Molecular screening of Enterococcus virulence determinants and potential for genetic exchange between food and medical isolates

Probiotic potential of LAB strains from native Kashmir Flavorella chickens of northwestern Himalayas: A focus on safety and gut health

Lactic acid bacteria (LAB) possess notable functional characteristics, making them promising candidates for probiotic applications due to their ability to endure low pH and high bile salt concentrations while inhibiting enteric pathogens. This study evaluates the probiotic potential and safety of LAB strains isolated from the gastrointestinal tract of indigenous chickens of the Northwestern Himalayas. We assessed features such as antimicrobial activity, auto-aggregation, co-aggregation, haemolytic activity, antibiotic resistance, and virulence gene presence. Multivariate analysis using Principal Component Analysis (PCA) and heat mapping was conducted to evaluate variability among strains based on traits like pH and bile salt tolerance, autoaggregation and co-aggregation and antimicrobial activity. Five LAB strains were identified through 16S rDNA analysis: Lactobacillus johnsonii, Ligilactobacillus salivarius, Lactobacillus kitasatonis, Rummeliibacillus suwonensis, and Enterococcus faecalis. All strains demonstrated significant tolerance to acidic and bile salt conditions, robust aggregation abilities, and strong antibacterial activity. Safety evaluations revealed no haemolytic activity or virulence genes, except for Enterococcus faecalis, which harboured the esp gene. PCA and heat mapping identified strain NC10 as the most promising probiotic isolate due to its superior antimicrobial activity and bile tolerance. This study highlights the potential of indigenous LAB strains, particularly Ligilactobacillus salivarius NC10, as safe probiotics for enhancing poultry health. To the best of our knowledge, this study is the first to evaluate the probiotic attributes of LAB strains derived from native chickens of the Northwestern Himalayas in the Indian subcontinent. IMPORTANCE: This study underscores the potential of utilizing lactic acid bacteria (LAB) strains from indigenous chickens of the Northwestern Himalayas as safe and effective probiotics. Native breeds, such as the Kashmir Flavorella, have adapted to the region's unique environment, offering a rich source of microbiota with distinct probiotic traits. The identification of LAB strains, particularly Ligilactobacillus salivarius NC10, with exceptional antimicrobial activity and bile tolerance, opens avenues for improving poultry gut health and productivity. As antibiotic resistance emerges as a global challenge, exploring natural and safe alternatives like probiotics becomes increasingly vital. Additionally, the comprehensive safety evaluation, including the absence of haemolytic activity and virulence genes in most strains, highlights their suitability for probiotic applications. This research not only contributes to sustainable poultry farming practices but also emphasizes the need to preserve and harness the microbial diversity of indigenous animal breeds, ensuring food security and environmental sustainability.

Evaluation of the virulence of enterococcal strains isolated from high touch surfaces in a hospital in Bejaia (Algeria)

Biofilms are key drivers of healthcare-associated infections (HAIs). Recently, the emergence of Enterococcus strains as major contributors to HAIs has been linked to their high antibiotic resistance and biofilm formation capabilities. In this study, we report for the first time the isolation and characterisation of Enterococcus strains (5 E. faecalis, 2 E. faecium and 1 E. hirae), from hospital surfaces in Algeria. We evaluated their biofilm-forming ability under different culture conditions, cytotoxicity on Caco-2/TC7 epithelial cells, antibiotic resistance profiles and the presence of key virulence genes (agg, gelE, vanA, vanB). Results showed that the biofilm formation capacity was enhanced in the presence of sucrose and all strains were slime-positive. They were non-hemolytic but cytotoxic on epithelial cells; 75 % and 62.5 % of the strains harbored the gelE and agg genes respectively. No strain carried vanA and vanB genes. Seven strains were resistant to cefotaxime and penicillin G, and all of them were resistant to ciprofloxacin but sensitive to ofloxacin. Importantly, we evaluated the anti-biofilm efficacy of benzalkonium chloride (BAK) against mature biofilms on stainless steel coupons, complete biofilm removal required BAK >1250 × MIC, highlighting the limitations of standard biocide use. This study provides one of the few comprehensive characterisations of environmental Enterococcus strains, including E. hirae, with a focus on their resistance, virulence and tolerance to biocides. Our findings highlight the importance of contamination control of inanimate surfaces and equipment in hospitals and inefficacy of commonly used biocides against biofilm-embedded cells, posing a threat for HAIs and call for improved disinfection strategies targeting biofilm-embedded bacteria.

Biofilm inhibition and antagonism of Klebsiella pneumoniae by probiotic lactic acid bacteria (LAB) isolated from raw cow milk

Lactic acid bacteria (LAB) with their potential health benefits are naturally prevalent in dairy and fermented food products. This probiotic microbiota can be an alternative biological tool for controlling other pathogenic bacteria. The study aimed to isolate lactic acid bacteria (LAB) from raw cow milk and evaluate their probiotic potential. Twelve gram-positive isolates showing tolerance to bile salt, acid, and low pH were identified by 16S rRNA sequencing, which revealed the isolates belong to the genera including Lactococcus, Enterococcus, Streptococcus, Bacillus, and Weissella. In case of probiotic potential, the isolates exhibited arrays of probiotic properties: autoaggregation (33.65-84.63 %), co-aggregation (8.17-83.22 %), cell surface hydrophobicity for both polar (13.37-90.24 %) and non-polar solvents (5.52-53.58 %) and able to form biofilm (75 % weak, 16.67 % moderate and 8.33 % strong). Statistical analysis revealed the correlation pattern between the probiotic properties and showed a significant strong positive correlation between cell surface hydrophobicity and aggregation. Additionally, three isolates L. lactis, W. confusa, and E. gallinarum that were sensitive to antibiotics, able to produce biofilm, and did not contain virulence genes were able to reduce the biofilm formation of pathogen K. pneumoniae (1.3-4 log) in the co-culture assay. These Findings suggest that LAB from the raw cow milk could serve as a natural biocontrol agent for preventing and controlling K. pneumoniae biofilm formation and pave the way for innovative intervention of LAB in food safety and clinical settings.

Safety Assessment of Levilactobacillus brevis KU15006: A Comprehensive Analysis of its Phenotypic and Genotypic Properties

Levilactobacillus brevis KU15006, isolated from kimchi, exhibits pathogen-antagonistic and anti-diabetic activities; however, the safety of this strain has not been assessed. In the present study, L. brevis KU15006 was evaluated to elucidate its safety as a probiotic strain using phenotypic and genotypic analyses. Its safety was assessed using a minimum inhibitory concentration test comprising nine antibiotics, 26 antibiotic resistance genes, a single conjugative element, virulence gene analysis, hemolysis, cell cytotoxicity, mucin degradation, and toxic metabolite production. L. brevis KU15006 exhibited equal or lower minimum inhibitory concentration for the nine antibiotics than the cut-off value established by the European Food Safety Authority. It did not harbor antibiotic resistance and virulence genes. L. brevis KU15006 lacked β-hemolysis, mucin degradation, cytotoxicity against Caco-2 cells, gelatin liquefaction, bile salt deconjugation, and toxic metabolite production abilities. Based on the results, L. brevis KU15006, which has antagonistic and anti-diabetic effects, could be marketed as a probiotic in the future.

Assessment of Factors Contributing to Infection Severity and High Levels of Drug Resistance in Clinical Enterococcus Isolates

BACKGROUND

Various factors, including virulence determinants, biofilm formation, and antimicrobial resistance, contribute to the severity of infections caused by Enterococcus spp.

METHODS

Enterococcus isolates were obtained from hospitalized patients in Yazd, Iran, and identified using microbiological and molecular tests. High-level resistance, biofilm formation, and the genes encoding virulence factors and resistance were investigated following standard methods.

RESULTS

Enterococcus faecalis was the most prevalent species (60.7%), followed by Enterococcus faecium (30.4%). Linezolid was highly effective, with 94.6% of isolates being susceptible. However, more than 76% of isolates exhibited resistance to rifampin, erythromycin, tetracycline, and ciprofloxacin, and 94.6% were multidrug-resistant (MDR). Additionally, 39.3% of the isolates were vancomycin-resistant enterococci (VRE) with a MIC > 32 μg/mL, and the vanA gene was detected in 35.7% of the isolates. High-level resistance to gentamicin and streptomycin was seen in 60.7% and 50% of the isolates, respectively. The most prevalent aminoglycoside resistance gene was aph(3')-IIIa (62.5%) followed by ant(6')-Ia (58.9%), and aac(6')-Ie-aph(2″)-Ia (50%). The ant(3″)-Ia was found in only one isolate. Most of the isolates (87.5%) were biofilm producers, and the distribution of virulence-encoding genes was as follows: gelE (66.1%), efaA (57.1%), asa1 (51.8%), esp (25%), cylA (19.6%), and hyl (8.9%). Furthermore, the ace gene was present in 79.4% of E. faecalis isolates, while the fnm and acm genes were found in 76.5% and 23.5% of E. faecium isolates, respectively.

CONCLUSION

The study highlights the significant role of notable drug resistance and the widespread presence of virulence traits in the development of enterococcal infections.

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.

Antimicrobial Activity, Genetic Diversity and Safety Assessment of Lactic Acid Bacteria Isolated from European Hakes (Merluccius merluccius, L.) Caught in the Northeast Atlantic Ocean

Background/Objectives: The overuse and misuse of antibiotics has contributed significatively to the growing problem of the emergence and spread of antibiotic resistance genes among bacteria, posing a serious global challenge to the treatment of bacterial infectious diseases. For these reasons, there is a current and growing interest in the development of effective alternative or complementary strategies to antibiotic therapy for the prevention of fish diseases, which are mainly based on the use of probiotics-in particular, those belonging to the Lactic Acid Bacteria (LAB) group. In this context, the aim of the present study was to characterise, evaluate the genetic diversity and assess the safety of candidate probiotic LAB strains for aquaculture isolated from faeces and intestines of European hakes (Merluccius merluccius, L.) caught in the Northeast Atlantic Ocean (Ireland). Methods: The direct antimicrobial activity of the LAB isolates was tested by the Stab-On-Agar method against key ichthyopathogens. Subsequently, their taxonomic classification and genetic diversity were determined by 16SrDNA sequencing and Enterobacterial Repetitive Intergenic Consensus-PCR (ERIC-PCR), respectively. To ensure the in vitro safety of the LAB isolates, their biofilm-forming ability was assessed by a microtiter plate assay; their sensitivity to major antibiotics used in aquaculture, human and veterinary medicine by a broth microdilution method and their haemolytic and gelatinase activity by microbiological assays. Results: All LAB isolates were biofilm producers and susceptible to chloramphenicol, oxytetracycline, flumequine and amoxicillin. A total of 30 isolates (85.7%) were resistant to at least one of the tested antibiotics. None of the 35 LAB isolates showed haemolytic or proteolytic activity. Conclusions: Among the isolated strains, five LAB strains exhibiting the highest antimicrobial activity against aquaculture-relevant ichthyopathogens, taxonomically identified as Streptococcus salivarius, Enterococcus avium and Latilactobacillus sakei, were selected for further characterisation as potential probiotic candidates to promote sustainable aquaculture. To our knowledge, this is the first study to report that hake intestines and faeces represent viable ecological niches for the isolation of LAB strains with antimicrobial activity.

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.

Review of Enterococcus faecalis Infections of Poultry

Enterococcus faecalis organisms are Gram-positive cocci that are ubiquitous in the environment, occurring in water and soil, and are commensal inhabitants of the intestinal tracts of both vertebrate and invertebrate animals. They are considered opportunists and possess many virulence-encoding traits, including the formation of biofilms and toxins. Enterococcus faecalis produces cytolysin, which is a unique toxin having activity against both eukaryotic and prokaryotic cells. Cytolysin causes hemolysis of red blood cells and has also been termed hemolysin. Enterococcus faecalis organisms are intrinsically resistant to some antibiotics and can transmit antimicrobial resistance to other microorganisms. In poultry, there is ample evidence to indicate that E. faecalis can be egg transmitted, causing decreased hatchability of eggs. Enterococcus faecalis has been found to rapidly spread among hatchlings that are exposed in the hatcher. In older birds, some E. faecalis isolates cause amyloid arthropathy. Various methods have been developed to assess E. faecalis isolates for virulence-encoding traits, including Multilocus sequence typing and embryo lethality assays. However, much variability occurs in interpreting the results of these methods and the correlation between genotypes, phenotypes, and virulence has not been well established. The virulence traits and pathogenesis of E. faecalis in poultry need to be elucidated further.

Fecal strains Enterococcus mundtii from wild ruminants, their safety and postbiotic potential

Roe and red deers represent inhabitants in European forests but also in agricultural areas. In general, microbiota can have a significant impact on health. E. g. the genus Enterococcus was detected in more or less high abundance percentage in feces of red deers. To preserve negative impact of some microbiota, beneficial autochthonous strains can be selected for this purpose. The aim of this study was to assess safety, postbiotic activity and character of the fecal strains Enterococcus mundtii from roe and red deers living in Poland to spread basic microbiology research in this field and to select application candidate. Taxonomy of seven E. mundtii was determined using MALDI-TOF mass spectrometry and 16S rRNA sequence analysis. The evaluation score responded mostly with secure genus identification/probable species identification. Strains showed identity up to 100% with the sequence MK414812.1 of E. mundtii in GenBank. They were deoxyribonuclease and gelatinase- negative, with low-grade biofilm formation (0.100 ± 0.31 to 0.181 ± 0.43). E. mundtii were susceptible to antibiotics without production of damaging enzymes. They were absent of virulence factors genes (gelE, agg, esp, efaAfm, efaAfs). Postbiotic potential of the bacteriocin substance produced by E. mundtii revealed inhibition of indicator strains growth up to 48%. The most active substance was from the strain EM 1/90/2; inhibitory activity against enterococci, staphylococci and listeriae up to 86% (up to 1600 AU mL) was noted. The substance from the strain EM 6/123/1 reached inhibitory activity up to 81% with activity up to 400 AU/mL. It remained active at -20 ˚C for one month. E. mundtii were assessed with no and/or low- grade virulence factor rate and with postbiotic potential for further studies.

Isolation of vanA-Mediated Vancomycin-Resistant Enterococcus faecalis (ST1912/CC116) and Enterococcus faecium (ST80/CC17), optrA-Positive Linezolid-Resistant E. faecalis (ST32, ST1902) from Human Clinical Specimens in Bangladesh

BACKGROUND/OBJECTIVES

Enterococcus is one of the major nosocomial pathogens. The present status of antimicrobial resistance determinants and virulence factors was analyzed for current Enterococcus causing infectious diseases in Bangladesh.

METHODS

Clinical isolates of Enterococcus recovered from various specimens in a tertiary care hospital were analyzed. Antimicrobial susceptibility was measured by a broth microdilution test, and resistance genes/virulence factors were detected by uniplex/multiplex PCR, along with sequencing analysis as required. The sequence type (ST) of E. faecalis and E. faecium was identified based on a multilocus sequence typing (MLST) scheme.

RESULTS

For a one-year period, a total of 143 isolates (135 E. faecalis, 7 E. faecium, and 1 E. hirae) were collected. Although all E. faecalis isolates were susceptible to penicillin, high resistance rates were noted against erythromycin (87%) and levofloxacin (62%). High-level resistance to gentamicin was detected in 30% of E. faecalis and 86% of E. faecium. Vancomycin resistance due to vanA was identified in one isolate each of E. faecalis (ST1912, CC116) and E. faecium (ST80, CC17). Three E. faecalis isolates (2.2%) with ST32 or ST1902 were resistant to linezolid, harboring optrA-fexA.

CONCLUSIONS

The present study identifies the vancomycin-resistant Enterococcus harboring vanA from humans in Bangladesh and shows the potential spread of optrA in multiple lineages of E. faecalis.

Detection of glycopeptide resistance and virulence genes in enterococci isolated from cheese and investigation of the clonal relationship of E. faecium species with rectal surveillance isolates

OBJECTIVE

This study aimed to investigate the presence of glycopeptide resistance and virulence genes in Enterococcus spp. isolated from cheese and the clonal relationship of E. faecium species with rectal surveillance isolates.

MATERIALS AND METHOD

The study included 50 E. faecium species identified by the BD Phoenix 100 automatic identification system from surveillance cultures sent to the Kahramanmaraş Sütçü İmam University's microbiology laboratory and Enterococcus species from various packaged and unpackaged cheese samples. Multiplex polymerase chain reaction was used to investigate the presence of glycopeptide resistance and virulence genes in enterococci isolates. The clonal relationship between E. faecium isolates was evaluated using the Enterobacterial Repetitive Intergenic Consensus polymerase chain reaction method.

RESULTS

Bacterial growth was detected in 33 of the cheese samples. The study included E. faecium and E. faecalis species. Glycopeptide resistance genes were detected in 11 E. faecalis isolates, including vanD (61.1 %) and vanB (44.4 %). None of the glycopeptide resistance genes were detected in E. faecium isolates. Additionally, virulence genes were detected in 5 (31.25 %) E. faecium and 12 (66.6 %) E. faecalis isolates. Glycopeptide resistance genes were more common in isolates from packaged cheeses (p = 0.045).

CONCLUSION

Four E. faecium strains isolated from cheeses were closely related to the rectal surveillance isolates. This suggests that the health risks associated with enterococci in cheese must be carefully analyzed.

Isolation of Enterococcus hirae From Fresh White Yak Milk in Ledu District, Qinghai Province, China: A Comparative Genomic Analysis

Yak milk is a widely consumed dairy product rich in lactic acid bacteria. Although Enterococcus hirae (E. hirae) is commonly found in dairy products and other foods, there is limited information available on its genetic makeup in yak milk. In the present study, 10 E. hirae strains isolated and identified from fresh white yak milk samples, along with 442 E. hirae strains obtained from the NCBI database (totaling 452 strains), were subjected to comparative genomic analysis. The findings of this study revealed that E. hirae has an open pan-genomic structure that allows for its high adaptability and environmental plasticity. Notably, E. hirae isolates from fresh white yak milk had smaller genomes, encoded more functional genes, and had fewer copies of genes encoding carbohydrate-active enzymes involved in the degradation of oligosaccharide metabolism and autolysin synthesis (CE1, GH73, GH23, and GT4 families) than those from animal and human isolates (P < 0.05). Additionally, fresh white yak milk isolates carried only three intrinsic bacteriocins and lacked virulence factors, CRISPR-Cas systems, and resistance genes linked to pathogenicity, which may be attributed to their specialization in the milk-derived environment. This study provides new insights into the genetic and functional gene diversity of E. hirae and how it adapts to milk-derived habitats.

Relationship Between CRISPR-Cas Systems and Acquisition of Tetracycline Resistance in Non-Clinical Enterococcus Populations in Bulgaria

Non-clinical enterococci are relatively poorly studied by means of acquired antibiotic resistance to tetracycline and by the distribution, functionality and role of their CRISPR systems. Background: In our study, 72 enterococcal strains, isolated from various non-clinical origins, were investigated for their phenotypic and genotypic (tet(M), tet(O), tet(S), tet(L), tet(K), tet(T) and tet(W)) tetracycline resistance. Methods: The genetic determinants for HGT (MGEs (Int-Tn and prgW), inducible pheromones (cpd, cop and cff), aggregation substances (agg, asa1, prgB and asa373) and CRISPR-Cas systems were characterized by PCR and whole-genome sequencing. Results: Four tet genes (tetM, tetO, tetS and tetT) were detected in 39% (n = 28) of our enterococcal population, with tetM (31%) being dominant. The gene location was linked to the Tn6009 transposon. All strains that contained tet genes also had genes for HGT. No tet genes were found in E. casseliflavus and E. gilvus. In our study, 79% of all tet-positive strains correlated with non-functional CRISPR systems. The strain E. faecalis BM15 was the only one containing a combination of a functional CRISPR system (cas1, cas2, csn2 and csn1/cas9) and tet genes. The CRISPR subtype repeats II-A, III-B, IV-A2 and VI-B1 were identified among E. faecalis strains (CM4-II-A, III-B and VI-B1; BM5-IV-A2, II-A and III-B; BM12 and BM15-II-A). The subtype II-A was the most present. These repeats enclosed a great number of spacers (1-10 spacers) with lengths of 31 to 36 bp. One CRISPR locus was identified in plasmid (p.Firmicutes1 in strain E. faecalis BM5). We described the presence of CRISPR loci in the species E. pseudoavium, E. pallens and E. devriesei and their lack in E. gilvus, E. malodoratus and E. mundtii. Conclusions: Our findings generally describe the acquisition of foreign DNA as a consequence of CRISPR inactivation, and self-targeting spacers as the main cause.

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.

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.

Isolation and identification of probiotic Bacillus subtilis AJQ03 from the intestinal tract of Anguilla japonica (Japanese eel)

In recent years, the use of fish-derived probiotics in aquaculture has become more widespread. However, research on Anguilla japonica-derived probiotics is still limited. To evaluate the potential of probiotics for disease control in eel aquaculture, isolates were obtained from the intestinal tract of healthy Anguilla japonica. These isolates were assessed for their adhesion properties, inhibition of pathogen adhesion, and hydrolytic enzyme production. Morphological characteristics and 16S rRNA sequence analysis were used for identification. Results showed that the AJQ03 strain adhered to the intestinal mucus and inhibited common pathogenic bacteria through adhesion inhibition, and further produced amylase, lipase, protease, and cellulase. Based on morphological characteristics and 16S rRNA sequencing, AJQ03 was identified as Bacillus subtilis. The strain demonstrated tolerance to various extreme conditions, as well as survival in simulated gastrointestinal fluids and superior growth in intestinal fluid compared to Luria-Bertani (LB) broth. In vitro safety tests showed that AJQ03 was not resistant to 32 antibiotics and exhibited γ hemolysis on blood plate. In vivo safety tests demonstrated a 100% survival rate for the fish, with stable organ indices, reduced bacterial loads in the liver and spleen, and complete bacterial clearance by day 7 without residue. Intestinal bacterial load results confirmed effective colonization by strain AJQ03. Analysis of the impact of AJQ03 on the gut microbiota of A. japonica revealed a significant increase in the relative abundance of Bacillus at the genus level, corroborating the colonization efficiency of AJQ03. Additionally, the relative abundances of Klebsiella, Pseudomonas, and Aeromonas were significantly lower compared to the controls, indicating that strain AJQ03 effectively reduced harmful bacteria and improved gut microbiota composition. This study confirms that B. subtilis AJQ03, isolated from the intestine of A. japonica, can serve as a probiotic candidate in A. japonica aquaculture.

Safety assessment of enterocin-producing Enterococcus strains isolated from sheep and goat colostrum

BACKGROUND

This study investigates the safety evaluation of enterocin-producing 11 E. mundtii and two E. faecium strains previously isolated from small livestock colostrums. Enterococcus species do not possess Generally Recognized as Safe (GRAS) status. Hence, it is critical to scrutinize enterococci's antibiotic resistance, virulence characteristics, and biogenic amine production capabilities in order to assess their safety before using them as starter or adjunct cultures.

RESULTS

Enterococcus strains showed susceptibility to medically significant antibiotics. Multiple-drug resistance (MDR) was found in only E. faecium HC121.4, and its multiple antibiotic resistance (MAR) index was detected to be 0.22. The tetL and aph(3')-IIIa were the most commonly found antibiotic resistance genes in the strains. However, E. mundtii strains HC56.3, HC73.1, HC147.1, and E. faecium strain HC121.4 were detected to lack any of the antibiotic resistance genes examined in this study. Only E. mundtii HC166.3 showed hemolytic activity, while none of the strains engage in gelatinase activity. The strains were identified to have virulence factor genes with a low rate. None of the virulence factor genes could be detected in E. mundtii HC26.1, HC56.3, HC73.1, HC165.3, HC166.8, and E. faecium HC121.4. The E. mundtii HC73.2 strain displayed the highest presence of virulence factor genes, namely gelE, efaAfs, cpd, and ccf. Similarly, the E. mundtii HC112.1 strain showed a significant presence of genes efaAfm, ccf, and acm. There was no decarboxylation of histidine, ornithine, or lysine seen in any of the strains. Nevertheless, E. faecium HC121.4 and HC161.1 strains could decarboxylate tyrosine, but E. mundtii HC26.1, HC56.3, HC73.1, HC73.2, HC112.1, HC147.1, HC155.2, HC165.3, HC166.3, HC166.5, and HC166.8 strains only showed a limited capacity for tyrosine decarboxylation. None of the strains possessed the hdc, odc, or ldc genes, but all of them had the tdc gene.

CONCLUSION

The E. mundtii HC56.3 and HC73.1 strains were deemed appropriate for utilization in food production. Using the remaining 11 strains as live cultures in food production activities could pose a possible risk to consumer health.

Insights into Genomic Characteristics and Biogenic Amine Degradation Potential and Mechanisms: A Strain of Pediococcus acidilactici Sourced from Doubanjiang

The control of excess biogenic amines (BAs) is crucial for the sustainable development of fermented foods. This study aimed to screen endogenous functional strains in Doubanjiang with the capacity to degrade BAs and to elucidate their application potential. Pediococcus acidilactici L-9 (PA), which was confirmed as a safe strain by phenotypic and genotypic analyses, exhibited an efficient degradation ability on BAs, particularly regarding tyramine. Notably, the degradation of tyramine was maintained at 24.03-50.60% at different temperatures (20-40 °C), pH values (4.0-9.0), and NaCl concentrations (3-18%, w/v). Additionally, genomic data revealed the presence of the laccase-coding gene, which was demonstrated to play a pivotal role in BA degradation by heterologous expression. Further, molecular docking results indicated that the degradation of BA by laccase is closely linked to the electron transfer pathway formed by the substrate and key amino acid residues. Finally, the degradation of tyramine by PA remained within the range of 8.19-64.19% under the simulated system with 6-12% salinity. This study provided valuable insights into the safety of PA and its potential degradation capacity on BAs, particularly in mitigating tyramine accumulation, which could improve the quality of Doubanjiang and other fermented foods.

Genomic diversity, antibiotic resistance, and virulence in South African Enterococcus faecalis and Enterococcus lactis isolates

This study presents the empirical findings of an in-depth genomic analysis of Enterococcus faecalis and Enterococcus lactis isolates from South Africa. It offers valuable insights into their genetic characteristics and their significant implications for public health. The study uncovers nuanced variations in the gene content of these isolates, despite their similar GC contents, providing a comprehensive view of the evolutionary diversity within the species. Genomic islands are identified, particularly in E. faecalis, emphasizing its propensity for horizontal gene transfer and genetic diversity, especially in terms of antibiotic resistance genes. Pangenome analysis reveals the existence of a core genome, accounting for a modest proportion of the total genes, with 2157 core genes, 1164 shell genes, and 4638 cloud genes out of 7959 genes in 52 South African E. faecalis genomes (2 from this study, 49 south Africa genomes downloaded from NCBI, and E. faecalis reference genome). Detecting large-scale genomic rearrangements, including chromosomal inversions, underscores the dynamic nature of bacterial genomes and their role in generating genetic diversity. The study uncovers an array of antibiotic resistance genes, with trimethoprim, tetracycline, glycopeptide, and multidrug resistance genes prevalent, raising concerns about the effectiveness of antibiotic treatment. Virulence gene profiling unveils a diverse repertoire of factors contributing to pathogenicity, encompassing adhesion, biofilm formation, stress resistance, and tissue damage. These empirical findings provide indispensable insights into these bacteria's genomic dynamics, antibiotic resistance mechanisms, and virulence potential, underlining the pressing need to address antibiotic resistance and implement robust control measures.

Identification of Enterococcus spp. from food sources by matrix-assisted laser desorption ionization-time of flight mass spectrometry and characterization of virulence factors, antibiotic resistance, and biofilm formation

The continuous detection of multi-drug-resistant enterococci in food source environments has aroused widespread concern. In this study, 198 samples from chicken products, animal feces, raw milk, and vegetables were collected in Japan and Egypt to investigate the prevalence of enterococci and virulence characterization. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was employed for species identification and taxonomic analysis of the isolates. The results showed that the rates of most virulence genes (efaA, gelE, asa1, ace, and hyl) in the Japanese isolates were slightly higher than those in the Egyptian isolates. The rate of efaA was the highest (94.9 %) among seven virulence genes detected, but the cylA gene was not detected in all isolates, which was in accordance with γ-type hemolysis phenotype. In Enterococcus faecalis, the rate of kanamycin-resistant strains was the highest (84.75 %) among the antibiotics tested. Moreover, 78 % of E. faecalis strains exhibited multi-drug resistance. Four moderately vancomycin-resistant strains were found in Egyptian isolates, but none were found in Japanese isolates. MALDI-TOF MS analysis correctly identified 98.5 % (68/69) of the Enterococcus isolates. In the principal component analysis dendrogram, strains isolated from the same region with the same virulence characteristics and similar biofilm-forming abilities were characterized by clustered distribution in different clusters. This finding highlights the potential of MALDI-TOF MS for classifying E. faecalis strains from food sources.

Prevalence and virulence factors of haemolytic Enterococcus faecalis isolated from root filled teeth associated with periradicular lesions: A laboratory investigation in Thailand

AIM

Previous endodontic research has provided limited understanding of the prevalence and roles of haemolytic and non-haemolytic Enterococcus faecalis strains in root filled teeth. This study aimed to determine the prevalence of these strains in root filled teeth with periradicular lesions and investigate their associated virulence factors.

METHODOLOGY

A total of 36 root canal samples were collected from 36 subjects. The prevalence of E. faecalis was determined using culture and PCR methods. Antibiotic susceptibility of haemolytic and non-haemolytic E. faecalis strains was assessed using the broth dilution assay. The cytokine stimulation in periodontal ligament (PDL) cells and neutrophil migration were evaluated using real-time PCR and migration assay, respectively. Cell invasion ability of the strains was assessed using a cell culture model. Additionally, the virulence gene expression of the haemolytic and non-haemolytic strains was investigated using real-time PCR. The Mann-Whitney U and Spearman's ρ tests were used to examine the significant difference between the two strains and to analyse the correlation between phenotype and gene expression, respectively.

RESULTS

Enterococcus faecalis was detected in 33.3% and 88.9% of samples by culture and real-time PCR, respectively. Haemolytic strains were found in 36.4% of subjects. Non-haemolytic strains exhibited susceptibility to erythromycin and varying susceptibility to tetracycline, while all haemolytic strains were resistant to both antibiotics. Haemolytic strains significantly upregulated the expression of IL-8, OPG and RANKL in PDL cells (p < .05). Notably, the fold increases in these genes were higher: IL-8 (556.1 ± 82.9 vs. 249.6 ± 81.8), OPG (2.2 ± 0.5 vs. 1.3 ± 0.2) and RANKL (1.8 ± 0.3 vs. 1.2 ± 0.1). Furthermore, haemolytic strains had a greater effect on neutrophil migration (68.7 ± 15.2% vs. 46.9 ± 11.4%) and demonstrated a higher level of internalization into oral keratinocyte cells (68.6 ± 0.4% vs. 33.8 ± 0.5%) (p < .05). They also showed enhanced expression of virulence genes associated with haemolysin, surface proteins, collagen-binding and aggregation substances. Gelatinase activity was only detectable in non-haemolytic strains.

CONCLUSIONS

This study revealed that haemolytic strains E. faecalis possessed enhanced abilities in host invasion and a higher abundance of virulence factors, suggesting their potential contribution to more severe disease manifestations.

Prevalence and Molecular Characteristics of Enterococci Isolated from Clinical Bovine Mastitis Cases in Ningxia

Purpose

This study aimed to investigate the prevalence and genetic characterization of enterococcal isolates (Enterococcus faecalis, Enterococcus faecium and Enterococcus hirae) isolated from clinical bovine mastitis cases in Ningxia, China.

Patients and Methods

The enterococci were identified by 16S rRNA amplification and sequencing. Antimicrobial resistance was determined by disc diffusion method. Virulence and antimicrobial resistance genes were detected by PCR assays.

Results

Overall, 198 enterococcal isolates were identified from 2897 mastitis samples, including 137 (4.7%) E. faecalis, 50 (1.7%) E. faecium and 11 (0.4%) E. hirae. E. faecalis, E. faecium and E. hirae isolates showed high resistance to tetracycline (92.7%, 68.0%, 90.9%), followed by erythromycin (86.9%, 76.0%, 72.7%). The multidrug-resistant strains of E. faecalis and E. faecium were 29 (21.2%) and 13 (26.0%), respectively. The resistance of E. faecalis, E. faecium and E. hirae isolates to tetracycline is mainly attributed to the presence of tetL (alone or combined with tetM and/or tetK), the erythromycin resistance to ermB (alone or combined with ermC and/or ermA). Moreover, cpd (94.2%), gelE (77.4%), efaAfs (93.4%), and esp (79.6%) were the most common virulence genes in E. faecalis. In E. faecium, except for the gene efaAfs (82.0%), other virulence genes are rarely found. Only two strains of E. hirae carrying asa1 gene were detected.

Conclusion

The results of this study can provide a reference for the prevention and treatment of bovine mastitis caused by enterococci.

The Impact of Enterococcus spp. in the Immunocompromised Host: A Comprehensive Review

The immunocompromised host is usually vulnerable to infectious diseases due to broad-spectrum treatments and immunological dysregulation. The Enterococcus genus consists of normal gut commensals, which acquire a leading role in infective processes among individuals with compromised immune systems. These microorganisms may express a potential virulence and resistance spectrum, enabling their function as severe pathogens. The Enterococcus spp. infections in immunocompromised hosts appear to be difficult to resolve due to the immunological response impairment and the possibility of facing antimicrobial-resistant strains. As regards the related risk factors, several data demonstrated that prior antibiotic exposure, medical device insertion, prolonged hospitalization and surgical interventions may lead to Enterococcus overgrowth, antibiotic resistance and spread among critical healthcare settings. Herein, we present a comprehensive review of Enterococcus spp. in the immunocompromised host, summarizing the available knowledge about virulence factors, antimicrobial-resistance mechanisms and host-pathogen interaction. The review ultimately yearns for more substantial support to further investigations about enterococcal infections and immunocompromised host response.

Autoprobiotics in the Treatment of Patients with Colorectal Cancer in the Early Postoperative Period

Despite great advances in the treatment of oncological diseases, the development of medical technologies to prevent or reduce complications of therapy, in particular, those associated with surgery and the introduction of antibiotics, remains relevant. The aim of this study is to evaluate the effectiveness of the use of autoprobiotics based on indigenous non-pathogenic strains of Enterococcus faecium and Enterococcus hirae as a personalized functional food product (PFFP) in the complex therapy of colorectal cancer (CRC) in the early postoperative period. A total of 36 patients diagnosed with CRC were enrolled in the study. Study group A comprised 24 CRC patients who received autoprobiotic therapy in the early postoperative period, while the control group C included 12 CRC patients without autoprobiotic therapy. Prior to surgery and between days 14 and 16 post-surgery, comprehensive evaluations were conducted on all patients, encompassing the following: stool and gastroenterological complaints analysis, examination of the gut microbiota (bacteriological study, quantitative polymerase chain reaction, metagenome analysis), and analysis of interleukins in the serum. Results: The use of autoprobiotics led to a decrease in dyspeptic complaints after surgery. It was also associated with the absence of postoperative complications, did not cause any side effects, and led to a decrease in the level of pro-inflammatory cytokines (IL-6 and IL-18) in the blood serum. The use of autoprobiotics led to positive changes in the structure of escherichia and enterococci populations, the elimination of Parvomonas micra and Fusobacterium nucleatum, and a decrease in the quantitative content of Clostridium perfringens and Akkermansia muciniphila. Metagenomic analysis (16S rRNA) revealed an increase in alpha diversity. Conclusion: The introduction of autoprobiotics in the postoperative period is a highly effective and safe approach in the complex treatment of CRC. Future studies will allow the discovery of additional fine mechanisms of autoprobiotic therapy and its impact on the digestive, immune, endocrine, and neural systems.

Antimicrobial Activity, Genetic Relatedness, and Safety Assessment of Potential Probiotic Lactic Acid Bacteria Isolated from a Rearing Tank of Rotifers (Brachionus plicatilis) Used as Live Feed in Fish Larviculture

Aquaculture is a rapidly expanding agri-food industry that faces substantial economic losses due to infectious disease outbreaks, such as bacterial infections. These outbreaks cause disruptions and high mortalities at various stages of the rearing process, especially in the larval stages. Probiotic bacteria are emerging as promising and sustainable alternative or complementary strategies to vaccination and the use of antibiotics in aquaculture. In this study, potential probiotic candidates for larviculture were isolated from a rotifer-rearing tank used as the first live feed for turbot larvae. Two Lacticaseibacillus paracasei and two Lactiplantibacillus plantarum isolates were selected for further characterization due to their wide and strong antimicrobial activity against several ichthyopathogens, both Gram-positive and Gram-negative. An extensive in vitro safety assessment of these four isolates revealed the absence of harmful traits, such as acquired antimicrobial resistance and other virulence factors (i.e., hemolytic and gelatinase activities, bile salt deconjugation, and mucin degradation, as well as PCR detection of biogenic amine production). Moreover, Enterobacterial Repetitive Intergenic Consensus-PCR (ERIC-PCR) analyses unveiled their genetic relatedness, revealing two divergent clusters within each species. To our knowledge, this work reports for the first time the isolation and characterization of Lactic Acid Bacteria (LAB) with potential use as probiotics in aquaculture from rotifer-rearing tanks, which have the potential to optimize turbot larviculture and to introduce novel microbial management approaches for a sustainable aquaculture.

Lactic Acid Bacteria isolated from traditional and innovative alheiras as potential biocontrol agents

From a selection of seven traditional and 14 innovative alheiras, 491 lactic acid bacteria (LAB) were isolated and tested for their antimicrobial activity against several food-borne pathogens. Among these, six strains revealed antimicrobial activity through potential bacteriocin production against 14 Listeria monocytogenes strains, Enterococcus faecalis ATCC 29212, Clostridium sporogenes ESB050, and Clostridium perfringens ESB054. Through whole genome sequencing (WGS), these strains were identified as Lactiplantibacillus plantarum (2), Leuconostoc mesenteroides (1), and Pediococcus acidilactici (3). Furthermore, several orthologues of class II bacteriocins genes were identified, including Plantaricin E, Plantaricin F, Pediocin PA, Enterocin X, Leucocin A, and Coagulin A. No virulence or antibiotic resistance genes' orthologues were detected by WGS analysis. However, the selected LAB strains showed variable phenotypic patterns related to virulence genes and antibiotic resistance when assessed through classical methodologies. None of these strains demonstrated the production of biogenic amines, gelatinase or DNase. Additionally, no hemolytic activity or lipase enzyme production was observed. However, only Lpb. plantarum 9A3 was sensitive to all tested antibiotics and was thus chosen for further examination. The bacteriocins produced by Lpb. plantarum (9A3) exhibited stability across a broad range of conditions, including temperatures from 4 to 100 °C, pH values ranging from 2 to 8, exposure to surfactants and detergents (Tween 20 and 80, SDS, EDTA 0.1, 2 and 5 mM, urea and sodium deoxycholate), and enzymes (papain and catalase). Their maximum activity (AU/mL = 12,800) against four L. monocytogenes strains was observed between 21 and 36 h of growth of Lbp. plantarum 9A3, indicating a bacteriostatic mode of action. Therefore, this strain appears to be a robust candidate for potential application as a protective strain to be used in the food industry. Not only is it safe, but it also produces stable bacteriocins (harbouring genes encoding for the production of three) effectively inhibiting significant pathogens such as L. monocytogenes and C. perfringens.

Antimicrobial resistance patterns, virulence genes, and biofilm formation in enterococci strains collected from different sources

BACKGROUND

Currently, antibiotic-resistant strains of Enterococcus are considered to be one of the critical health challenges globally. This study aimed to investigate the antibiotic susceptibility pattern, biofilm formation capacity, and virulence genes of enterococci isolated from different sources.

METHODS

In this cross-sectional study, environmental and fecal samples were collected from the hospital environment, volunteers, and hospital staff from October 2018 to August 2019. The isolates were identified by morphological and biochemical tests (gram staining, catalase, bile resistance, esculin hydrolysis, carbohydrate fermentation, growth in 6.5% NaCl, Pyrrolidonyl arylamidase, arginine dehydrolase), and PCR for ddl gene. An antimicrobial susceptibility test was performed by the standard disk agar diffusion method according to the Clinical and Laboratory Standards Institute (CLSI) guidelines. Quantitative microplate assays were used to assess biofilm production. The bacterial DNAs were extracted by alkaline lysis method and polymerase chain reaction technique was used detect the esp, ace, and efaA virulence genes.

RESULTS

Out of 145 isolates, 84 (57.9%) were identified as E. faecalis and 61 (42.1%) as E. faecium. Resistance to kanamycin and quinupristin-dalfopristin was 82.1% (69/84) and 85.7% (72/84), respectively, in E. faecalis isolates. Out of 61 E. faecalis isolates, 38 (62.4%) were resistant to kanamycin. Among the E. faecalis isolates, esp was the most dominant virulence gene (73.80%), followed by efaA, and ace, which were detected in 60.71%, and 30.95% isolates, respectively. In total, 68.27% of the strains were biofilm producers. Further, esp and efaA genes were more frequently found among E. faecalis strains with moderate and strong biofilm biomass.

CONCLUSIONS

According to the findings of our study, enterococci strains isolated from different samples possess distinctive patterns of virulence genes. The esp, ace, and efaA genes were more prevalent among E. faecalis than E. faecium. Besides, the high level antibiotic resistance of normal flora and environmental enterococci strains is alarming the researchers.

Genomic characterization of vancomycin-resistant Enterococcus faecium clonal complex 17 isolated from urine in tertiary hospitals in Northeastern Thailand

Vancomycin-resistant Enterococci (VREs) have increasingly become a major nosocomial pathogen worldwide, earning high-priority category from the World Health Organization (WHO) due to their antibiotic resistance. Among VREs, vancomycin-resistant Enterococcus faecium (VREfm) is particularly concerning, frequently isolated and resistant to many antibiotics used in hospital-acquired infections. This study investigated VREfm isolates from rural tertiary hospitals in Northeastern Thailand based both antibiotic susceptibility testing and whole-genome sequencing. All isolates showed resistance to vancomycin, ampicillin, erythromycin, tetracycline, ciprofloxacin, norfloxacin, and rifampin. Nitrofurantoin and tigecycline resistance were also observed in nearly all isolates. Conversely, all isolates remained susceptible to chloramphenicol, daptomycin, and linezolid. Genomic characterization revealed that all VREfm isolates belonged to clonal complex 17 (CC17), primarily consisting of sequence type (ST) 80, followed by ST17, ST761, and ST117. Additionally, all isolates harbored numerous antimicrobial-resistant genes, including vanA, tet(L), tet(M), aac(6')-li, ant(6)-Ia, aph(3')-III, aac(6')-aph(2″), aph(2″)-la, ant(9)-la, erm(B), msr(C), erm(T), erm(A), fosB, dfrG, and cfr(B). Notably, all isolates contained virulence genes, for collagen adhesin (acm) and cell wall adhesin (efafm), while hylEfm (glycosyl hydrolase) was detected in VREfm ST80. This study provided important information for understanding the genomic features of VREfm isolated from urine.

Pathogenic Potential and Antibiotic Susceptibility: A Comprehensive Study of Enterococci from Different Ecological Settings

The pathway and the lifestyle of known enterococcus species are too complicated. The aim of the present study is to trace the path of pathogenicity of enterococci isolated from seven habitats (Cornu aspersum intestine; Bulgarian yoghurt; goat and cow feta cheese-mature and young, respectively; Arabian street food-doner kebab; cow milk; and human breast milk) by comparing their pathogenic potential. In total, 72 enterococcal strains were isolated and identified by MALDI-TOF, sequencing, and PCR. Hemolytic and gelatinase activity were biochemically determined. PCR was carried out for detection of virulence factors (cylB, esp, gls24, nucl, psaA, agg, gelE, and ace) and antibiotic resistance (erm, ermB, blaZ, vanA, aphA, mefA, gyrA, catpIP501, and aac6'-aph2″). Phenotypic antibiotic resistance was assigned according to EUCAST. Eleven representatives of the genus Enterococcus were identified: E. mundtii, E. casseliflavus, E. gilvus, E. pseudoavium, E. pallens, E. malodoratus, E. devriesei, E. gallinarum, E. durans, E. faecium, and E. faecalis. Twenty-two strains expressed α-hemolysis. Thirteen strains had the cylB gene. Only two strains expressed α-hemolysis and possessed the cylB gene simultaneously. Positive amplification for gelE was found in 35% of the isolates, but phenotypic gelatinase activity was observed only in three strains. All isolates showed varying antibiotic resistance. Only E. faecalis BM15 showed multiple resistance (AMP-HLSR-RP). Correlation between genotypic and phenotypic macrolide resistance was revealed for two E. faecalis strains.

Prevalence of antibiotic resistance in lactic acid bacteria isolated from traditional fermented Indian food products

The emergence of antimicrobial resistance (AMR) in lactic acid bacteria (LAB) raises questions on qualified presumptive safety status and poses challenge of AMR transmission in food milieu. This study focuses on isolation, identification and characterization of AMR in LAB prevalent in traditional fermented Indian food products. The analysis of 16SrRNA based phylogenetic tree showed placements of isolates among four different genera Lactobacillus, Enterococcus, Weissella and Leuconostoc. In E-strip gradient test of susceptibility to 14 different antibiotics, over 50% of isolates showed resistance to ampicillin, chloramphenicol, ciprofloxacin, erythromycin, kanamycin, linezolid, streptomycin, trimethoprim and vancomycin. A multivariate principal component analysis, an antibiogram and multiple antibiotic resistance index-values (> 0.2) indicated presence of multidrug-resistance among the isolates. This study reports prevalence of an alarmingly high rate of AMR LAB strains in traditional fermented foods and is important to regulators and public health authorities for developing strategies to control transmission in food systems.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-023-01305-1.

Comparative study of virulence factor genes, β-hemolysis and biofilm production in invasive and colonizing enterococci

Objectives: In humans, enterococci are among the most important opportunistic pathogens. This study aims to compare invasive isolates obtained from blood cultures of patients with sepsis and endocarditis with colonizing isolates obtained from healthy donors’ stool samples.

Methods: A case-by-case assessment was conducted on invasive infection cases to determine whether enterococci were involved in their pathogenesis. They were tested for the presence of virulence factor genes, β-hemolysis on agars supplemented with human and sheep blood, and biofilm forming capacity.

Results: Three species of enterococci were identified among invasive isolates: Enterococcus faecalis, Enterococcus faecium, and Enterococcus durans. All endocarditis isolates were biofilm producers. Genes esp, gelE, asa1, ace, hyl, cylB, and cylA were present in 7 (41.2%), 11 (64.7%), 11 (64.7%), 13 (76.5%), 0, 3 (17.6%), and 1 (5.9%) invasive isolate, but none of them could be linked to a particular infection (sepsis or endocarditis). Colonizing isolates proved to have had more virulence factor genes, but the differences were not statistically significant. Members of that group produced a greater amount of biofilm when the ace gene was absent ( p = 0.047). The production of β-hemolysis by noninvasive strains was detected more frequently when agar was supplemented with human blood ( p = 0.021). In general, the presence of either cyl gene on that specific agar was in direct connection with the production of β-hemolysis: cylA ( p = 0.047) or cylB ( p = 0.020).

Conclusion: We have been unable to establish any correlation between invasive isolates and any virulence gene carriage and biofilm formation. β-hemolysis was produced significantly more often by colonizing strains when agar had been supplemented with human blood.

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.

Molecular characterization of tetracycline and vancomycin-resistant Enterococcus faecium isolates from healthy dogs in Egypt: a public health threat

BACKGROUND

Vancomycin-resistant enterococci (VRE) are among the most common causative pathogens for nosocomial infections worldwide. Moreover, strains of VRE have been isolated from several domestic livestock in Egypt.

METHODS

This study examined if healthy dogs are a potential source of VRE infection by isolating and characterizing Enterococcus faecium strains from stool samples on a morphological basis and biochemical activities. Subsequently, it was confirmed by genotypic characterization using polymerase chain reaction (PCR), followed by the detection of antibiotic resistance genes, virulence determinants, and genes contributing to enterocin production by PCR. Furthermore, the phylogenetic relationships among vanB and tetL genes were analyzed.

RESULTS

All ten fecal samples were identified as E. faecium and confirmed by PCR. In addition, 90% of the isolates tested were positive for the virulence genes gelE and esp, and all the isolates tested were positive for the antibiotic resistance genes tetL and vanB. Only three of the five enterocin genes examined were detected. Ent As-48, bacteriocin 31, and Ent L50 were identified in 100%, 80%, and 60% of the samples, respectively.

CONCLUSION

Dogs should be regarded as a reservoir of E. faecium that carries vancomycin resistance and virulence determinants that may affect public health in Egypt, considering a "One Health" task force approach to restrict their spread.

Safety evaluation of enterococci isolated from raw milk and artisanal cheeses made in Slovenia and Serbia

Enterococci represent a significant part of the non-starter LAB microbiota of artisanal cheeses produced mainly from raw milk. Common approaches to safety evaluation of enterococci isolates include assessment of antimicrobial resistance and virulence potential. Hence, a collection of 47 (n = 22, Serbia; n = 25, Slovenia) dairy enterococcal isolates, of which E. faecalis (n = 28), E. faecium (n = 11), E. durans (n = 5), E. casseliflavus (n = 2), and E. gallinarum (n = 1), was analyzed. The susceptibility to 12 antimicrobials was tested using a broth microdilution method, and the presence of the selected antimicrobial resistance and virulence genes was investigated using PCR. Isolates were resistant to tetracycline (TET) (25.5%), erythromycin (ERY) (17.0%), gentamycin and chloramphenicol (CHL) (∼6%). No resistance to ampicillin (AMP), ciprofloxacin (CIP), daptomycin (DAP), linezolid (LZD), teicoplanin (TEI), tigecycline (TGC) and vancomycin (VAN) was detected. Among all the resistance determinants analyzed, ermB gene was detected most frequently. All 10 virulence genes analyzed were detected with a distribution of cpd (72.3%), cob and ccf (70.2%), gelE (68.1%), hyl (59.6%), agg (53.2%) and esp (46.8%). The genes encoding cytolysin (cylA, cylM and cylB) were amplified to a lesser extent (21.3%, 21.3% and 12.8%, respectively). However, due to the limited number of enterococci isolates analyzed in the present study, further studies are still required in order to better document the safety status of dairy enterococci.

Exploiting Potential Probiotic Lactic Acid Bacteria Isolated from Chlorella vulgaris Photobioreactors as Promising Vitamin B12 Producers

Lactic acid bacteria (LAB) have been documented as potential vitamin B12 producers and may constitute an exogenous source of cobalamin for the microalga Chlorella vulgaris, which has been described as being able to perform vitamin uptake. Hence, there is an interest in discovering novel B12-producing probiotic LAB. Therefore, the purpose of the current work was to perform a phenotype-genotype analysis of the vitamin B12 biosynthesis capacity of LAB isolated from C. vulgaris bioreactors, and investigate their probiotic potential. Among the selected strains, Lactococcus lactis E32, Levilactobacillus brevis G31, and Pediococcus pentosaceus L51 demonstrated vitamin B12 biosynthesis capacity, with the latter producing the highest (28.19 ± 2.27 pg mL-1). The genomic analysis confirmed the presence of pivotal genes involved in different steps of the biosynthetic pathway (hemL, cbiT, cobC, and cobD). Notably, P. pentosaceus L51 was the only strain harboring cobA, pduU, and pduV genes, which may provide evidence for the presence of the cobalamin operon. All strains demonstrated the capability to withstand harsh gastrointestinal conditions, although P. pentosaceus L51 was more resilient. The potential for de novo cobalamin biosynthesis and remarkable probiotic features highlighted that P. pentosaceus L51 may be considered the most promising candidate strain for developing high-content vitamin B12 formulations.

Evaluation of Enterococcal Probiotic Usage and Review of Potential Health Benefits, Safety, and Risk of Antibiotic-Resistant Strain Emergence

Enterococci are often used in probiotics but can also cause nosocomial infections. As such, enterococcal consumption may have beneficial health effects, but a thorough evaluation of virulence absence and risk of antibiotic resistance spread is needed at the strain level. This article reviewed ten online health product shopping websites in the US. On these websites, 23 probiotic products using enterococci were found across 12 companies. In addition, this article reviewed studies that demonstrated the probiotic potential of enterococcal consumption (e.g., gastrointestinal and respiratory disease, hyperlipidemia alleviation, as well as infection prevention). To investigate the safety aspects of enterococci, the present work examined studies evaluating virulence factors and antibiotic resistance. Furthermore, this article assessed research that explored these virulent factors, specifically in probiotics containing enterococci, as well as the potential transfer mechanism of their antibiotic resistance. Based on reviewed data, enterococcal probiotic consumption has been proven beneficial for conditions or symptoms of multiple diseases without any apparent adverse effects. However, due to the plasmid- or transposon-mediated gene transfer ability of enterococci, surveillance monitoring and further studies regarding enterococcal consumption are warranted. Future studies that identify enterococcal strains safe to use in probiotics without virulence factors and antibiotic resistance are imperative for evidence-based decisions by health organizations and government agencies.

Molecular Characterization of Enterococcus faecalis and Enterococcus faecium Isolated from a Meat Source in Shahrekord Local Markets, Iran

Enterococcus faecalis (E. faecalis) and E. faecium (E. faecium) are commensals of the gastrointestinal biota of humans and animals and are considered opportunistic pathogens. This study aimed to improve the knowledge about E. faecalis and E. faecium isolated from meat. To this end, 104 meat samples were collected from sheep, goats, cattle, and calves from Shahrekord local markets in Iran. Presumptive colonies of E. faecalis and E. faecium were isolated from the samples and subjected to identification tests. Antimicrobial susceptibility was determined using the Kirby-Bauer disc diffusion method, and polymerase chain reaction (PCR) was performed to detect some virulence genes. Furthermore, randomly amplified polymorphic DNA typing and repetitive element sequence-based PCR fingerprinting were used to show the clonal relatedness of the isolates. The results revealed that enterococci were present in 90 out of 104 samples. Specifically, E. faecalis and E. faecium were the commonly isolated species, with the predominance of E. faecalis, which exhibited high resistance to streptomycin (95%) but was susceptible to vancomycin (85.6%). Virulence genes detection showed that ccf and cpd genes were the most prevalent genes in both species. In addition, the molecular typing method indicated that the isolates belonged to separate subgroups. This study shows the contamination of meat products by potential pathogens and resistant enterococci. There is a need to implement regular surveillance to monitor the emergence of antimicrobial-resistant E. faecalis and E. faecium in food, particularly in meat production.

Prevalence of Enterococcus species in adults with periodontal health or with periodontitis: a systematic review

The aim of this study was to evaluate the prevalence of Enterococcus species in the mouth of adults with periodontal health and periodontitis. A systematic search was made in databases in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines. The search for articles was conducted in Medline/PubMed, Latin American and Caribbean Health Sciences Literature Database (LILACS), Cochrane Library, Scopus, Embase, Web of Science databases and in the System of Information on Grey Literature in Europe (SINGLE) and included articles published in English up to April 25th, 2021. Observational studies in humans with and without periodontitis were evaluated to identify the prevalence of Enterococcus species. Articles that met the inclusion criteria were analyzed and classified to determine the quality rating in good, fair, and poor. A new detailed checklist for quality assessment was developed based on the information required for applicable data extraction in reviews. The study design, sample size, demographic data, periodontal clinical parameters, microbial analysis method, biological sample, prevalence of Enterococcus spp., and correlations with periodontal clinical parameters were assessed. After screening and full-text reading, 8 articles met the inclusion criteria. All selected studies showed a significantly higher prevalence of Enterococcus spp. in patients with periodontitis compared with periodontally healthy patients. Thus, the present systematic review suggests that the prevalence of Enterococcus faecalis in the mouth of periodontitis individuals is higher than that of periodontally healthy individuals.

The Emergence of Antimicrobial Resistance and Virulence Characteristics in Enterococcus Species Isolated from Bovine Milk

Enterococcus spp., including E. faecalis and E. faecium, pose risks to dairy farms as opportunistic pathogens. The study evaluates antimicrobial resistance (AMR) and virulence characteristics of Enterococcus spp. isolated from bovine milk. Bile esculin agar was used to assess 1471 milk samples, followed by colony identification, gram staining, catalase tests, and 45 °C incubation. PCR analysis targeted E. faecalis and E. faecium in characteristic Enterococcus spp. colonies, with MALDI-TOF used for negative samples. Multiple tests, including disk diffusion, chromogenic VRE agar for vancomycin resistance, Vancomycin Etest® for MIC determination, and PCR for virulence factors (cylA, esp, efaA, ace, asa1, gelE, and hyl genes), were performed. Out of 100 identified strains, E. durans (30.66%), E. faecium (26.28%), and E. faecalis (18.25%) were predominant. AMR in Enterococcus spp. varied, with the highest rates against rifampicin (27%), tetracycline (20%), and erythromycin (18%). Linezolid (5%), vancomycin, ciprofloxacin, and teicoplanin (3% each) had lower prevalence. E. faecium and E. faecalis showed high AMR to rifampicin, erythromycin, and tetracycline. Thirty-two strains (18.98%) grew on VRE Chromoselect agar, while 4 (2 E. faecalis and 2 E. faecium) showed vancomycin resistance by MIC values. E. faecalis carried gelE (45.5%) and asa1 (36%), and E. gallinarum had 9.1% with the asa1 gene. Detecting resistant Enterococcus in bovine milk supports control strategies for enterococci on dairy farms, highlighting AMR concerns in the food chain.

An Overview of the Factors Involved in Biofilm Production by the Enterococcus Genus

Enterococcus species are known for their ability to form biofilms, which contributes to their survival in extreme environments and involvement in persistent bacterial infections, especially in the case of multi-drug-resistant strains. This review aims to provide a comprehensive understanding of the mechanisms underlying biofilm formation in clinically important species such as Enterococcus faecalis and the less studied but increasingly multi-drug-resistant Enterococcus faecium, and explores potential strategies for their eradication. Biofilm formation in Enterococcus involves a complex interplay of genes and virulence factors, including gelatinase, cytolysin, Secreted antigen A, pili, microbial surface components that recognize adhesive matrix molecules (MSCRAMMs), and DNA release. Quorum sensing, a process of intercellular communication, mediated by peptide pheromones such as Cob, Ccf, and Cpd, plays a crucial role in coordinating biofilm development by targeting gene expression and regulation. Additionally, the regulation of extracellular DNA (eDNA) release has emerged as a fundamental component in biofilm formation. In E. faecalis, the autolysin N-acetylglucosaminidase and proteases such as gelatinase and serin protease are key players in this process, influencing biofilm development and virulence. Targeting eDNA may offer a promising avenue for intervention in biofilm-producing E. faecalis infections. Overall, gaining insights into the intricate mechanisms of biofilm formation in Enterococcus may provide directions for anti-biofilm therapeutic research, with the purpose of reducing the burden of Enterococcus-associated infections.

Analysis of Antibiotic-Resistant and Virulence Genes of Enterococcus Detected in Calf Colostrum-One Health Perspective

Enterococci are considered among the most prevalent global multidrug-resistant microorganisms globally. Their dissemination is a global concern, particularly by food-producing animals for both animals and humans. The aim of this study was to identify the species and investigate the antibiotic resistance and virulence profile of Enterococcus in bovine colostrum. Out of 88 presumptive Enterococcus isolates, species identification and susceptibility to 14 antimicrobials were tested using the disk diffusion method. An analysis of the antibiotic resistance and virulence genes was performed on the most prevalent species, using specific PCR assays. Enterococcus faecalis (54.5%), E. faecium (14.8%) and E. gallinarum (6.8%) were the identified species. To the best of our knowledge, this is the first report of E. gallinarum in bovine colostrum. The majority of the isolates showed resistance to quinupristin-dalfopristin (95.9%), erythromycin (80.7%), tetracycline (80.7%) and streptomycin (58%). Ninety-two percent of isolates were classified as multidrug-resistant. The most frequently detected resistance genes were tet(K) (61.1%), tet(M) (75.9%), tet(L) (90.7%), erm(B) (55.6%) and ant(6)-Ia (46.3%). The most prevalent virulence factors were cpd, esp, agg and cylL_L. Enterococcus faecium showed a higher probability of carrying the erm(C), tet(M), ace and gel(E) genes (p < 0.05). These results demonstrated that colostrum can constitute an important reservoir and vehicle for the dissemination of antibiotic resistance and virulence genes to the three niches included in a One Health perspective (humans, animals and the environment), highlighting the importance of hygiene sanitary measures to mitigate colostrum microbial contamination.

Antibiotic Susceptibility Patterns and Virulence-Associated Factors of Vancomycin-Resistant Enterococcal Isolates from Tertiary Care Hospitals

This study explored the prevalence of multi-drug resistance and virulence factors of enterococcal isolates obtained from various clinical specimens (n = 1575) including urine, blood, pus, tissue, catheter, vaginal wash, semen, and endotracheal secretions. Out of 862 enterococcal isolates, 388 (45%), 246 (29%), 120 (14%), and 108 (13%) were identified as Enterococcus faecalis, Enterococcus faecium, Enterococcus durans, and Enterococcus hirae, respectively, using standard morphological and biochemical methods. The antibiotic resistance profile of all these enterococcal isolates was checked using the disc diffusion technique. High-level resistance was observed for benzylpenicillin (70%) and vancomycin (43%) among E. faecalis and E. faecium isolates, respectively. This study also revealed the prevalence of 'multi-drug resistance (resistant to 3 antibiotic groups)' among the vancomycin-resistant enterococcal strains, and this was about 11% (n = 91). The virulence determinants associated with vancomycin resistance (VR) were determined phenotypically and genotypically. About 70 and 39% of E. faecalis and E. faecium isolates showed to be positive for all four virulence factors (gelatinase, protease, hemolysin, and biofilm). Among the several virulence genes, gelE was the most common virulence gene with a prevalence rate of 76 and 69% among E. faecalis and E. faecium isolates, respectively. More than 50% of VRE isolates harbored other virulence genes, such esp, asa, ace, and cylA. Similarly, the majority of the VR enterococcal isolates (n = 88/91) harbored vanA gene and none of them harbored vanB gene. These results disclose the importance of VR E. faecalis and E. faecium and the associated virulence factors involved in the persistence of infections in clinical settings.

Antibiotic Resistance of Enterococcus Species in Ornamental Animal Feed

Enterococcus is a bacterial genus that is strongly associated with nosocomial infections and has a high capacity to transfer and acquire resistance genes. In this study, the main objective was to evaluate the presence of Enterococcus species in ornamental animal feed and characterize their antimicrobial resistance and virulence factors. Antimicrobial susceptibility was determined using 14 antimicrobial agents by the disk diffusion method, complemented by genotypic analysis to identify Enterococcus species and the presence of 14 antimicrobial resistance and 10 virulence genes. From 57 samples of ornamental animal feed, 103 Enterococcus isolates were recovered from 15 bird, 9 fish and 4 reptile feed samples. Enterococcus isolates were highly resistance to rifampicin (78%) and erythromycin (48%), and 48% of isolates were classified as multidrug-resistant. Enterococcus faecalis (36.7%) and E. faecium (31.7%) were the species most frequently identified. Most isolates carried the resistance genes ermB (57%) and tetL (52%) and the virulence genes, cylL (52%) and esp (40%). Enterococcus gallinarum was the species with the highest number of multidrug-resistant isolates (50%) and virulence genes (80%). These results highlight the high levels of antibiotic-resistant Enterococcus spp. present in ornamental animal feed and the growing interaction of these animals with humans as a public health concern.

Safety assessment of Enterococcus lactis based on comparative genomics and phenotypic analysis

Enterococcus faecium is sometimes used in food production; however, its acquisition of antibiotic resistance has become an alarming health concern. The E. lactis species is closely related to E. faecium and has good probiotic potential. This study aimed to investigate the antibiotic resistance of E. lactis. We analyzed the antibiotic resistance phenotype and whole-genome sequences of 60 E. lactis isolates (23, 29, and 8 isolates from dairy products, Rice wine Koji, and human feces, respectively). These isolates showed varying degree of resistance to 13 antibiotics, and were sensitive to ampicillin and linezolid. The E. lactis genomes carried only a subset of commonly reported antibiotic resistance genes (ARGs) in E. faecium. Five ARGs were detected across the investigated E. lactis, including two universally present genes (msrC and AAC(6')-Ii) and three rarely detected ARGs (tet(L), tetM, and efmA). To identify other undescribed antibiotic resistance-encoding genes, a genome-wide association study was performed, returning 160 potential resistance genes that were associated with six antibiotics, namely chloramphenicol, vancomycin, clindamycin, erythromycin, quinupristin-dalfopristin, and rifampicin. Only around one-third of these genes encode known biological functions, including cellular metabolism, membrane transport, and DNA synthesis. This work identified interesting targets for future study of antibiotic resistance in E. lactis. The fact that the lower number of ARGs present in E. lactis supports that it may be an alternative to E. faecalis for use in the food industry. Data generated in this work is of interest to the dairy industry.

Differences in Virulence Factors and Antimicrobial Susceptibility of Uropathogenic Enterococcus spp. Strains in a Rural Area of Uganda and a Spanish Secondary Hospital

Enterococcus faecalis and Enterococcus faecium have become two of the most important agents of nosocomial diseases due to their constantly growing resistance. Enterococcal infections are associated with biofilms, which are intrinsically sensitive to antimicrobials. The main goal of this study was to compare and relate their capacity to form biofilm and their antimicrobial sensitivity, as well as their virulence factors and their implicated genes, of strains isolated from patients with urinary tract infection (UTI) in a rural hospital in Uganda and a secondary hospital in Spain. A prospective study was conducted with 104 strains of E. faecalis and E. faecium isolated from patients with suspected UTI and who presented leukocyturia at the Saint Joseph Kitgum hospital (Uganda) and at the Hospital Universitario Principe de Asturias (Spain). All microorganisms were identified in Spain by MALDI-TOF mass spectrometry. Antimicrobial susceptibility studies were carried out using the Vitek^® 2 system (Biomériux, France). The biofilm formation capacity was studied by photospectrometry. Phenotypic and genotypic virulence factors were studied in all cases by PCR or expression techniques. In Uganda, we found a higher incidence of E. faecium (65.3%, n = 32), contrary to the situation found in Spain where most of the bacteria found belonged to E. faecalis (92.7%, n = 51). All E. faecalis strains were found to have very low levels of resistance to ampicillin, imipenem, and nitrofurantoin. However, E. faecium exhibited more than 25% resistance to these antibiotics. Although the esp gene has been shown in the results obtained to be an important initial agent in biofilm formation, we have also demonstrated in this study the intervention of other genes when esp is not present, such as the ace1 gene. No statistically significant relationships were found between the presence of agg and gelE genes and increased biofilm formation. The significant difference between the incidence of E. faecalis and E. faecium and biofilm formation, between samples from Spain and Uganda, shows us very different profiles between countries.

Evaluation of the effectiveness of personalised therapy for the patients with irritable bowel syndrome

Intestinal microbiota correction in the therapy of irritable bowel syndrome (IBS) is an important medical problem. We conducted a laboratory and pilot clinical trial to investigate the effect of autoprobiotic bacteria, indigenous bifidobacteria and enterococci isolated from faeces and grown on artificial media to use as personified food additives in IBS treatment. Convincing evidence of the clinical efficacy of autoprobiotic was demonstrated by the disappearance of dyspeptic symptoms. The microbiome of patients with IBS was compared to a group of healthy volunteers and changes in the microbiome after autoprobiotic use were detected by quantitative polymerase chain reaction and 16S rRNA metagenome analysis. The possibility of reducing opportunistic microorganisms in the treatment of IBS with autoprobiotics has been convincingly proven. The quantitative content of enterococci in the intestinal microbiota was higher in IBS patients than in healthy volunteers and increased after therapy. An increase in the relative abundance of genera Coprococcus, Blautia and a decrease in the relative abundance of Paraprevotella spp. were found at the end of therapy. A metabolome study which was performed by gas chromatography and mass spectrometry demonstrated an increase in the content of oxalic acid, a decrease of dodecanoate, lauric acid, and other metabolome components after taking autoprobiotics. Some of these parameters correlated with the relative abundances of Paraprevotella spp., Enterococcus spp., and Coprococcus spp. representative of the microbiome. Apparently, they reflected the peculiarities of metabolic compensation and changes in the microbiota. Therefore, the use of autoprobiotics for treatment of IBS may lead to a stable positive clinical effect, associated with compensatory changes in the intestinal microbiota, and accompanied by corresponding changes in metabolic processes in the organism.

Determination of the Prevalence and Antimicrobial Resistance of Enterococcus faecalis and Enterococcus faecium Associated with Poultry in Four Districts in Zambia

The presence of antimicrobial-resistant Enterococci in poultry is a growing public health concern worldwide due to its potential for transmission to humans. The aim of this study was to determine the prevalence and patterns of antimicrobial resistance and to detect drug-resistant genes in Enterococcus faecalis and E. faecium in poultry from four districts in Zambia. Identification of Enterococci was conducted using phenotypic methods. Antimicrobial resistance was determined using the disc diffusion method and antimicrobial resistance genes were detected using polymerase chain reaction and gene-specific primers. The overall prevalence of Enterococci was 31.1% (153/492, 95% CI: 27.1–35.4). Enterococcus faecalis had a significantly higher prevalence at 37.9% (58/153, 95% CI: 30.3–46.1) compared with E. faecium, which had a prevalence of 10.5% (16/153, 95% CI: 6.3–16.7). Most of the E. faecalis and E. faecium isolates were resistant to tetracycline (66/74, 89.2%) and ampicillin and erythromycin (51/74, 68.9%). The majority of isolates were susceptible to vancomycin (72/74, 97.3%). The results show that poultry are a potential source of multidrug-resistant E. faecalis and E. faecium strains, which can be transmitted to humans. Resistance genes in the Enterococcus species can also be transmitted to pathogenic bacteria if they colonize the same poultry, thus threatening the safety of poultry production, leading to significant public health concerns.