtained from deer (n = 38), wild boar (n = 29), hare (n = 19), roe deer (n = 12), fallow deer (n = 5), raccoon dog (n = 4), fox (n = 4), moose (n = 2), polecat (n = 2), rabbit (n = 1), wolf (n = 1) and marten (n = 1). Antibiotic resistance assessments were performed using the disk diffusion method following the recommendations of the European Committee on Antimicrobial Susceptibility Testing (EUCAST). The frequency of occurrence of vancomycin-resistant enterococci (VRE) phenotypes, high-level streptomycin resistance (HLSR), high-level gentamicin resistance (HLGR), and high-level aminoglycoside resistance (HLAR) was also determined. The PCR was used to detect virulence genes (VGs) (agg, gelE, EfaAfs, ace, pil, ebpA, ebpB, ebpC, srtA, hyl, asa, cylA and cylB). The study revealed a high species diversity of Enterococcus spp. Among the 118 strains collected, 70 were resistant to at least one antibiotic. The majority of strains exhibited resistance to eravacycline, while the least resistance was observed against ampicillin. Strains with VRE, HLSR, HLGR, and HLAR phenotypes were identified. Multidrug resistant (MDR) strains were detected. However, extensively drug-resistant (XDR) and pandrug-resistant (PDR) strains were not observed. The virulence factors were present in the tested strains, and the most frequently detected gene was agg encoding aggregation substance. We have provided evidence that healthy wild animals can be reservoirs of pathogenic Enterococcus strains, including MDR strains and with many VGs, which can be transmitted to humans.

Exploring the bioactive landscape: peptides and non-peptides from the human microbiota

The human microbiota, consisting of trillions of bacteria from six main phyla, produces peptide and non-peptide secondary metabolites which have antibacterial properties vital to medicine and biotechnology. These metabolites influence biological processes linked to diseases, yet much remains unknown. This review explores their structures and functions, aiming to spur novel metabolite discovery and advance drug development.

Bladder Microbiota Snapshots Help to Monitor Urinary Tract Infections in Vulnerable Patients

The development of next generation sequencing technology has undoubtedly impairs the classic microbiological approach even though main questions remain still elusive. To date, nobody can define the existence of a unique healthy microbial community, nor a diagnostic application can be definitely assessed. In this context, “snapshots” of the microbiota contribute to reveal factors associated with a disease, even though lacking longitudinal data and the association with results obtained from gold standard microbiological tests. Here we show how the information obtained by microbiota can be a promising additional tool to monitor urinary tract infections revaluating beneficial communities or attention to particularly microbial patterns.

Enterococci for human health: A friend or foe?

Enterococci are widely distributed in nature and exhibit good temperature and pH tolerance, making them suitable for industrial fermentation. It can produce bacteriocins, natural antibacterial substances utilized in food preservation. Some Enterococci are employed as probiotics to regulate human immunity and maintain healthy intestinal environments. However, recent scientific studies have highlighted the pathogenicity and multidrug resistance of Enterococci, classifying it as an important pathogen in clinical infections. Moreover, increasing evidence has linked Enterococcus sp., particularly Enterococcus faecalis and Enterococcus faecium, to clinical diseases, raising concerns about their safety and posing the question, how should we approach the conflicting nature of the pathogenic and beneficial effects of Enterococci? This review provides the recent advancements in Enterococci research and incorporates the perspectives of international authoritative organizations and institutions to comprehensively analyze the beneficial and harmful characteristics of Enterococci in the fields of science, clinical and industrial applications, aiming to address three important questions: whether Enterococci are beneficial or harmful to humans, their potential use in medical treatments, and the criteria to evaluate their safety. The goal is to explore the feasibility of the standardized use of Enterococci and provide guidance on the scientific selection and utilization of probiotics.

Exploring the dark side of probiotics to pursue light: Intrinsic and extrinsic risks to be opportunistic pathogens

Probiotics, live microorganisms with multiple health benefits, have gained popularity for their roles in maintaining daily health and treating a variety of diseases. However, they have the potential to be opportunistic pathogens in some conditions. This review delves into the intrinsic and extrinsic risks associated with probiotics. Intrinsic risks involve the production of harmful substances, such as toxins and invasive factors, biofilm formation, bacteria emboli, antibiotic resistance with relevant genetic materials, genetic plasticity, and metabolic issues, while extrinsic risks include problems in regulatory oversight and public awareness, host health status and appropriately administration. It emphasizes the need for a balanced view of their therapeutic benefits and potential hazards, advocating for further research to understand the complex interactions between probiotics and the human microbiome, to optimize the safety and efficacy of probiotics.

A Meta-Analysis on the In Vitro Antagonistic Effects of Lactic Acid Bacteria from Dairy Products on Foodborne Pathogens

Raw milk and traditional fermented foods such as artisanal cheese represent a natural source of lactic acid bacteria (LAB). They can produce antimicrobial compounds, such as bacteriocins and lactic acid, which may be exploited in dairy biopreservation. This study aimed to conduct a systematic review and meta-analysis to synthesize the inhibition diameter (ID) of LAB against L. monocytogenes, S. aureus, and Salmonella spp. Literature electronic searches were performed on PubMed, Scopus, and Web of Science, to identify articles that reported data on in-vitro antimicrobial activity by LAB isolated from dairy foods. A total of 1665 papers were retrieved, and 20 primary studies were selected according to the selection criteria, of which 397 observations were extracted. Random-effects meta-regression models were employed to describe the effects of LAB genus, pathogen concentration, susceptibility method, incubation time, inoculation volume, agar type and pH on the IDs for L. monocytogens, S. aureus, and Salmonella spp. L. monocytogens was the most susceptible pathogen (p < 0.05) to the LAB effects, followed by S. aureus and Salmonella spp. As a whole, LAB from the Lacticaseibacillus genus were the most effective (p < 0.05) in inhibiting L. monocytogens (21.49 ± 2.654 mm), followed by S. aureus (21.06 ± 2.056 mm). Salmonella spp. presented higher (p < 0.05) susceptibility to Lactobacillus genus (19.93 ± 2.456 mm). From the results, a general trend could be observed for the well-diffusion method to produce higher (p < 0.05) ID estimates than the spot and disk methods (30.73 ± 2.530 mm vs. 21.98 ± 1.309 mm vs. 13.39 ± 1.403 mm for L. monocytogenes; 22.37 ± 1.073 mm vs. 14.91 ± 2.312 mm vs. 20.30 ± 2.319 mm for Salmonella spp.), respectively. Among the tested moderators, the pathogen's inoculum concentration, the in vitro susceptibility assay itself, incubation time and inoculation volume on agar are determinant parameters to be looked at when designing a robust and reproducible experimental plan. The in vitro results reinforced that LAB can be useful in controlling the development of pathogenic bacteria frequently found in the dairy industry.

Antibiotic Resistance Gene Expression in Veterinary Probiotics: Two Sides of the Coin

The rapid proliferation of antimicrobial resistance has emerged as one of the most pressing animal and public health challenges of our time. Probiotics, extensively employed in human and veterinary medicine, are instrumental in maintaining a balanced microbiome and mitigating its disruption during antibiotic therapy. While their numerous benefits are well documented, probiotics also present potential risks, notably the capacity to harbor antimicrobial resistance genes. This genetic reservoir could contribute to the emergence and spread of antimicrobial resistance by facilitating the horizontal transfer of resistance genes to pathogenic bacteria within the gut. This review critically examines the presence of antimicrobial resistance genes in commonly used probiotic strains, explores the underlying mechanisms of resistance, and provides a balanced analysis of the benefits and risks associated with their use. By addressing these dual aspects, this paper highlights the need for vigilant evaluation of probiotics to preserve their therapeutic potential while minimizing public health risks.

Navigating a challenging path: precision disease treatment with tailored oral nano-armor-probiotics

Oral probiotics have significant potential for preventing and treating many diseases. Yet, their efficacy is often hindered by challenges related to survival and colonization within the gastrointestinal tract. Nanoparticles emerge as a transformative solution, offering robust protection and enhancing the stability and bioavailability of these probiotics. This review explores the innovative application of nanoparticle-armored engineered probiotics for precise disease treatment, specifically addressing the physiological barriers associated with oral administration. A comprehensive evaluation of various nano-armor probiotics and encapsulation methods is provided, carefully analyzing their respective merits and limitations, alongside strategies to enhance probiotic survival and achieve targeted delivery and colonization within the gastrointestinal tract. Furthermore, the review explores the potential clinical applications of nano-armored probiotics in precision therapeutics, critically addressing safety and regulatory considerations, and proposing the innovative concept of 'probiotic intestinal colonization with nano armor' for brain-targeted therapies. Ultimately, this review aspires to guide the advancement of nano-armored probiotic therapies, driving progress in precision medicine and paving the way for groundbreaking treatment modalities.

Molecular Assessment and Validation of the Selected Enterococcal Strains as Probiotics

Probiotics are live microorganisms which confer health benefits to the host. Lactic acid bacteria (LAB) are used as probiotics since decades. Enterococci being the member of LAB have proven probiotic strains; therefore, this study was aimed at finding out the potential probiotic candidates from the pool of locally isolated strains. For initial screening, one hundred and twenty-two strains were selected and subjected to different confirmatory and phenotypic tests to choose the best strains that have potential probiotic criteria, i.e., no potential virulence traits, antibiotic resistance, and having tolerance properties. Keeping this criterion, only eleven strains (n = 11) were selected for further assessment. All virulence traits such as production of hemolysin, gelatinase, biofilm, and DNase were performed and not found in the tested strains. The molecular assessment indicates the presence of few virulence-associated genes in Enterococcus faecalis strains with variable frequency. The phenotypic and genotypic assessments of antibiotic resistance profile indicate that the selected strain was susceptible to ten commonly used antibiotics, and there were no transferrable antibiotic resistance genes. The presence of CRISPR-Cas genes also confirmed the absence of antibiotic resistance genes. Various enterocin-producing genes like EntP, EntB, EntA, and EntQ were also identified in the selected strains which make them promising probiotic lead strains. Different tolerance assays like acid, NaCl, and gastric juice tolerance that mimic host conditions was also evaluated by providing artificial conditions. Cellular adhesion and aggregation properties like auto- and co-aggregation were also checked and their results reflect all in the favor of lead probiotic strains.

The Enterococcus secretome inhibits the growth of vancomycin-resistant Enterococcus faecalis V853 with their antiproliferative properties and nanoencapsulation effects

In our study, the secretome of the clinical isolate Enterococcus faecalis HY7 displayed antibacterial activity against the vancomycin-resistant Enterococcus faecalis V853. These bacteriocin-like substances showed thermal stability at a wide range of temperatures up to 121 °C, while proteinase K treatment resulted in a total loss of their activity. PCR-based screening for bacteriocin biosynthetic genes revealed that Enterococcus faecalis HY7 harbored multiple enterocin-producing genes, including ent A, avc A, and as-48. The production kinetics demonstrated the highest levels of bacteriocins production at 16 h, whereas the activity was diminished after 32 h of microbial growth. Notably, the partially purified bacteriocins exhibited anti-proliferative activity on the colon cancer cells, Caco2, with an IC50 value of 172.8 μg/mL. Remarkably, the nanoencapsulation of our bacteriocins in liposome showed a fourfold increase in its anti-vancomycin-resistant Enterococcus activity, which is the first report of liposome encapsulation with anti-vancomycin resistant Enterococcus bacteriocin.

Analysis of Olive Oil Mill Wastewater from Conventionally Farmed Olives: Chemical and Microbiological Safety and Polyphenolic Profile for Possible Use in Food Product Functionalization

This study aimed to perform an in-depth investigation of olive oil mill wastewater (OOMW). Two OOMW samples (OOMW-A and OOMW-B) from conventionally farmed olives were collected from two different olive oil mills in Palermo province (Italy). Multiresidual analysis indicated that both OOMW samples were unsuitable for food production due to pesticide residues. Specifically, OOMW-A contained 4 active compounds totaling 5.7 μg/L, while OOMW-B had 16 analytes with a total content of 65.8 μg/L. However, polyphenol analysis in the OOMW revealed 23 compounds with high concentrations of hydroxytyrosol, secoiridoid derivatives, phenolic acids, flavones, and total polyphenol content ranging from 377.5 μg/mL (for OOMW-B) to 391.8 μg/mL (for OOMW-A). The microbiological analysis of OOMW samples revealed only detectable viable bacteria (102 CFU/mL) of the lactic acid bacteria (LAB) group. Two distinct LAB strains, Lactiplantibacillus plantarum OMW1 and Leuconostoc mesenteroides OMW23, were identified. These strains demonstrated notable acidification capabilities and produced antibacterial compounds. In conclusion, despite the high polyphenolic content and microbiological suitability of OOMW, the presence of micro-contaminants hinders their use in food production. Thus, further studies are underway to investigate OOMW from organically farmed olives for bakery product functionalization, employing the two selected LAB strains resistant to olive polyphenols as leavening agents.

Human microbiota peptides: important roles in human health

Covering: 1974 to 2024Human microbiota consist of a diverse array of microorganisms, such as bacteria, Eukarya, archaea, and viruses, which populate various parts of the human body and live in a cooperatively beneficial relationship with the host. They play a crucial role in supporting the functional balance of the microbiome. The coevolutionary progression has led to the development of specialized metabolites that have the potential to substitute traditional antibiotics in combating global health challenges. Although there has been a lot of research on the human microbiota, there is a considerable lack of understanding regarding the wide range of peptides that these microbial populations produce. Particularly noteworthy are the antibiotics that are uniquely produced by the human microbiome, especially by bacteria, to protect against invasive infections. This review seeks to fill this knowledge gap by providing a thorough understanding of various peptides, along with their in-depth biological importance in terms of human disorders. Advancements in genomics and the understanding of molecular mechanisms that control the interactions between microbiota and hosts have made it easier to find peptides that come from the human microbiome. We hope that this review will serve as a basis for developing new therapeutic approaches and personalized healthcare strategies. Additionally, it emphasizes the significance of these microbiota in the field of natural product discovery and development.

Potentially probiotic NPL 1334 strain of Enterococcus durans benefits rats with diet-induced hypercholesterolemia

PURPOSE

To study the potential of a candidate probiotic strain belonging to the Enterococcus durans species in alleviating hypercholesterolemia and improving the microbial milieu of rat gut.

METHODS

A previously isolated and characterized E. durans strain NPL 1334 was further screened in vitro for its bile salt hydrolyzation and cholesterol assimilation ability. An in vivo trial using diet-induced hypercholesterolemic rats was conducted to evaluate the effects of the administered test probiotic strain on the animal's blood biochemical parameters such as total cholesterol (TC), high-density lipopolysaccharides (HDL), low-density lipopolysaccharides (LDL), triglycerides (TG), on body weight, oxidative stress markers, and its impact on intestinal and fecal microbiota as well as a histopathological examination of the test animal's livers.

RESULTS

E. durans strain showed good bile salt hydrolyzing ability and ample cholesterol assimilation in vitro. Probiotic-fed hypercholesterolemic rats showed significantly lowered cholesterol, triglyceride and LDL levels. The body weight of probiotic-fed rats was reduced as compared to the control. E. durans also stimulated the growth of beneficial LAB in the intestine of experimental rats and did not harm the liver of the experimental rats.

CONCLUSION

E. durans can be a natural therapeutic alternative to manage diet-induced hypercholesterolemia and may eventually enhance anti-cholesterolemic therapies.

Evaluating the antibacterial efficacy of bee venom against multidrug-resistant pathogenic bacteria: Escherichia coli, Salmonella typhimurium, and Enterococcus faecalis

Bee venom (BV) represents a promising natural alternative to conventional antibiotics, particularly significant given its broad-spectrum antimicrobial activity and potential to address the growing challenge of antimicrobial resistance. The prevalence of antimicrobial-resistant microorganisms (AMR) is a global burden that affects human health and the economies of different countries. As a result, several scientific communities around the world are searching for safe alternatives to antibiotics. In this context, the present study represents a comprehensive investigation to evaluate the antibacterial effect of bee venom (BV) against Escherichia coli ATCC8739, Salmonella typhimurium ATCC14028, and Enterococcus faecalis ATCC25923. One mg of BV was extracted using 1 mL of DMSO to obtain a 1000 µg/mL solution. The chemical profile of the BV extract was determined using GC-MS, which revealed the presence of bioactive molecules with antimicrobial properties, such as astaxanthin, hycanthone, and fucoxanthin. The BV extract was tested against bacterial strains using different concentrations to obtain the minimum inhibitory concentrations (MIC) and minimum bactericidal concentrations (MBC). The results obtained revealed a high antibacterial activity of BV against the three strains with the highest MIC/MBC values of 12.5/25 µgml- 1 against S. typhimurium. The antibacterial activity of the BV extract was compared to five conventional antibiotics using the disc diffusion method. The results showed a high antibacterial activity of the BV extract compared to different antibiotics with the largest inhibition zone obtained against E. faecalis at a value of 15 ± 0.22 mm compared to 9 ± 0.13 for azithromycin. The mode of action of BV, examined using scanning electron microscopy, proved a high effect of BV on the permeability of the bacterial plasma membrane. This study demonstrates bee venom's promising potential as a natural and eco-friendly antimicrobial agent, with activity against multiple bacterial strains, suggesting it may serve as an alternative to conventional antibiotics. The findings highlight the potential applications of BV in medical, agricultural, and veterinary fields, offering a sustainable solution to combat antimicrobial resistance. However, further studies are needed to fully assess its broad-spectrum antibacterial potential.Clinical trial number Not applicable.

Probiotics and Food Bioactives: Unraveling Their Impact on Gut Microbiome, Inflammation, and Metabolic Health

This review paper delves into the role of probiotics and food bioactives in influencing gut health and overall well-being, within the context of probiotics and food bioactives, emphasizing their roles in modulating inflammation, gut microbiota, and metabolic health. Probiotics are defined as live microorganisms that confer health benefits to the host, primarily through their impact on the gut microbiome; a complex community of microorganisms crucial for maintaining health. The review aims to elucidate how probiotics, incorporated into both traditional and modern food systems, can enhance gut health and address metabolic disorders. It examines the types of probiotics present in various foods and their mechanisms of action, including their effects on immune function and metabolic health. By exploring the links between probiotics and health outcomes such as digestive health, immune support, and mental health, the review identifies specific conditions where probiotics show significant promise. Hurldes such as inconsistencies in research findings, variability in probiotic strains, and dosages are addressed. The paper also suggests future research directions, including the potential for personalized probiotic interventions. The review concludes by summarizing key findings and emphasizing the critical role of probiotics in food systems for promoting overall health and mitigating metabolic diseases.

Antimicrobial activity of Monascus purpureus-derived red pigments against Salmonella typhimurium, Escherichia coli, and Enterococcus faecalis

The rise of antimicrobial-resistant microorganisms (AMR) poses a significant global challenge to human health and economic stability. In response, various scientific communities are seeking safe alternatives to antibiotics. This study comprehensively investigates the antibacterial effects of red dye derived from Monascus purpureus against three bacterial pathogens: Salmonella typhimurium ATCC14028, Escherichia coli ATCC8739, and Enterococcus faecalis ATCC25923. The dye was extracted from the Monascus purpureus ATCC16436 strain, using 1 mg of red dye in 1 ml of DMSO to achieve a concentration of 1000 µg/ml. The chemical profile of the red dye extract was analyzed using GC-MS analysis, confirming the presence of several bioactive antimicrobial compounds, including aspidospermidin-17-ol, 1-acetyl-16-methoxy, octanoic acid, and hexadecanoic acid methyl ester. The extract was tested against the bacterial strains at varying concentrations to determine the minimum inhibitory concentrations (MIC) and minimum bactericidal concentrations (MBC). The results demonstrated significant antibacterial activity, with the highest MIC and MBC values of 6.25/12.5 µg/ml against S. typhimurium. The antibacterial activity of the red dye was compared to five conventional antibiotics using the disc diffusion method, revealing superior effectiveness, particularly against S. typhimurium, with an inhibition zone measuring 20 ± 0.22 mm. Scanning electron microscopy was employed to explore the mechanism of action of the red dye extract, highlighting its impact on bacterial plasma membrane permeability and its interference with cellular energy production. These findings suggest that the Monascus purpureus-derived red dye extract represents a promising natural alternative to conventional antibiotics, demonstrating potent antibacterial activity and potential as a novel therapeutic agent in combating antimicrobial resistance.

Metagenomic Insights into Pigeon Gut Microbiota Characteristics and Antibiotic-Resistant Genes

BACKGROUND

Antibiotics were extensively used in the pigeon breeding industry previously to promote growth and prevent disease, leading to the spread of antibiotic-resistant genes (ARGs) in gut microbes, which has become a major public health concern.

METHODS

A metagenomic analysis was performed to investigate the gut microbial communities and ARGs in young and older pigeons in Nanjing, Jiangsu Province, China.

RESULTS

There were obviously distinct gut microbiota and functional compositions between young and older pigeons. Both Pseudomonadota and Uroviricota were dominant in young and older pigeons. Although sharing 24 gut microbiota phyla between young and older pigeons, Bacillota and Pseudomonadota were the dominant microbial phyla in them, respectively. Besides the shared metabolic pathways and biosynthesis of secondary metabolites, biosynthesis of amino acids was the most abundant Kyoto Encyclopedia of Genes and Genomes (KEGG) function in young pigeons, while microbial metabolism in diverse environments was abundant in older pigeons. A total of 142 ARGs conferring multidrug resistance, tetracycline, and aminoglycoside resistance were identified; the most abundant gene in young pigeons was tetracycline-tetW, while in older pigeons, it was multidrug-acrB.

CONCLUSIONS

Our findings revealed significant differences in the gut microbial communities and ARGs between young and older pigeons. This study enhances our understanding of pigeon gut microbiota and antibiotic resistomes, contributing to knowledge-based sustainable pigeon meat production.

Distinct phenotypes of salivaricin-producing Ligilactobacillus salivarius isolated from the gastrointestinal tract of broiler chickens and laying hens

Ligilactobacillus salivarius harbors bacteriocin genes in its repA-type megaplasmid, specifically salivaricin P (salP), a class IIb bacteriocin. This study aimed to differentiate 25 salP-positive Lig. salivarius strains isolated from the gastrointestinal tract (GIT) of broilers and laying hens. Results showed that 12 isolates were classified as Type A, with active bacteriocins, while the rest were Type B, with no active bacteriocins. In vitro and in silico characterization of salP bacteriocins revealed narrow-spectrum antibacterial activity against Listeria monocytogenes and Enterococcus faecalis. SalP bacteriocins were predicted as positively charged, hydrophobic, small molecular weight (α, 4.097 kDa; ß, 4.285 kDa) bacteriocins with characteristic GXXXG motif. Investigation of the salP gene cluster based on genomic data revealed that Type B strains lacked the lanT and hlyD genes that encode export proteins dedicated to the modification and extracellular transport of mature salP peptides. However, two Type B strains (B4311 and B5258) showed inhibitory activity against L. monocytogenes ATCC19114. Multiplex PCR analysis and synteny mapping analysis revealed that B4311 and B5258 strains harbored the lanT gene, highlighting the importance of LanT protein in the cleavage of leader peptide and excretion of mature peptides. Further analysis revealed that the resistance of Type B strains to salP was attributable to the presence of a dedicated immunity protein, blurring the evolutionary significance of producing active bacteriocins for competitive advantage. Additionally, the loss of export proteins occurred in a polyphyletic manner, consistent with the genetic plasticity of the repA-type megaplasmid. This suggests that the loss of lanT and hlyD is likely in the presence of limited nutritional competitors. In conclusion, the observed differences in salivaricin production of Lig. salivarius exist independent of isolation host and that Type A and Type B strains can coexist in the same environment. Finally, the functional characterization of active salP allows for a better understanding of its potential to control specific bacteria in human food and animal production.

Antibiotic Resistance in Fermented Foods Chain: Evaluating the Risks of Emergence of Enterococci as an Emerging Pathogen in Raw Milk Cheese

Fermented foods, particularly fermented dairy products, offer significant health benefits but also present serious concerns. Probiotic bacteria, such as lactic acid bacteria (LAB), found in these foods have been strongly linked to the selection and dissemination of antibiotic resistance genes (ARGs). This study aims to examine the potential risks associated with fermented foods, despite their importance in human nutrition, by analyzing the entire production chain from raw material acquisition to storage. Focusing on cheese production as a key fermented food, the study will investigate various aspects, including dairy farm management, milk acquisition, milk handling, and the application of good manufacturing practices (GMP) and good hygiene practices (GHP) in cheese production. The findings of this review highlight that ARGs found in LAB are similar to those observed in hygiene indicator bacteria like E. coli and pathogens like S. aureus. The deliberate use of antibiotics in dairy farms and the incorrect use of disinfectants in cheese factories contribute to the prevalence of antibiotic-resistant bacteria in cheeses. Cheese factories, with their high frequency of horizontal gene transfer, are environments where the microbiological diversity of raw milk can enhance ARG transfer. The interaction between the raw milk microbiota and other environmental microbiotas, facilitated by cross-contamination, increases metabolic communication between bacteria, further promoting ARG transfer. Understanding these bacterial and ARG interactions is crucial to ensure food safety for consumers.

High prevalence and plasmidome diversity of optrA-positive enterococci in a Shenzhen community, China

Background

The emergence of optrA, which can confer resistance to phenicols and oxazolidinones in Enterococcus spp., poses a growing public health threat.

Methods

102 optrA-positive enterococci (OPEs) including various species were isolated from feces of 719 healthy volunteers in a Shenzhen community, China. Antimicrobial susceptibility of these isolates was tested. Whole-genome sequencing and bioinformatics analysis were performed to characterize molecular epidemiology of OPEs.

Results

Compared to optrA-negative enterococci (ONEs), antimicrobial resistance (linezolid, florfenicol, doxycycline, erythromycin and ciprofloxacin) and presence of antimicrobial resistance genes (ARGs) (fexA, cat, tet(M), erm(A), erm(B) and etc) were higher in OPEs. Phylogenetic analysis revealed that high similarly (19-338 SNPs) was observed between the optrA-positive E. faecalis from community and the strains from patients, animals, and environment. In 102 OPEs, the optrA gene was detected on the chromosome (n = 36), on plasmids (n = 62), or both (n = 4). A diverse range of optrA-carrying plasmid types was identified. The rep9-plasmid replicons were widely detected in E. faecalis (44/66), whereas repUS1-plasmid replicons were widely identified in other enterococcal species (7/66). Most of all ARGs harbored by isolates were co-existed on optrA-carrying plasmids, suggesting that the acquisition of optrA-carrying plasmids will pose a greater threat to public health. Notably, the pAD1 (rep9 family) + DOp1-type plasmids should receive more attention for the transfer of optrA given their high prevalence (36.36%), high number of co-located ARGs with optrA (83.87% of total ARGs) and presence in multiple sources. Tn6674, IS1216E, ISEnfa1 and ISEnfa5 are related to the transfer of chromosomal and plasmids-derived optrA, respectively. The bcrABDR gene cluster, fexA, and erm(A) were frequently identified surrounding optrA and may be transferred with optrA via IS1216E or ISEnfa1.

Conclusion

The transfer of optrA gene is related to a variety of mobile elements (including plasmids, insertion sequences, transposons), which will promote the horizontal transfer of optrA. Moreover, many ARGs co-exist with optrA and could co-transfer with optrA. The acquisition of OPEs and optrA-carrying plasmids will pose a greater threat to public health and should be obtained more attention, especially optrA-positive E. faecalis and pAD1 + DOp1-type plasmids.

Biofunctional attributes and storage study of milk fermented by Enterococcus italicus

Lactic acid bacteria are probiotics in the intestines and have been widely used as natural antioxidants in the food industry. In this study, Enterococcus italicus FM5 with strong antioxidant ability was isolated from fresh milk. The safety evaluation showed that E. italicus FM5 was sensitive to ampicillin, chloramphenicol, erythromycin, vancomycin, rifampicin, and tetracycline, and was not hemolytic. Meanwhile, the whole genome information and biofunctional attributes of this strain were determined and analyzed. Subsequently, E. italicus FM5 was co-cultured with traditional yogurt starters (Streptococcus thermophilus and Lactobacillus bulgaricus) to make fermented milk. The results showed that the addition of E. italicus FM5 could improve the oxygen free radical scavenging ability of the fermented milk, and the scavenging rates of DPPH, ABTS, OH-, and O2- radicals reaching up to 95.54 %, 88.35 %, 93.65 %, and 60.29 %, respectively. Furthermore, the addition of E. italicus FM5 reduced the curd time and improved the water holding capacity of the fermented milk. Besides, the growth of Lb. bulgaricus was significantly promoted when co-cultured with E. italicus FM5, thus the survival cells were increased compared with the traditional fermentation processes. Therefore, this study emphasized the potential to manufacture fermented milk by the co-cultivation of E. italicus with traditional yogurt starters.

Antioxidative and immunity-enhancing effects of heat-killed probiotic Enterococcus faecium KU22001 without toxin or antibiotic resistance

This study evaluated the probiotic properties, safety profile, and antioxidative and immune system-enhancing effects of Enterococcus faecium strains isolated from human infant feces. E. faecium KU22001, E. faecium KU22002, and E. faecium KU22005 exhibited potential probiotic properties; however, to eliminate concerns about toxin production and antibiotic resistance, the E. faecium strains were heat-treated prior to experimental usage. E. faecium KU22001 showed the highest antioxidant activity and lowest reactive oxygen species production among the three strains. The immune system-enhancing effects of heat-killed E. faecium strains were evaluated using a nitric oxide assay. E. faecium KU22001 induced an increase in the mRNA expression of inducible nitric oxide synthase, cyclooxygenase-2, and proinflammatory cytokines, including tumor necrosis factor-α, interleukin-1β, and interleukin-6 in RAW 264.7 cells. Furthermore, E. faecium KU22001 activated the mitogen-activated protein kinase pathway, which was a key regulator of the immune system. These results demonstrate the potential use of E. faecium KU22001 as a multifunctional food material.

A rationally designed antigen elicits protective antibodies against multiple nosocomial Gram-positive pathogens

ESKAPE pathogens are responsible for complicated nosocomial infections worldwide and are often resistant to commonly used antibiotics in clinical settings. Among ESKAPE, vancomycin-resistant Enterococcus faecium (VREfm) and methicillin-resistant Staphylococcus aureus (MRSA) are two important Gram-positive pathogens for which non-antibiotic alternatives are urgently needed. We previously showed that the lipoprotein AdcA of E. faecium elicits opsonic and protective antibodies against E. faecium and E. faecalis. Prompted by our observation, reported here, that AdcA also elicits opsonic antibodies against MRSA and other clinically relevant Gram-positive pathogens, we identified the dominant epitope responsible for AdcA cross-reactive activity and designed a hyper-thermostable and multi-presenting antigen, Sc(EH)3. We demonstrate that antibodies raised against Sc(EH)3 mediate opsonic killing of a wide-spectrum of Gram-positive pathogens, including VREfm and MRSA, and confer protection both in passive and active immunisation models. Our data indicate that Sc(EH)3 is a promising antigen for the development of vaccines against different Gram-positive pathogens.

The Probiotic Enterococcus Lactis SF68 as a Potential Food Fermentation Microorganism for Safe Food Production

Due to the reports describing virulent and multidrug resistant enterococci, their use has become a topic of controversy despite most of them being safe and commonly used in traditionally fermented foods worldwide. We have characterized Enterococcus lactis SF68, a probiotic strain approved by the European Food Safety Authority (EFSA) for use in food and feed, and find that it has a remarkable potential in food fermentations. Genome analysis revealed the potential of SF68 to metabolize a multitude of carbohydrates, including lactose and sucrose, which was substantiated experimentally. Bacteriocin biosynthesis clusters were identified and SF68 was found to display a strong inhibitory effect against Listeria monocytogenes. Fermentation-wise, E. lactis SF68 was remarkably like Lactococcus lactis and displayed a clear mixed-acid shift on slowly fermented sugars. SF68 could produce the butter aroma compounds, acetoin and diacetyl, the production of which was enhanced under aerated conditions in a strain deficient in lactate dehydrogenase activity. Overall, E. lactis SF68 was found to be versatile, with a broad carbohydrate utilization capacity, a capacity for producing bacteriocins, and an ability to grow at elevated temperatures. This is key to eliminating pathogenic and spoilage microorganisms that are frequently associated with fermented foods.

Chemical Profile and In Vitro Gut Microbiota Modulation of Wild Edible Mushroom Phallus atrovolvatus Fruiting Body at Different Maturity Stages

Phallus atrovolvatus, a wild edible mushroom, has attracted increasing interest for consumption due to its unique taste and beneficial health benefits. This study determined the chemical components in the so-called fruiting body during the egg and mature stages and investigated its gut microbiota-modulating activities. The egg stage contained higher total carbohydrates, dietary fiber, glucans, ash, and fat, while the total protein content was lower than in the mature stage. Two consumption forms, including cooked mushrooms and a mushroom aqueous extract from both stages, were used in this study. An in vitro gut fermentation was performed for 24 h to assess gut microbiota regulation. All mushroom-supplemented fermentations increased short-chain fatty acid (SCFA) production compared to the blank control. Furthermore, all mushroom supplementations promoted the growth of Bifidobacterium and Streptococcus. Samples from the mature stage increased the relative abundance of Clostridium sensu stricto 1, while those from the egg stage increased the Bacteroides group. The inhibition of harmful bacteria, including Escherichia-Shigella, Klebsiella, and Veillonella, was only observed for the mature body. Our findings demonstrate that P. atrovolvatus exhibits potential benefits on gut health by promoting SCFA production and the growth of beneficial bacteria, with the mature stage demonstrating superior effects compared to the egg stage.

Assessing the impact of hatching system and body weight on the growth performance, caecal short-chain fatty acids, and microbiota composition and functionality in broilers

BACKGROUND

Variations in body weight (BW) remain a significant challenge within broiler flocks, despite uniform management practices. Chicken growth traits are influenced by gut microbiota, which are in turn shaped by early-life events like different hatching environments and timing of first feeding. Chicks hatched in hatcheries (HH) experience prolonged feed deprivation, which could adversely impact early microbiota colonization. Conversely, hatching on-farm (HOF) allows early feeding, potentially fostering a more favorable gut environment for beneficial microbial establishment. This study investigates whether BW differences among broilers are linked to the disparities in gut microbiota characteristics and whether hatching systems (HS) impact the initial microbial colonization of broilers differing in BW, which in turn affects their growth patterns. Male Ross-308 chicks, either hatched in a hatchery or on-farm, were categorized into low (LBW) and high (HBW) BW groups on day 7, making a two-factorial design (HS × BW). Production parameters were recorded periodically. On days 7, 14, and 38, cecal volatile fatty acid (VFA) and microbiota composition and function (using 16 S rRNA gene sequencing and PICRUSt2) were examined.

RESULTS

HOF chicks had higher day 1 BW, but HH chicks caught up within first week, with no further HS-related performance differences. The HBW chicks remained heavier attributed to higher feed intake rather than improved feed efficiency. HBW group had higher acetate concentration on day 14, while LBW group exhibited higher isocaproate on day 7 and isobutyrate on days 14 and 38. Microbiota analyses revealed diversity and composition were primarily influenced by BW than by HS, with HS having minimal impact on BW-related microbiota. The HBW group on various growth stages was enriched in VFA-producing bacteria like unclassified Lachnospiraceae, Alistipes and Faecalibacterium, while the LBW group had higher abundances of Lactobacillus, Akkermansia and Escherichia-Shigella. HBW microbiota presented higher predicted functional potential compared to the LBW group, with early colonizers exhibiting greater metabolic activity than late colonizers.

CONCLUSIONS

Despite differences in hatching conditions, the effects of HS on broiler performance were transient, and barely impacting BW-related microbiota. BW variations among broilers are likely linked to differences in feed intake, VFA profiles, and distinct microbiota compositions and functions.

Dissemination, virulence characteristic, antibiotic resistance determinants of emerging linezolid and vancomycin-resistant Enterococcus spp. in fish and crustacean

Enterococci are emerging nosocomial pathogens. Their widespread distribution causes them to be food contaminants. Furthermore, Enterococci can colonize various ecological niches and diffuse into the food chain via contaminated animals and foods because of their remarkable tolerance to unfavorable environmental circumstances. Due to their potential dissemination to humans, antimicrobial-resistant Enterococci in fish are a worldwide health issue. This study characterized AMR, ARGs, VAGs, gelatinase activity, and biofilm formation in Enterococcus spp. recovered from fish and seafood and evaluated potential correlations. 54 Enterococcus spp. strains(32.73 %)were isolated from 165 samples (75 Oreochromis niloticus, 30 Argyrosomus regius, and 60 Shrimp), comprising 30 Enterococcus faecalis (55.6 %) and 24 Enterococcus faecium (44.4 %) with total 32.73 % (54/165), The maximum prevalence rate of Enterococcus spp. was observed in Nile tilapia (34/54; 63 %), followed by shrimp (14/54; 25.9 %) and Argyrosomus regius (6/54; 11.1 %). The maximum prevalence rate of E. faecalis was observed in Nile tilapia (22/30; 73.3 %), followed by shrimp (8/30; 26.7 %) with significant differences. The prevalence rate of E. faecium was observed in Nile tilapia (12/24; 50 %), followed by shrimp (6/24,25 %). E. faecium is only isolated from Argyrosomus regius (6/24,25 %). Isolates exhibited high resistance against both tetracycline (90.7 %) and erythromycin(88.9 %), followed by gentamycin (77.8 %), ciprofloxacin (74.1 %), levofloxacin (72.2 %), penicillin (44.4 %), vancomycin (37 %), and linezolid (20.4 %). 50 strains (92.6 %) exhibited resistance to more than two antibiotics, 5 strains (10 %) were XDR, and the remaining 45 strains (90 %) were classified as MDR. 92.6 % of the isolates had MARindices >0.2, indicating they originated in settings with a high risk of contamination. Additionally, ten ARGs were identified, with tet(M) 92.6 %, followed by erm(B) (88.9 %), aac(6')-Ie-aph(2″)-Ia(77.8 %), tet(K) (75.9 %), gyrA (74.1 %), blaZ (48.1 %), vanA (37 %), vanB (31.5 %), optrA (20.4 %), and catA(3.7 %). Biofilm formation and gelatinase activity were observed in 85.2 %, and 61.1 % of the isolates, respectively. A total of 11 VAGs were detected, with gelE as the most prevalent (83.3 %) followed by agg(79.6 %), pil (74.1 %), both sprE and asa1 (72.2 %), hyl (70.4 %), eps(68.5 %), EF3314 (57.4 %), ace (50 %), and cylA (35.2 %) with no detection of cylB. In conclusion, the emergence of linezolid-resistant -vancomycin-resistant enterococci recovered from Egyptian fish and shrimp, suggests that fish and seafood might participate a fundamental part in the emergence of antimicrobial resistance among humans.

Species prevalence, virulence genes, and antibiotic resistance of enterococci from food-producing animals at a slaughterhouse in Turkey

Healthy cattle, sheep, and goats can be reservoirs for gastrointestinal pathogenic fecal enterococci, some of which could be multidrug-resistant to antimicrobials. The objective of this study was to determine the prevalence and diversity of Enterococcus species in healthy sheep, goat, and cattle carcasses, as well as to analyze the antimicrobial resistance phenotype/genotype and the virulence gene content. During 2019-2020, carcass surface samples were collected from 150 ruminants in a slaughterhouse. A total of 90 enterococci, comprising five species, were obtained. The overall prevalence of enterococci was found to be 60%, out of which 37.7% were identified as Enterococcus (E.) hirae, 33.3% as E. casseliflavus, 15.5% as E. faecium, 12.2% as E. faecalis, and 1.1% as E. gallinarum. Virulence-associated genes of efaA (12.2%) were commonly observed in the Enterococcus isolates, followed by gelE (3.3%), asaI (3.3%), and ace (2.2%). High resistance to quinupristin-dalfopristin (28.8%), tetracycline (21.1%), ampicillin (20%), and rifampin (15.5%) was found in two, four, four, and five of the Enterococcus species group, respectively. The resistance of Enterococcus isolates to 11 antibiotic groups was determined and multidrug resistant (MDR) strains were found in 18.8% of Enterococcus isolates. Characteristic resistance genes were identified by PCR with an incidence of 6.6%, 2.2%, 1.1%, 1.1%, 1.1%, and 1.1% for the tetM, ermB, ermA, aac(6')Ie-aph(2")-la, VanC1, and VanC2 genes in Enterococcus isolates, respectively. Efflux pump genes causing multidrug resistance were detected in Enterococcus isolates (34.4%). The results showed that there were enterococci in the slaughterhouse with a number of genes linked to virulence that could be harmful to human health.

Bad to the bone? - Genomic analysis of Enterococcus isolates from diverse environments reveals that most are safe and display potential as food fermentation microorganisms

Enterococci comprise a group of lactic acid bacteria (LAB) with considerable potential to serve as food fermentation microorganisms. Unfortunately, enterococci have received a lot of negative attention, due to the occurrence of pathogenic and multidrug resistant strains. In this study, we used genomics to select safe candidates among the forty-four studied enterococcal isolates. The genomes of the forty-four strains were fully sequenced and assessed for presence of virulence and antibiotic resistance genes. Nineteen isolates belonging to the species Enterococcus lactis, Enterococcus faecium, Enterococcus durans, and Enterococcus thailandicus, were deemed safe from the genome analysis. The presence of secondary metabolite gene clusters for bacteriocins was assessed, and twelve candidates were found to secrete antimicrobial compounds effective against Listeria monocytogenes isolated from cheese and Staphylococcus aureus. Physiological characterization revealed nineteen industrial potentials; all strains grew well at 42 °C and acidified 1.5 hours faster than their mesophilic counterpart Lactococcus lactis, with which they share metabolism and flavor forming ability. We conclude that a large fraction of the examined enterococci were safe and could serve as excellent food fermentation microorganisms with inherent bioprotective abilities.

Identification and Safety Assessment of Enterococcus casseliflavus KB1733 Isolated from Traditional Japanese Pickle Based on Whole-Genome Sequencing Analysis and Preclinical Toxicity Studies

The present study involves the precise identification and safety evaluation of Enterococcus casseliflavus KB1733, previously identified using 16S rRNA analysis, through whole-genome sequencing, phenotypic analysis, and preclinical toxicity studies. Analyses based on the genome sequencing data confirm the identity of KB1733 as E. casseliflavus and show that the genes related to vancomycin resistance are only present on the chromosome, while no virulence factor genes are present on the chromosome or plasmid. Phenotypic analyses of antibiotic resistance and hemolytic activity also indicated no safety concerns. A bacterial reverse mutation test showed there was no increase in revertant colonies of heat-killed KB1733. An acute toxicity test employing heat-killed KB1733 at a dose of 2000 mg/kg body weight in rats resulted in no deaths and no weight gain or other abnormalities in the general condition of the animals, with renal depression foci and renal cysts only occurring at the same frequency as in the control. Taking the background data into consideration, the effects on the kidneys observed in the current study were not caused by KB1733. Our findings suggest that KB1733 is non-pathogenic to humans/animals, although further studies involving repeated oral toxicity tests and/or clinical tests are required.

Silk-derived sericin/fibroin mixture drink fermented with plant-derived Lactococcus lactis BM32-1 improves constipation and related microbiota: a randomized, double-blind, and placebo-controlled clinical trial

We previously showed through clinical trials that one plant-derived lactic acid bacteria (LAB) can improve constipation. We preliminarily found that the plant-derived LAB Lactococcus lactis BM32-1 can grow in a mixture of sericin and fibroin, which are extracted from silk and have been reported to help promote health. Thus, in the present study, we evaluated the favorable effect of a sericin/fibroin mixture (S/F-M), which was extracted from silk prepared from cocoons reared in an aseptic rearing system using an artificial diet, fermented with the BM32-1 strain through a clinical trial. The trial was conducted at Hiroshima University from June to October 2022 as a double-blind, placebo-controlled, randomized parallel-group comparative study with 50 eligible subjects (aged 23-71) who had an average defecation frequency of less than 5 times per week. The subjects were instructed to drink 100 mL of fermented S/F-M or placebo every day. After the 12 weeks of the clinical trial period, the average defecation frequency increased significantly-1.4 times higher than that at baseline in the test group-as compared with the placebo group. Furthermore, the fecal microbiota was also compared before and after treatment, revealing that intake of the fermented S/F-M significantly multiplied the relative abundance of the genera Enterococcus and Clostridium, which have been reported to contribute to the amelioration of constipation by improving the gut microbiota and producing butyric acid, respectively. In conclusion, the S/F-M fermented using the BM32-1 strain improves defecation frequency through alteration of the gut microbiota.

Enterococcus faecalis: implications for host health

The microbiota represents a crucial area of research in maintaining human health due to its potential for uncovering novel biomarkers, therapies, and molecular mechanisms relevant to population identification and experimental model characterization. Among these microorganisms, Enterococcus faecalis, a Gram-positive bacterium found in the gastrointestinal tract of humans and animals, holds particular significance. Strains of this bacterial species have sparked considerable debate in the literature due to their dual nature; they can either be utilized as probiotics in the food industry or demonstrate resistance to antibiotics, potentially leading to severe illness, disability, and death. Given the diverse characteristics of Enterococcus faecalis strains, this review aims to provide a comprehensive understanding of their impact on various systems within the host, including the immunological, cardiovascular, metabolic, and nervous systems. Furthermore, we summarize the bacterium-host interaction characteristics and molecular effects to highlight their targets, features, and overall impact on microbial communities and host health.

In Vitro Profiling of Potential Fish Probiotics, Enterococcus hirae Strains, Isolated from Jade Perch, and Safety Properties Assessed Using Whole Genome Sequencing

The demands of intensified aquaculture production and escalating disease prevalence underscore the need for efficacious probiotic strategies to enhance fish health. This study focused on isolating and characterising potential probiotics from the gut microbiota of the emerging aquaculture species jade perch (Scortum barcoo). Eighty-seven lactic acid bacteria and 149 other bacteria were isolated from the digestive tract of five adult jade perch. The screening revealed that 24 Enterococcus hirae isolates inhibited the freshwater pathogens Aeromonas sobria and Streptococcus iniae. Co-incubating E. hirae with the host gut suspensions demonstrated a two- to five-fold increase in the size of growth inhibition zones compared to the results when using gut suspensions from tilapia (a non-host), indicating host-specificity. Genome analysis of the lead isolate, E. hirae R44, predicted the presence of antimicrobial compounds like enterolysin A, class II lanthipeptide, and terpenes, which underlay its antibacterial attributes. Isolate R44 exhibited desirable probiotic characteristics, including survival at pH values within the range of 3 to 12, bile tolerance, antioxidant activity, ampicillin sensitivity, and absence of transferable antimicrobial resistance genes and virulence factors commonly associated with hospital Enterococcus strains (IS16, hylEfm, and esp). This study offers a foundation for sourcing host-adapted probiotics from underexplored aquaculture species. Characterisation of novel probiotics like E. hirae R44 can expedite the development of disease mitigation strategies to support aquaculture intensification.

Evaluating Enterococcus faecium9 N-2 as a probiotic candidate from traditional village white cheese

In this study, various functional and probiotic attributes of the Enterococcus faecium 9 N-2 strain isolated from village-style white cheese were characterized, while also assessing its safety. To achieve this, we conducted an in vitro analysis of several key probiotic properties exhibited by the 9 N-2 strain. Notably, this strain demonstrated robust resilience to low pH, high bile salt concentrations, lysozyme, pepsin, pancreatin, and phenol. Furthermore, this strain displayed exceptional auto-aggregation capabilities and moderate co-aggregation tendencies when interacting with Escherichia coli. The cell-free supernatant derived from strain 9 N-2 exhibited significant antimicrobial activity against the tested pathogens. The strain exhibited resistance to gentamicin, meropenem, and bacitracin, while remaining susceptible to vancomycin and various other antibiotics. Furthermore, it was found that E. faecium 9 N-2 possessed the capacity to produce the phytase enzyme. When all the results of this study are evaluated, it is thought that 9 N-2 strain has superior probiotic properties, and therefore it can be used as probiotic in food, medicine, and animal feed in the future. In addition, further in vivo tests should be performed to fully understand its effects and mechanisms of action and to confirm its safety and probiotic effects. Further research and clinical trials are also needed to identify new strains with potential probiotic properties.

Study of an Enterococcus faecium strain isolated from an artisanal Mexican cheese, whole-genome sequencing, comparative genomics, and bacteriocin expression

Enterococci are ubiquitous microorganisms in almost all environments, from the soil we step on to the food we eat. They are frequently found in naturally fermented foods, contributing to ripening through protein, lipid, and sugar metabolism. On the other hand, these organisms are also leading the current antibiotic resistance crisis. In this study, we performed whole-genome sequencing and comparative genomics of an Enterococcus faecium strain isolated from an artisanal Mexican Cotija cheese, namely QD-2. We found clear genomic differences between commensal and pathogenic strains, particularly in their carbohydrate metabolic pathways, resistance to vancomycin and other antibiotics, bacteriocin production, and bacteriophage and CRISPR content. Furthermore, a bacteriocin transcription analysis performed by RT-qPCR revealed that, at the end of the log phase, besides enterocins A and X, two putative bacteriocins not reported previously are also transcribed as a bicistronic operon in E. faecium QD-2, and are expressed 1.5 times higher than enterocin A when cultured in MRS broth.

Genomic and phenotypic characterisation of Enterococcus mundtii AM_AQ_BC8 for its anti-biofilm, antimicrobial and probiotic potential

Enterococcus mundtii AM_AQ_BC8 isolated from biofouled filtration membrane was characterised as a potential probiotic bacterium showing strong L-lactic acid-producing capability. Experimental studies revealed that E. mundtii AM_AQ_BC8 possess antibiofilm and antimicrobial ability too, as tested against strong biofilm-forming bacteria like Pseudomonas spp. The present study has evaluated the genetic potential of E. mundtii AM_AQ_BC8 through genome sequencing. Whole genome analysis revealed the presence of key genes like ldh_1 and ldh_2 responsible for lactic acid production along with genes encoding probiotic features such as acid and bile salt resistance (dnaK, dnaJ, argS), fatty acid synthesis (fabD, fabE) and lactose utilisation (lacG, lacD). The phylogenomic analysis based on OrthoANI (99.85%) and dDDH (96.8%) values revealed that the strain AM_AQ_BC8 shared the highest homology with E. mundtii. The genome sequence of strain AM_AQ_BC8 has been deposited to NCBI and released with GenBank accession no. SAMN32531201. The study primarily demonstrated the probiotic potential of E. mundtii AM_AQ_BC8 isolate, for L-lactate synthesis in high concentration (8.98 g/L/day), which also showed anti-biofilm and antimicrobial activities.

Antimicrobial Activity of Synthetic Enterocins A, B, P, SEK4, and L50, Alone and in Combinations, against Clostridium perfringens

Multidrug-resistant Clostridium perfringens infections are a major threat to the poultry industry. Effective alternatives to antibiotics are urgently needed to prevent these infections and limit the spread of multidrug-resistant bacteria. The aim of the study was to produce by chemical synthesis a set of enterocins of different subgroups of class II bacteriocins and to compare their spectrum of inhibitory activity, either alone or in combination, against a panel of twenty C. perfringens isolates. Enterocins A, P, SEK4 (class IIa bacteriocins), B (unsubgrouped class II bacteriocin), and L50 (class IId leaderless bacteriocin) were produced by microwave-assisted solid-phase peptide synthesis. Their antimicrobial activity was determined by agar well diffusion and microtitration methods against twenty C. perfringens isolates and against other pathogens. The FICINDEX of different combinations of the selected enterocins was calculated in order to identify combinations with synergistic effects. The results showed that synthetic analogs of L50A and L50B were the most active against C. perfringens. These peptides also showed the broadest spectrum of activity when tested against other non-clostridial indicator strains, including Listeria monocytogenes, methicillin-resistant Staphylococcus aureus, Streptococcus suis, Streptococcus pyogenes, Enterococcus cecorum, Enterococcus faecalis, as well as Gram-negative bacteria (Campylobacter coli and Pseudomonas aeruginosa), among others. The selected synthetic enterocins were combined on the basis of their different mechanisms of action, and all combinations tested showed synergy or partial synergy against C. perfringens. In conclusion, because of their high activity against C. perfringens and other pathogens, the use of synthetic enterocins alone or as a consortium can be a good alternative to the use of antibiotics in the poultry sector.

Context matters: environmental microbiota from ice cream processing facilities affected the inhibitory performance of two lactic acid bacteria strains against Listeria monocytogenes

IMPORTANCE

Antilisterial LAB strains have been proposed as biological control agents for application in food processing environments. However, the effect of resident food processing environment microbiota on the performance on antilisterial LAB strains is poorly understood. Our study shows that the presence of microbiota collected from ice cream processing facilities' environmental surfaces can affect the attachment and inhibitory effect of LAB strains against L. monocytogenes. Further studies are therefore needed to assess whether individual microbial taxa affect antilisterial properties of LAB strains and to characterize the underlying mechanisms.

Effective microorganism water treatment method for rapid eutrophic reservoir restoration

Since reservoirs perform many important functions, they are exposed to various types of unfavorable phenomena, e.g., eutrophication which leads to a rapid growth of algae (blooms) that degrade water quality. One of the solutions to combat phytoplankton blooms are effective microorganisms (EM). The study aims to evaluate the potential of EM in improving the water quality of the Turawa reservoir on the Mała Panew River in Poland. It is one of the first studies providing insights into the effectiveness of using EM in the bioremediation of water in a eutrophic reservoir. Samples for the study were collected in 2019-2021. The analysis showed that EM could be one of the most effective methods for cleaning water from unfavorable microorganisms (HBN22, HBN36, CBN, FCBN, FEN) - after the application of EM, a reduction in their concentration was observed (from 46.44 to 58.38% on average). The duration of their effect ranged from 17.6 to 34.1 days. The application of EM improved the trophic status of the Turawa reservoir, expressed by the Carlson index, by 7.78%. As shown in the literature review, the use of other methods of water purification (e.g., constructed wetlands, floating beds, or intermittent aeration) leads to an increase in the effectiveness and a prolongation of the duration of the EM action. The findings of the study might serve as a guide for the restoration of eutrophic reservoirs by supporting sustainable management of water resources. Nevertheless, further research should be conducted on the effectiveness of EM and their application in the remediation of eutrophic water reservoirs.

Metabolic response of broiler chickens to different doses of Enterococcus faecium ICIS 96 in the diet

The competitiveness and profitability of the poultry industry in market conditions are hampered by growing problems with the safety and quality of poultry meat. The use of targeted microbial preparations can assist in resolving these problems. Numerous studies of the properties of bacteria of the genus Enterococcus have shown their effectiveness in the practice of poultry farming. The objectives of this study were to identify the effect of various doses of Enterococcus faecium ICIS 96 added to the diet of broiler chickens on their metabolism and to evaluate the productive qualities of the chickens when different doses are used. The experiment was carried out on 72 Cobb-500 cross broiler chickens, divided into 3 groups. Chickens in the first group received a suspension of E. faecium ICIS 96 containing 1 × 108 cells in 1 mL of sterile saline, at a dose of 0.1 mL per 1 kg of live weight. The second group of chickens received a double dose of enterococcus, that is 0.2 mL of the suspension per 1 kg of live weight per day. The results demonstrated that 0.1 mL of a 1 × 108 per mL enterococcus culture suspension in the poultry diet per 1 kg of live weight per day intensified metabolism and increased the live weight of chickens after 40 d of treatment.

Commensal Enterococcus faecalis W5 ameliorates hyperuricemia and maintains the epithelial barrier in a hyperuricemia mouse model

OBJECTIVE

The intestine is responsible for approximately one-third of uric acid (UA) excretion. The effect of commensal Enterococcus faecalis (E. faecalis), one of the most colonized bacteria in the gut, on UA excretion in the intestine remains to be investigated. The aim of this study was to evaluate the effect of commensal E. faecalis on UA metabolism and gut microbiota.

METHODS

The 16S rRNA gene sequencing was used to examine the species of Enterococcus in mouse fecal content. E. faecalis strain was isolated from mouse feces and identified to be E. faecalis W5. The hyperuricemia (HUA) animal model was established with yeast-rich forage and 250 mg·kg-1 ·day-1 potassium oxonate. Oral administration of E. faecalis W5 was given for 20 days, serving as the Efa group.

RESULTS

Disrupted intestinal barrier, activated proinflammatory response and low UA excretion in the intestine were found in HUA mice. After E. faecalis W5 treatment, the gut barrier was restored and serum UA level was decreased. Additionally, fecal and intestinal UA levels were elevated, intestinal urate transporter ABCG2 and purine metabolism were upregulated. Moreover, short-chain fatty acid levels were increased, and intestinal inflammation was ameliorated.

CONCLUSIONS

Commensal E. faecalis W5 ameliorated HUA through reversing the impaired gut barrier, promoting intestinal UA secretion by regulating ABCG2 expression, and decreasing intestinal UA synthesis by regulating purine metabolism. The results may provide the potential for developing treatments for HUA through the intestine.

Distribution and association of antimicrobial resistance and virulence characteristics in Enterococcus spp. isolates from captive Asian elephants in China

Enterococcus spp., as an opportunistic pathogen, are widely distributed in the environment and the gastrointestinal tracts of both humans and animals. Captive Asian elephants, popular animals at tourist attractions, have frequent contact with humans. However, there is limited information on whether captive Asian elephants can serve as a reservoir of antimicrobial resistance (AMR). The aim of this study was to characterize AMR, antibiotic resistance genes (ARGs), virulence-associated genes (VAGs), gelatinase activity, hemolysis activity, and biofilm formation of Enterococcus spp. isolated from captive Asian elephants, and to analyze the potential correlations among these factors. A total of 62 Enterococcus spp. strains were isolated from fecal samples of captive Asian elephants, comprising 17 Enterococcus hirae (27.4%), 12 Enterococcus faecalis (19.4%), 8 Enterococcus faecium (12.9%), 7 Enterococcus avium (11.3%), 7 Enterococcus mundtii (11.3%), and 11 other Enterococcus spp. (17.7%). Isolates exhibited high resistance to rifampin (51.6%) and streptomycin (37.1%). 50% of Enterococcus spp. isolates exhibited multidrug resistance (MDR), with all E. faecium strains demonstrating MDR. Additionally, nine ARGs were identified, with tet(M) (51.6%), erm(B) (24.2%), and cfr (21.0%) showing relatively higher detection rates. Biofilm formation, gelatinase activity, and α-hemolysin activity were observed in 79.0, 24.2, and 14.5% of the isolates, respectively. A total of 18 VAGs were detected, with gelE being the most prevalent (69.4%). Correlation analysis revealed 229 significant positive correlations and 12 significant negative correlations. The strongest intra-group correlations were observed among VAGs. Notably, we found that vancomycin resistance showed a significant positive correlation with ciprofloxacin resistance, cfr, and gelatinase activity, respectively. In conclusion, captive Asian elephants could serve as significant reservoirs for the dissemination of AMR to humans.

Multidrug Resistance in Enterococci Isolated from Cheese and Capable of Producing Benzalkonium Chloride-Resistant Biofilms

This study aimed to investigate enterococci recovered from eight Portuguese cheeses made with raw ewe's milk, regarding antibiotic resistance, virulence genes, minimum inhibitory concentration (MIC) of benzalkonium chloride (BAC), biofilm formation capacity, and biofilm eradication (MBEC) by BAC. Antimicrobial resistance against seven antibiotics of five groups was evaluated using the disk diffusion method. The presence of the genes that encode resistance to the antibiotics penicillin (blaZ), erythromycin (ermA, ermB, and ermC), vancomycin (vanA and vanB), aminoglycoside (aac(6')-Ie-aph(2″)-Ia), and β-lactam (pbp5) and the genes that encode virulence factors, frsB, cylA, gelE, esp, and agg, were investigated via multiplex PCR. The susceptibility of planktonic cells to BAC was evaluated by the MIC and MBC values of the isolates, using the broth microdilution method. To assess the biofilm-forming ability and resistance of biofilms to BAC, biofilms were produced on stainless steel coupons, followed by exposure to BAC. The results showed a high resistance to the antibiotics vancomycin (87.5%), erythromycin (75%), tetracycline (50%), and penicillin (37.5%). Multidrug resistance was observed in 68.8% of the isolates. Genes encoding the virulence factors FrsB (frsB) and gelatinase E (gelE) were detected in all isolates. The esp and cylA genes were found in 56.3% and 37.5% of the isolates, respectively. All isolates exhibited a biofilm-forming ability, regardless of incubation time and temperature tested. However, after 72 h at 37 °C, E. faecium and E. faecalis biofilms showed significant differences (p ≤ 0.05). Although most isolates (62.5%) were susceptible to BAC (MIC ≤ 10 mg/L), biofilms of the same isolates were, generally, resistant to the higher concentration of BAC (80 mg/mL) tested. This study using Enterococcus isolates from a ready-to-eat food, such as cheese, reveals the high percentages of vancomycin resistance and multidrug resistance, associated with the presence of virulence genes, in isolates also capable of producing biofilms resistant to BAC, an important active ingredient of many disinfectants. These results emphasize the need for effective control measures to ensure the safety and quality of dairy products.

Antimicrobial overproduction sustains intestinal inflammation by inhibiting Enterococcus colonization

Loss of antimicrobial proteins such as REG3 family members compromises the integrity of the intestinal barrier. Here, we demonstrate that overproduction of REG3 proteins can also be detrimental by reducing a protective species in the microbiota. Patients with inflammatory bowel disease (IBD) experiencing flares displayed heightened levels of secreted REG3 proteins that mediated depletion of Enterococcus faecium (Efm) from the gut microbiota. Efm inoculation of mice ameliorated intestinal inflammation through activation of the innate immune receptor NOD2, which was associated with the bacterial DL-endopeptidase SagA that generates NOD2-stimulating muropeptides. NOD2 activation in myeloid cells induced interleukin-1β (IL-1β) secretion to increase the proportion of IL-22-producing CD4+ T helper cells and innate lymphoid cells that promote tissue repair. Finally, Efm was unable to protect mice carrying a NOD2 gene variant commonly found in IBD patients. Our findings demonstrate that inflammation self-perpetuates by causing aberrant antimicrobial activity that disrupts symbiotic relationships with gut microbes.

Avidumicin, a novel cyclic bacteriocin, produced by Cutibacterium avidum shows anti-Cutibacterium acnes activity

The prevalence of antimicrobial-resistant Cutibacterium acnes in acne patients has increased owing to inappropriate antimicrobial use. Commensal skin bacteria may play an important role in maintaining the balance of the skin microbiome by producing antimicrobial substances. Inhibition of Cu. acnes overgrowth can prevent the development and exacerbation of acne vulgaris. Here, we evaluated skin bacteria with anti-Cu. acnes activity. Growth inhibition activity against Cu. acnes was tested using 122 strains isolated from the skin of healthy volunteers and acne patients. Comparative genomic analysis of the bacterium with or without anti-Cu. acnes activity was conducted. The anti-Cu. acnes activity was confirmed by cloning an identified gene cluster and chemically synthesized peptides. Cu. avidum ATCC25577 and 89.7% of the Cu. avidum clinical isolates (26/29 strains) inhibited Cu. acnes growth. The growth inhibition activity was also found against other Cutibacterium, Lactiplantibacillus, and Corynebacterium species, but not against Staphylococcus species. The genome sequence of Cu. avidum showed a gene cluster encoding a novel bacteriocin named avidumicin. The precursor protein encoded by avdA undergoes post-translational modifications, supposedly becoming a circular bacteriocin. The anti-Cu. acnes activity of avidumicin was confirmed by Lactococcus lactis MG1363 carrying avdA. The C-terminal region of the avidumicin may be essential for anti-Cu. acnes activity. A commensal skin bacterium, Cu. avidum, producing avidumicin has anti-Cu. acnes activity. Therefore, avidumicin is a novel cyclic bacteriocin with a narrow antimicrobial spectrum. These findings suggest that Cu. avidum and avidumicin represent potential alternative agents in antimicrobial therapy for acne vulgaris.