Controversial Aspects Displayed by Enterococci: Probiotics or Pathogens?

Occurrence of Enterococci in the Process of Artisanal Cheesemaking and Their Antimicrobial Resistance

Enterococci are a group of microorganisms that have a controversial position from some scientific points of view. The species of the greatest clinical importance are E. faecalis and E. faecium, which are common agents of nosocomial infections. However, enterococci also have important applications in the dairy industry, as they are used as non-starter lactic acid bacteria (NSLAB) in a variety of cheeses, especially artisanal cheeses. The aim of this study was to determine the presence of representatives from the Enterococcus genus using PCR and MALDI-TOF MS methods on samples of raw milk, processing environment swabs, and cheese from four different artisanal dairy plants in Slovakia. Among the 136 isolates of enterococci, 9 species of genus Enterococci (E. faecalis, E. faecium, E. durans, E. devriesi, E. hirae, E. italicus, E. casseliflavus, E. malodoratus, and E. gallinarum) were identified and were tested for their antimicrobial resistance (AMR) to 8 antibiotics (amoxicillin, penicillin, ampicillin, erythromycin, levofloxacin, vancomycin, rifampicin, and tetracycline); most of them were resistant to rifampicin (35.3%), ampicillin (22.8%), and tetracycline (19.9%). A PCR analysis of vanA (4.41%) and tetM (14.71%) revealed that antimicrobial resistance genes were present in not only phenotypic resistant isolates of enterococci but also susceptible isolates. The investigation of antimicrobial resistance in enterococci during the cheesemaking process can be a source of valuable information for public health in the concept of "One Health".

Enterococcus durans 98D alters gut microbial composition and function to improve DSS-induced colitis in mice

Enterococcus durans, is a potential functional strain with the capacity to regulate intestinal health and ameliorate colonic inflammation. However, the strain requires further investigation regarding its safety profile and potential mechanisms of colitis improvement. In this study, the safety of E. durans 98D (Ed) as a potential probiotic was studied using in vitro methods. Additionally, a dextran sulfate sodium (DSS)-induced murine colitis model was employed to investigate its impact on the intestinal microbiota and colitis. In vitro antimicrobial assays revealed Ed sensitivity to common antibiotics and its inhibitory effect on the growth of Escherichia coli O157, Streptococcus pneumoniae CCUG 37328, and Staphylococcus aureus ATCC 25923. To elucidate the functional properties of Ed, 24 weight-matched 6-week-old female C57BL/6J mice were randomly divided into three groups (n = 8): NC group, Con group (DSS), and Ed group (DSS + Ed). Ed administration demonstrated a protective effect on colitis mice, as evidenced by improvements in body weight, colonic length, reduced disease activity index, histological scores, diminished splenomegaly, and decreased goblet cell loss. Furthermore, Ed downregulated the expression of the pro-inflammatory cytokine genes (IL-6, IL-1β, and TNF-α) and upregulated the expression of the anti-inflammatory cytokine gene IL-10. The 16S rRNA gene sequencing revealed significant alterations in microbial α-diversity, with principal coordinate analysis indicating distinct differences in microbial composition among the three groups. At the phylum level, the relative abundance of Actinomycetota significantly increased in the Ed-treated group. At the genus level, Ed treatment markedly elevated the relative abundance of Paraprevotella, Rikenellaceae_RC9, and Odoribacter in DSS-induced colitis mice. In conclusion, Ed exhibits potential as a safe and effective therapeutic agent for DSS-induced colitis by reshaping the colonic microbiota.

Enterocins Produced by Enterococci Isolated from Breast-Fed Infants: Antilisterial Potential

Enterocins are bacteriocins synthesized by Enterococcus strains that show an interesting antimicrobial effectiveness against foodborne pathogens such as Listeria monocytogenes. The objectives of this study were to identify and analyze the expression of enterocin genes of Enterococcus isolated from breast-fed infants and evaluate their ability to inhibit three human isolates of virulent L. monocytogenes, as well as some probiotic bacteria. The susceptibility of the strains of L. monocytogenes to fifteen antibiotics was tested, detecting their resistance to cefoxitin (constitutively resistant), oxacillin, and clindamycin. The production of enterocins A, B, and P was observed in Enterococcus faecium isolates, while enterocin AS-48 was detected in an Enterococcus faecalis isolate. AS-48 showed antilisterial activity by itself, while the joint action of enterocins A and B or B and P was necessary for inhibiting L. monocytogenes, demonstrating the synergistic effect of those combinations. The presence of multiple enterocin genes does not assure the inhibition of L. monocytogenes strains. However, the expression of multiple enterocin genes showed a good correlation with the inhibition capacity of these strains. Furthermore, the potential beneficial strains of lactobacilli and bifidobacteria examined were not inhibited by any of the enterocins produced individually or in combination, with the exception of Bifidobacterium longum BB536, which was inhibited by enterocin AS-48 and the joint production of enterocins A and B or B and P. The enterocins studied here could be candidates for developing alternative treatments against antibiotic-resistant bacterial infections. Moreover, these selected enterocin-producing E. faecium strains isolated from breast-fed infants could be used as probiotic strains due to their antilisterial effect, as well as the absence of virulence factors.

Genomic Landscape of Multidrug Resistance and Virulence in Enterococcus faecalis IRMC827A from a Long-Term Patient

We report on a highly virulent, multidrug-resistant strain of Enterococcus faecalis IRMC827A that was found colonizing a long-term male patient at a tertiary hospital in Khobar, Saudi Arabia. The E. faecalis IRMC827A strain carries several antimicrobial drug resistance genes and harbours mobile genetic elements such as Tn6009, which is an integrative conjugative element that can transfer resistance genes between bacteria and ISS1N via an insertion sequence. Whole-genome-sequencing-based antimicrobial susceptibility testing on strains from faecal samples revealed that the isolate E. faecalis IRMC827A is highly resistant to a variety of antibiotics, including tetracycline, doxycycline, minocycline, dalfopristin, virginiamycin, pristinamycin, chloramphenicol, streptomycin, clindamycin, lincomycin, trimethoprim, nalidixic acid and ciprofloxacin. The isolate IRMC827A carries several virulence factors that are significantly associated with adherence, biofilm formation, sortase-assembled pili, manganese uptake, antiphagocytosis, and spreading factor of multidrug resistance. The isolate also encompasses two mutations (G2576T and G2505A) in the 23S rRNA gene associated with linezolid resistance and three more mutations (gyrA p.S83Y, gyrA p.D759N and parC p.S80I) of the antimicrobial resistance phenotype. The findings through next-generation sequencing on the resistome, mobilome and virulome of the isolate in the study highlight the significance of monitoring multidrug-resistant E. faecalis colonization and infection in hospitalized patients. As multidrug-resistant E. faecalis is a serious pathogen, it is particularly difficult to treat and can cause fatal infections. It is important to have quick and accurate diagnostic tests for multidrug-resistant E. faecalis, to track the spread of multidrug-resistant E. faecalis in healthcare settings, and to improve targeted interventions to stop its spread. Further research is necessary to develop novel antibiotics and treatment strategies for multidrug-resistant E. faecalis infections.

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.

Enterococcal bacteriophage: A survey of the tail associated lysin landscape

Bacteriophages are viruses that exclusively infect bacteria which require local degradation of cell barriers. This degradation is accomplished by various lysins located mainly within the phage tail structure. In this paper we surveyed and analysed the genomes of 506 isolated bacteriophage and prophage infecting or harboured within the genomes of the medically important Enterococcus faecalis and faecium. We highlight and characterise the major features of the genomes of phage in the morphological groups podovirus, siphovirus and myovirus, and explore their categorisation according to the new ICTV classifications, with a focus on putative extracellular lysins chiefly within tail modules. Our analysis reveals a range of potential cell-wall targeting enzyme domains that are part of tail, tape measure or other predicted base structures of these phages or prophages. These largely fall into protein domains targeting pentapeptide or glycosidic linkages within peptidoglycan but also potentially the enterococcal polysaccharide antigen (EPA) and wall teichoic acids of these species (i.e., Pectinesterases and Phosphodiesterases). Notably, there is a great variety of domain architectures that reveal the diversity of evolutionary solutions to attack the Enterococcus cell wall. Despite this variety, most phage and prophage possess a putative endopeptidase (70%), reflecting the ubiquity of this cell surface barrier. We also identified a predicted lytic transglycosylase domain belonging to the glycosyl hydrolase (GH) family 23 and present exclusively within tape measure proteins. Our data also reveal distinct features of the genomes of podo-, sipho- and myo-type viruses that most likely relate to their size and complexity. Overall, we lay a foundation for expression of recombinant TAL proteins and engineering of enterococcal and other phage that will be invaluable for researchers in this field.

Isolation and phenotypic characterization of bacteriophage SA14 with lytic- and anti-biofilm activity against multidrug-resistant Enterococcus faecalis

Background

Antimicrobial resistance is a growing global health concern demanding more attention and action at the international-, national- and regional levels. In the present study, bacteriophage was sought as a potential alternative to traditional antibiotics.

Results

Vancomycin-resistant Enterococcus faecalis was isolated from a urine sample. Partial 16S rRNA-gene sequencing and VITEK®2 system were employed for its identification, biochemical characterization, and antibiotic susceptibility testing. The isolate was resistant to eight antibiotics (out of 11): vancomycin, gentamicin (high-level synergy), streptomycin (high-level synergy), ciprofloxacin, levofloxacin, erythromycin, quinupristin/dalfopristin, and tetracycline. Bacteriophage SA14 was isolated from sewage water using the multidrug-resistant isolate as a host. Transmission electron micrographs revealed that phage SA14 is a member of the Siphoviridae family displaying the typical circular head and long non-contractile tail. The phage showed characteristic stability to a wide range of solution pH and temperatures, with optimal stability at pH 7.4 and 4 °C, while showing high specificity toward their host. Based on the one-step growth curve, the phage's latent period was 25 min, and the burst size was 20 PFU/ml. The lytic activity of phage SA14 was evaluated at various multiplicities of infection (MOI), all considerably suppressed the growth of the host organism. Moreover, phage SA14 displayed a characteristic anti-biofilm activity as observed by the reduction in adhered biomass and -viable cells in the pre-formed biofilm by 19.1-fold and 2.5-fold, respectively.

Conclusion

Phage therapy can be a valuable alternative to antibiotics against multi-drug resistant microorganisms.

Genomic insights into antibiotic-resistance and virulence genes of Enterococcus faecium strains from the gut of Apis mellifera

Enterococcus faecium is a lactic acid bacterium that confers beneficial health effects in humans. However, lately, a number of E. faecium strains have been linked to the spread of nosocomial infections in the hospital environment. Therefore, any potential commercial usage of E. faecium isolates should be preceded by an assessment of infection risk. In the current study, the genomes of two novel E. faecium strains Am1 (larval isolate) and Bee9 (adult bee isolate) isolated from the gut of Apis mellifera L. (honeybee) were sequenced to allow evaluation of their safety. In particular, their genomes were screened for antibiotic-resistance and virulence genes. In addition, their potential to spread resistance in the environment was evaluated. The analysis revealed that Am1 and Bee9 possess 2832 and 2844 protein-encoding genes, respectively. In each case, the genome size was 2.7 Mb with a G+C content of 37.9 mol%. Comparative analysis with probiotic, non-pathogenic and pathogenic enterococci revealed that there are variations between the two bee E. faecium isolates and pathogenic genomes. They were, however, closely linked to the probiotic comparison strains. Phenotypically, the Am1 and Bee9 strains were susceptible to most antibiotics tested, but showed intermediate sensitivity towards erythromycin, linezolid and trimethoprim/sulfamethoxazole. Notably, no genes associated with antibiotic resistance in clinical isolates (e.g. vancomycin resistance: vanA, vanB, vanS, vanX and vanY) were present. In addition, the insertion sequences (IS16, ISEfa11 and ISEfa5), acting as molecular pathogenicity markers in clinically relevant E. faecium strains, were also absent. Moreover, the analysis revealed the absence of three key pathogenicity-associated genes (acm, sgrA, ecbA) in the Am1 and Bee9 strains that are found in the prominent clinical isolates DO, V1836, Aus0004 and Aus0085. Overall, the findings of this investigation suggest that the E. faecium isolates from the bee gut have not suffered any recent clinically relevant antibiotic exposure. It also suggests that E. faecium Am1 and Bee9 are safe potential probiotic strains, because they lack the phenotypic and genetic features associated with strains eliciting nosocomial infections.

Enterocin M in Interaction in Broiler Rabbits with Autochthonous, Biofilm-Forming Enterococcus hirae Kr8 Strain

Young rabbits are susceptible to gastrointestinal diseases caused by bacteria. Enterococcus hirae can be associated with diseases. But enterocins produced by some enterococcal species can prevent/reduce this problem. Therefore, the interaction of enterocin M with a biofilm-forming, autochthonous E. hirae Kr8⁺ strain was tested in rabbits to assess enterocin potential in vivo. Rabbits (96), aged 35 days, both sexes, meat line M91 breed were divided into four groups, control C and three experimental groups. The rabbits in C received the standard diet, rabbits in experimental group 1 (E1) received 10⁸ CFU/mL of Kr8⁺, a dose 500 µL/animal/day, E2 received Ent M (50 µL/animal/day), and E3 received both Kr8⁺ and Ent M in their drinking water over 21 days. The experiment lasted 42 days. Feces and blood were sampled at day 0/1 (at the start of the experiment, fecal mixture of 96 animals, n = 10), at day 21 (five fecal mixtures per group, n = 5), and at day 42 (21 days after additives cessation, the same). At days 21 and 42, four rabbits from each group were slaughtered, and cecum and appendix were sampled for standard microbial analysis. Ent M showed decreased tendency of Kr8⁺. Using next-generation sequencing, the phyla detected with the highest abundance were Firmicutes, Verrucomicrobia, Bacteroidetes, Tenericutes, Proteobacteria, Cyanobacteria, Saccharibacteria, and Actinobacteria. Interaction of Ent M with some phyla resulted in reduced abundance percentage. At day 21, significantly increased phagocytic activity (PA) was found in E1 and E2 (p < 0.001). Kr8⁺ did not attack PA and did not stimulate oxidative stress. But Ent M supported PA. The prospective importance of this study lies in beneficial interaction of enterocin in host body.

Norepinephrine and Serotonin Can Modulate the Behavior of the Probiotic Enterococcus faecium NCIMB10415 towards the Host: Is a Putative Surface Sensor Involved?

The human gut microbiota has co-evolved with humans by exchanging bidirectional signals. This study aims at deepening the knowledge of this crucial relationship by analyzing phenotypic and interactive responses of the probiotic Enterococcus faecium NCIMB10415 (E. faecium SF68) to the top-down signals norepinephrine (NE) and serotonin (5HT), two neuroactive molecules abundant in the gut. We treated E. faecium NCIMB10415 with 100 µM NE and 50 µM 5HT and tested its ability to form static biofilm (Confocal Laser Scanning Microscopy), adhere to the Caco-2/TC7 monolayer, affect the epithelial barrier function (Transepithelial Electrical Resistance) and human dendritic cells (DC) maturation, differentiation, and cytokines production. Finally, we evaluated the presence of a putative hormone sensor through in silico (whole genome sequence and protein modelling) and in vitro (Micro-Scale Thermophoresis) analyses. The hormone treatments increase biofilm formation and adhesion on Caco-2/TC7, as well as the epithelial barrier function. No differences concerning DC differentiation and maturation between stimulated and control bacteria were detected, while an enhanced TNF-α production was observed in NE-treated bacteria. Investigations on the sensor support the hypothesis that a two-component system on the bacterial surface can sense 5HT and NE. Overall, the data demonstrate that E. faecium NCIMB10415 can sense both NE and 5HT and respond accordingly.

Slovak Local Ewe's Milk Lump Cheese, a Source of Beneficial Enterococcus durans Strain

Slovak ewe's milk lump cheese is produced from unpasteurized ewe's milk without any added culture. Because of the traditional processing and shaping by hand into a lump, this cheese was given the traditional specialty guaranteed (TSG) label. Up till now, there have existed only limited detailed studies of individual microbiota and their benefits in ewe's milk lump cheese. Therefore, this study has been focused on the beneficial properties and safety of Enterococcus durans strains with the aim to contribute to basic dairy microbiology but also for further application potential and strategy. The total enterococcal count in cheeses reached 3.93 CFU/g (log 10) ± 1.98 on average. Based on a MALDI-TOF mass spectrometry evaluation, the strains were allotted to the species E. durans (score, 1.781-2.245). The strains were gelatinase and hemolysis-negative (γ-hemolysis) and were mostly susceptible to commercial antibiotics. Among the strains, E. durans ED26E/7 produced the highest value of lactase enzyme β-galactosidase (10 nmoL). ED26E/7 was absent of virulence factor genes such as Hyl (hyaluronidase), IS 16 element and gelatinase (GelE). To test safety, ED26E/7 did not cause mortality in Balb/c mice. Its partially purified bacteriocin substance showed the highest inhibition activity/bioactivity against Gram-positive indicator bacteria: the principal indicator Enterococcus avium EA5 (102,400 AU/mL), Staphylococcus aureus SA5 and listeriae (25,600 AU/mL). Moreover, 16 staphylococci (out of 22) were inhibited (100 AU/mL), and the growth of 36 (out of 51) enterococcal indicators was as well. After further technological tests, E. durans ED26E/7, with its bacteriocin substance, can be supposed as a promising additive to dairy products.

Safety and metabolic characteristics of 17 Enterococcus faecium isolates

In the present study, metabolic characteristics, such as lactic acid, hydrogen peroxide, exopolysaccharide (EPS) production, and antimicrobial activities, of 17 Enterococcus faecium isolates from white cheese samples were assessed. In E. faecium isolates, the amount of lactic acid obtained between in MRS medium 0.61-1.22% and in skim milk 0.75-1.08%, and the amount of H2O2 was found between 0.57 and 3.17 µg mL-1. In MRS and skim milk, the amount of EPS production was 59-185 mg L-1, 155-255 mg L-1 for isolates, respectively. The antimicrobial activities of E. faecium isolates on eight different pathogenic bacteria were also performed by an agar well diffusion method. The highest inhibition zones 8.60 mm were observed with culture supernatants of RI-71 isolate against Escherichia coli ATCC 35218. The safety of the E. faecium isolates was assessed by determining gelatinase activity, hemolytic activity, the resistance to ten different antibiotics, biofilm forming, and virulence genes (van A, van B, gelE, cylA, cylB, esp, agg, and asa1, efaAfm, cob, ccf, hyl). The isolates did not show gelatinase activity, β-hemolysis, and biofilm formation. All E. faecium isolates were susceptible to vancomycin, penicillin-G, tetracycline, ampicillin, and chloramphenicol. The efaAfm gene was detected most frequently (94%) followed by cob (82%), van B (59%), and ccf (53%). For enterococci to be recommended as co-starter or probiotic adjunct cultures, it is necessary to determine whether they have virulence genes and resistance to antibiotics.

Ready-to-Eat Sandwiches as Source of Pathogens Endowed with Antibiotic Resistance and Other Virulence Factors

The aim of this study was to evaluate and characterize the bacterial load present in twenty-four Ready-To-Eat (RTE) sandwiches, purchased at refrigerated vending machines and supermarkets in the province of Modena (Italy). We isolated 54 bacterial strains, including pathogens of interest in food safety, such as Listeria, Staphylococcus, Enterococcus, Yersinia, Aeromonas and Acinetobacter spp. Phenotypic tests have been performed on these pathogens to detect the presence of virulence factors, such as gelatinase production and hemolytic capability. To test their antibiotic resistance features, the minimum inhibitory concentration (MIC) against eight commonly used antibiotics (Amikacin, Ciprofloxacin, Ampicillin, Oxacillin, Imipenem, Tetracycline, Erythromycin and Vancomycin) was also evaluated. The results showed that among the 54 isolates, fifty percent (50%) belonged to harmless microorganisms (Leuconostoc and Lactococcus), whereas the remaining fifty percent (50%) included pathogenic bacteria (Listeria ivanovii, Listeria monocytogenes, Staphylococcus aureus, Yersinia, and Citrobacter spp.), species responsible for pathologies often difficult to treat due to the presence of antibiotic resistance features. This study demonstrates the importance of thorough controls, both during the production and marketing of RTE food like sandwiches, to avoid reaching the infectious load and the onset of pathologies, particularly dangerous for old and immunocompromised patients.

Molecular Characterization of Enterococcus Isolates From Different Sources in Estonia Reveals Potential Transmission of Resistance Genes Among Different Reservoirs

In this study, we aimed to characterize the population structure, drug resistance mechanisms, and virulence genes of Enterococcus isolates in Estonia. Sixty-one Enterococcus faecalis and 34 Enterococcus faecium isolates were collected between 2012 and 2014 across the country from various sites and sources, including farm animals and poultry (n = 53), humans (n = 12), environment (n = 24), and wild birds (n = 44). Clonal relationships of the strains were determined by whole-genome sequencing and analyzed by multi-locus sequence typing. We determined the presence of acquired antimicrobial resistance genes and 23S rRNA mutations, virulence genes, and also the plasmid or chromosomal origin of the genes using dedicated DNA sequence analysis tools available and/or homology search against an ad hoc compiled database of relevant sequences. Two E. faecalis isolates from human with vanB genes were highly resistant to vancomycin. Closely related E. faecalis strains were isolated from different host species. This indicates interspecies spread of strains and potential transfer of antibiotic resistance. Genomic context analysis of the resistance genes indicated frequent association with plasmids and mobile genetic elements. Resistance genes are often present in the identical genetic context in strains with diverse origins, suggesting the occurrence of transfer events.