A PCR assay for identification of Enterococcus faecium

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.

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.

Antimicrobial overproduction sustains intestinal inflammation by inhibiting Enterococcus colonization

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

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.

Identification and phylogenetic analysis of Enterococcus isolates using MALDI-TOF MS and VITEK 2

The bacterial genus Enterococcus encompasses 38 species. Two of the most common species are E. faecalis and E. faecium. Recently, however, there has been an increase in clinical reports concerning less prevalent Enterococcus species, such as E. durans, E. hirae, and E. gallinarum. Rapid and accurate laboratory methods are needed to facilitate the identification of all these bacterial species. In the present study, we compared the relative accuracy of matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS), VITEK 2, and 16S rRNA gene sequencing using 39 enterococci isolates from dairy samples, and compared the resultant phylogenetic trees. We found that MALDI-TOF MS correctly identified all isolates at the species level except for one, whereas the VITEK 2 system, which is an automated identification system using biochemical characteristics of species, misidentified ten isolates. However, phylogenetic trees constructed from both methods showed all isolates in similar positions. Our results clearly showed that MALDI-TOF MS is a reliable and rapid tool for identifying Enterococcus species with greater discriminatory power than the biochemical assay method of VITEK 2.

Molecular epidemiology of bacteraemic vancomycin-resistant Enterococcus faecium isolates and in vitro activities of SC5005 and other comparators against these isolates collected from a medical centre in northern Taiwan, 2019-2020

OBJECTIVES

The global prevalence of vancomycin-resistant Enterococcus faecium (VREfm) highlights the need for new anti-enterococcal agents. Here, we assessed the molecular epidemiology of clinical VREfm bacteraemic isolates from a medical centre in northern Taiwan in 2019-2020 and to evaluate their susceptibility to last-line antibiotics and a new antimicrobial agent, SC5005.

METHODS

The molecular epidemiology of VREfm was investigated using van genotyping, MLST and PFGE. The susceptibilities of VREfm strains to antibiotics and SC5005 were determined using the agar dilution and broth microdilution methods. The capability of E. faecium to develop resistance to antibiotics and SC5005 was evaluated using frequency of resistance and multipassage resistance assays. The mode of action of SC5005 was assessed by time-kill, bacterial membrane integrity and membrane potential assays.

RESULTS

All 262 VREfm isolates harboured vanA gene, and the most prevalent sequence type was ST17 (51%, n = 134, 84 pulsotypes), followed by ST78 (25%, n = 65, 54 pulsotypes). Additionally, we identified four new STs (ST2101, ST2102, ST2135 and ST2136) and observed the arrival of multidrug-resistant ST1885 in Taiwan. Moreover, SC5005 was effective against all VREfm isolates, including those non-susceptible to last-line antibiotics. SC5005 can disrupt and depolarize the bacterial membrane to kill E. faecium without detectable resistance.

CONCLUSIONS

The findings provide insights into the latest epidemiology and resistance profiles of bacteraemic-causing VREfm in northern Taiwan. Additionally, SC5005 has the potential for development as a new therapeutic to treat VREfm infections.

Vancomycin-variable enterococci in sheep and cattle isolates and whole-genome sequencing analysis of isolates harboring vanM and vanB genes

Background

Vancomycin resistance encoded by the vanA/B/M genes in enterococci is clinically important because of the transmission of these genes between bacteria. While vancomycin resistance is determined by detecting only vanA and vanB genes by routine analyses, failure to detect vanM resistance causes vancomycin resistance to be overlooked, and clinically appropriate treatment cannot be provided.

Aims

The study aimed to examine the presence of vanM-positive enterococcal isolates in Ankara, Turkey, and to have detailed information about them with sequence analyses.

Methods

Caecal samples were collected from sheep and cattle during slaughter at different slaughterhouses in Ankara, Turkey. Enterococci isolates were identified, confirmed, and analyzed for the presence of vanA/B/M genes. Antibiotic resistance profiles of isolates were determined by the broth microdilution method. A whole genome sequence analysis of the isolates harboring the vanM and vanB genes was performed.

Results

13.7% of enterococcal isolates were determined as Enterococcus faecium and Enterococcus faecalis. 15% of these isolates contained vanB, and 40% were vanM-positive. S98b and C32 isolates were determined to contain 16 CRISPR-Cas elements. 80% of the enterococci isolates were resistant to nitrofurantoin and 15% to ciprofloxacin. The first vanM-positive vancomycin-variable enterococci (VVE) isolates from food-producing animals were identified, and the S98b strain has been assigned to Genbank with the accession number CP104083.1.

Conclusion

Therefore, new studies are needed to facilitate the identification of vanM-resistant enterococci and VVE strains.

The Antimicrobial Effect of Various Single-Strain and Multi-Strain Probiotics, Dietary Supplements or Other Beneficial Microbes against Common Clinical Wound Pathogens

The skin is the largest organ in the human body and is colonized by a diverse microbiota that works in harmony to protect the skin. However, when skin damage occurs, the skin microbiota is also disrupted, and pathogens can invade the wound and cause infection. Probiotics or other beneficial microbes and their metabolites are one possible alternative treatment for combating skin pathogens via their antimicrobial effectiveness. The objective of our study was to evaluate the antimicrobial effect of seven multi-strain dietary supplements and eleven single-strain microbes that contain probiotics against 15 clinical wound pathogens using the agar spot assay, co-culturing assay, and agar well diffusion assay. We also conducted genera-specific and species-specific molecular methods to detect the DNA in the dietary supplements and single-strain beneficial microbes. We found that the multi-strain dietary supplements exhibited a statistically significant higher antagonistic effect against the challenge wound pathogens than the single-strain microbes and that lactobacilli-containing dietary supplements and single-strain microbes were significantly more efficient than the selected propionibacteria and bacilli. Differences in results between methods were also observed, possibly due to different mechanisms of action. Individual pathogens were susceptible to different dietary supplements or single-strain microbes. Perhaps an individual approach such as a 'probiogram' could be a possibility in the future as a method to find the most efficient targeted probiotic strains, cell-free supernatants, or neutralized cell-free supernatants that have the highest antagonistic effect against individual clinical wound pathogens.

Multiplexed colorimetric detection of SARS-CoV-2 and other pathogens in wastewater on a 3D printed integrated microfluidic chip

Severe acute respiratory coronavirus 2 (SARS-CoV-2) pandemic has become a global public health emergency. The detection of SARS-CoV-2 and human enteric pathogens in wastewater can provide an early warning of disease outbreak. Herein, a sensitive, multiplexed, colorimetric detection (termed "SMCD") method was established for pathogen detection in wastewater samples. The SMCD method integrated on-chip nucleic acid extraction, two-stage isothermal amplification, and colorimetric detection on a 3D printed microfluidic chip. The colorimetric signal during nucleic acid amplification was recorded in real-time and analyzed by a programmed smartphone without the need for complicated equipment. By combining two-stage isothermal amplification assay into the integrated microfluidic platform, we detected SARS-CoV-2 and human enteric pathogens with sensitivities of 100 genome equivalent (GE)/mL and 500 colony-forming units (CFU)/mL, respectively, in wastewater within one hour. Additionally, we realized smart, connected, on-site detection with a reporting framework embedded in a portable detection platform, which exhibited potential for rapid spatiotemporal epidemiologic data collection regarding the environmental dynamics, transmission, and persistence of infectious diseases.

Airborne bacterial emission fluxes from manure-fertilized agricultural soil

This is the first study to quantify the dependence on wind velocity of airborne bacterial emission fluxes from soil. It demonstrates that manure bacteria get aerosolized from fertilized soil more easily than soil bacteria, and it applies bacterial genomic sequencing for the first time to trace environmental faecal contamination back to its source in the chicken barn. We report quantitative, airborne emission fluxes of bacteria during and following the fertilization of agricultural soil with manure from broiler chickens. During the fertilization process, the concentration of airborne bacteria culturable on blood agar medium increased more than 600 000-fold, and 1 m3 of air carried 2.9 × 105 viable enterococci, i.e. indicators of faecal contamination which had been undetectable in background air samples. Trajectory modelling suggested that atmospheric residence times and dispersion pathways were dependent on the time of day at which fertilization was performed. Measurements in a wind tunnel indicated that airborne bacterial emission fluxes from freshly fertilized soil under local climatic conditions on average were 100-fold higher than a previous estimate of average emissions from land. Faecal bacteria collected from soil and dust up to seven weeks after fertilization could be traced to their origins in the poultry barn by genomic sequencing. Comparative analyses of 16S rRNA gene sequences from manure, soil and dust showed that manure bacteria got aerosolized preferably, likely due to their attachment to low-density manure particles. Our data show that fertilization with manure may cause substantial increases of bacterial emissions from agricultural land. After mechanical incorporation of manure into soil, however, the associated risk of airborne infection is low.

Administration of Enterococcus faecium HS-08 increases intestinal acetate and induces immunoglobulin A secretion in mice

A probiotic is considered a live microbial feed supplement that has beneficial effects on the host. In this study, the probiotic property by which Enterococcus faecium HS-08 strengthens the immune system was investigated. Using a murine model, we evaluated the abilities of this strain to increase intestinal short-chain fatty acid contents and to induce the production of mucosal immunoglobulin A (IgA), which are crucial for mucosal immune systems. Various amounts (0%, 0.0038%, 0.038%, or 0.38%) of strain HS-08 cells were administered to BALB/cAJcl mice, which resulted in a dose-dependent increase of fecal IgA levels. A qRT-PCR analysis of Peyer's patch cells revealed that the gene expression of retinal-dehydrogenase, interleukin 6, B-cell-activating factor, and a proliferation-inducing ligand were increased, which leads to IgA secretion via a T-cell-independent mechanism. The administration of 0.038% and 0.38% of strain HS-08 cells also increased fecal acetate levels, which plays an important role for maintaining immune functions. This cecal floral analysis and the stability of strain HS-08 against gastrointestinal digestion suggest that this strain can inhabit the host intestine. In conclusion, the administration of E. faecium HS-08 increased intestinal acetate levels and enhanced IgA secretion, which may result in strengthening of the mucosal immune system.

Antimicrobial resistance and genetic relationships of enterococci from siblings and non-siblings Heliconius erato phyllis caterpillars

BACKGROUND

Studies evaluating bacteria in insects can provide information about host-microorganism-environment interactions. The gut microbial community has a profound effect on different physiological functions of insects. Enterococcus spp. are part of the gut community in humans and other animals, as well as in insects. The presence and antimicrobial resistance profile of enterococci are well studied in different animals; however, data for Heliconius erato phyllis (Lepidoptera: Nymphalidae) do not yet exist. Therefore, the aims of this study were to evaluate the distribution of enterococcal species, their antimicrobial resistance profile and virulence genes, and the genetic relationships between enterococci isolated from fecal samples from sibling and non-sibling H. erato phyllis caterpillars collected from different sites in South Brazil.

METHODS

Three H. erato phyllis females were captured (two from a forest fragment and one from an urban area), and kept individually in open-air insectaries. Eggs were collected and caterpillars (siblings and non-siblings) were fed daily with Passiflora suberosa leaves. Fecal samples (n = 12) were collected from fifth-instar caterpillars, inoculated in selective medium, and 15 bacterial colonies were randomly selected from each sample. Enterococci were identified by PCR and MALDI-TOF, analyzed by disk diffusion antimicrobial susceptibility tests, and screened for resistance and virulence genes by PCR. The genetic relationships between the strains were determined using pulsed-field gel electrophoresis (PFGE).

RESULTS

A total of 178 enterococci strains were identified: E. casseliflavus (74.15%; n = 132), E. mundtii (21.34%; n = 38), E. faecalis (1.12%; n = 2) and Enterococcus sp. (3.37%; n = 6). High rates of resistance to rifampicin (56%) and erythromycin (31%) were observed; 120 (67.41%) of the isolates showed resistance to at least one antibiotic and six (3.37%) were multidrug-resistant.None of the erythromycin-resistant strains was positive for the erm(B) and msrC genes. The virulence genes esp, ace, and gelE were observed in 35%, 7%, and 1% of the strains, respectively. PFGE separated the enterococci into 22 patterns, four being composed of strains from sibling caterpillars.

CONCLUSION

Enterococcus casseliflavus was the dominant species in fecal samples of fifth-instar caterpillars. Resistant enterococci strains may be related to environmental pollution or the resistome. The PFGE analysis showed genetic relationships between some strains, suggesting that the enterococci isolated from fecal samples of the sibling caterpillars might have come from common sources, e.g., via diet (herbivory) and/or vertical transmission (through the egg surface). Further studies will be conducted to better understand the role of Enterococcus in the microbial community of the gastrointestinal tract of these insects, and the mechanisms involved in acquisition and maintenance of enterococci.

Using groEL as the target for identification of Enterococcus faecium clades and 7 clinically relevant Enterococcus species

BACKGROUND/PURPOSE

Accurate identification is important for effective treatment because Enterococcus species have talents to cope with various antibiotics either by intrinsic resistance or by acquisition of mobile genetic elements. The groEL gene is a permissive target in identification of bacteria. We aimed to develop simple assays based on groEL for identification of enterococci.

RESULTS

We continued our previous work and determined groEL gene sequences of Enterococcus species isolated from clinical specimens. Phylogenetic analysis based on groEL revealed that each strain clustered well with their reference strains (bootstrap value 100%), in which Enterococcusfaecium and Enterococcusgallinarum could be split into two clades. The divergence of E. faecium was coincident with hospital-associated clade, known as clade A, and community-associated clade, known as clade B. A PCR-restriction fragment length polymorphism (PCR-RFLP) assay was therefore designed to differentiate the two E. faecium clades, based on the specific RsaI cutting sites present in the two clades. To differentiate 7 clinical relevant Enterococcus species, the multiplex PCR assay was designed to identify Enterococcusavium, Enterococcuscasseliflavus, Enterococcusfaecalis, E. faecium, E. gallinarum, Enterococcushirae and Enterococcusraffinosus. Specificity was tested with other Enterococcus species including Enterococcuscecorum, Enterococcusdurans and Enterococcusmundtii. None of these bacterial species generated products of similar size to those of the seven Enterococcus species.

CONCLUSION

The simple PCR-RFLP and multiplex PCR assays on the basis of groEL gene provided an alternative way to identify Enterococcus species.

Frequency of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in non-clinical Enterococcus faecalis and Enterococcus faecium strains

The fidelity of the genomes is defended by mechanism known as Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) systems. Three Type II CRISPR systems (CRISPR1- cas, CRISPR2 and CRISPR3-cas) have been identified in enterococci isolates from clinical and environmental samples. The aim of this study was to observe the distribution of CRISPR1-cas, CRISPR2 and CRISPR3-cas in non-clinical strains of Enterococcus faecalis and Enterococcus faecium isolates from food and fecal samples, including wild marine animals. The presence of CRISPRs was evaluated by PCR in 120 enterococci strains, 67 E. faecalis and 53 E. faecium. It is the first report of the presence of the CRISPRs system in E. faecalis and E. faecium strains isolated from wild marine animal fecal samples. The results showed that in non-clinical strains, the CRISPRs were more frequently detected in E. faecalis than in E. faecium. And the frequencies of CRISPR1-cas and CRISPR2 were higher (60%) in E. faecalis strains isolated from animal feces, compared to food samples. Both strains showed low frequencies of CRISPR3-cas (8.95% and 1.88%). In conclusion, the differences in the habitats of enterococcal species may be related with the results observe in distribution of CRISPRs systems.

Study of the In Vitro Antagonistic Activity of Various Single-Strain and Multi-Strain Probiotics against Escherichia coli

Escherichia coli is an important commensal of our gut, however, many pathogenic strains exist, causing various severe infections in the gut or beyond. Due to several antibiotic resistance patterns of E. coli, research of alternative treatments or adjuvant therapy is important. One of these is the use of probiotics as antagonistic agents against E. coli. Most published studies investigate only one strain of E. coli and single-strain probiotics. The objectives of this study were to evaluate the antagonistic activity of selected single-strain and multi-strain probiotic supplements against selected clinical E. coli pathotypes using the in vitro agar spot test and the co-culturing method. Molecular methods were used to determine the presence of the genus lactobacilli and bifidobacteria as well as certain selected strains in the probiotic supplements. The agar-spot test showed that the multi-strain probiotics were more effective than the single-strain probiotics. On the other hand, the co-culturing method showed the opposite result, indicating that results are importantly influenced by the chosen method. The most effective single-strain probiotics against E. coli strains were Bifidobacterium animalis subsp. lactis BB-12 and Lactobacillus reuteri DSM 17938. The most effective multi-strain probiotics contained lactobacilli, bifidobacteria and enterococci strains, thus proving that most effective probiotics against E. coli strains are the lactic acid bacteria and bifidobacteria. The overall results from both in vitro tests reveal that all selected probiotics exhibited an antagonistic activity against all E. coli strains. From a public health perspective probiotics have thus proved to be successful in inhibiting the growth of E. coli and could therefore be used as adjuvant therapy or alternative therapy in E. coli infections.

Modulations in the offspring gut microbiome are refractory to postnatal synbiotic supplementation among juvenile primates

Background

We and others have previously shown that alterations in the mammalian gut microbiome are associated with diet, notably early life exposure to a maternal high fat diet (HFD). Here, we aimed to further these studies by examining alterations in the gut microbiome of juvenile Japanese macaques (Macaca fuscata) that were exposed to a maternal HFD, weaned onto a control diet, and later supplemented with a synbiotic comprised of psyllium seed and Enterococcus and Lactobacillus species.

Results

Eighteen month old offspring (n = 7) of 36% HFD fed dams were fed a control (14% fat) diet post weaning, then were synbiotic supplemented for 75 days and longitudinal stool and serum samples were obtained. All stool samples were subjected to 16S rRNA metagenomic sequencing, and microbiome profiles and serum lipids and triglycerides were compared to untreated, healthy age matched and diet matched controls (n = 7). Overall, 16S-based metagenomic analysis revealed that supplementation exerted minimal alterations to the gut microbiome including transient increased abundance of Lactobacillus species and decreased abundance of few bacterial genera, including Faecalibacterium and Anaerovibrio. However, serum lipid analysis revealed significant decreases in triglycerides, cholesterol, and LDL (p < 0.05). Nevertheless, supplemented juveniles challenged 4 months later were not protected from HFD-induced gut dysbiosis.

Conclusions

Synbiotic supplementation is temporally associated with alterations in the gut microbiome and host lipid profiles of juvenile Japanese macaques that were previously exposed to a maternal HFD. Despite these presumptive temporal benefits, a protective effect against later HFD-challenge gut dysbiosis was not observed.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1169-9) contains supplementary material, which is available to authorized users.

Microbiological and biochemical aspects of inland Pecorino Abruzzese cheese

Little is known on physicochemical and biochemical characteristics of “Pecorino” Abruzzese cheese in L’Aquila province, an artisanal cheese produced from ewe raw full-cream milk.

Three batches of inland “Pecorino” Abruzzese cheese were examined for microbiological, compositional, biochemical and sensory characteristics at the aim of isolating and storing in a bacterial collection, indigenous strain to preserve the microbial biodiversity present in this cheese, to a possible definition of a PDO. Cheese samples from three dairies, at different stages of production were collected and 148 colonies were characterized. Physicochemical assays, species-specific PCR and 16S rRNA gene sequencing revealed that the majority of the lactic acid bacteria (LAB) isolates were Enterococcus faecium and En. faecalis. They were highly prevalent, accounting for 48% of the isolates. The lactic microflora consisted of lactobacilli and lactococci from the species Lactobacillus plantarum (12.2%), Lactobacillus brevis (10.1%), Lactococcus lactis subsp. cremoris (11.5%), respectively.

Urea-PAGE electrophoresis showed extensive degradation of α_S1-casein (CN) and moderate hydrolysis of β-CN. Formation of γ-CNs from β-CN were highlighted. RP-HPLC profiles of the ethanol-soluble and ethanol-insoluble fractions of the pH 4.6-soluble nitrogen showed only minor differences between the three farms: lower proteolysis in the soluble fraction than the insoluble.

Leucine, glutamic acid, lysine, valine were the free amino acids present at the highest levels in all the cheeses. Flavour and texture profile were characterized through a sensory analysis.

Resistance to antimicrobial agents among enterococci isolated from fecal samples of wild marine species in the southern coast of Brazil

The purpose of this study was to evaluate species distribution, antimicrobial resistance profiles, and presence of resistance genes in enterococci isolated from fecal samples of wild marine species, including seabirds (n=12), sea turtles (n=8), and mammals (n=3) found alive or dead in southern coast of Brazil. Enterococci were classified based on phenotypic and genotypic characteristics, tested for antibiotic susceptibility, and the presence of tet(S), tet(M), tet(L), mrsC, and erm(B) genes by PCR. Enterococcus faecalis and Enterococcus faecium were the most common species. Single (37.09%), double (25.80%), and multiple (16.12%) antibiotic resistance patterns were observed. Resistance to rifampicin occurred most frequently. The msrC, tet(M), and/or tet(L) genes were detected in 60.15%, 73.07%, and 23.07% of the resistant strains, respectively. In conclusion, the presence of antibiotic resistant strains in these species could be related to food web interactions and aquatic pollutants or linked to environmental resistome.

Antimicrobial resistance and virulence factor gene profiles of Enterococcus spp. isolates from wild Arctocephalus australis (South American fur seal) and Arctocephalus tropicalis (Subantarctic fur seal)

Enterococci are natural inhabitants of the gastrointestinal tracts in humans and animals. Epidemiological data suggest that enterococci are important reservoirs of antimicrobial resistant genes that may be transmitted from other bacterial species The aim of this study was to investigate the species composition, antimicrobial resistance and virulence genes in enterococci recovered from fecal samples of wild Arctocephalus australis and A. tropicalis found dead along the South Coast of Brazil. From a total of 43 wild fur seals, eleven were selected for this study. Phenotypic and genotypic characterizations were used to classify Enterococcus species. Strains were tested for susceptibility to 10 antibiotics, presence of ace, gelE, asa, cylA, tet(L), tet(M) and erm(B) genes by PCR, and genetic variability using RAPD-PCR. Among the 50 enterococci isolated, 40% were Enterococcus faecalis, 40% E. hirae, 12% E. casseliflavus and 8 % other enterococcal species. Resistance profiles were observed to erythromycin, nitrofurantoin, tetracycline, norfloxacin and ciprofloxacin. The prevalence of virulence genes was ace (68%), gelE (54%), asa (22%) and cylA (4%). In erythromycin- and tetracycline strains, erm(B) and tet(M) were detected, respectively. The RAPD-PCR demonstrated a close phylogenetic relationship between the enterococci isolated from A. australis and A. tropicalis. In conclusion, different enterococcus species showing antimicrobial resistance and virulence determinates were isolated from fecal samples of fur seals. Antibiotic resistant strains in these animals could be related within food chain and aquatic pollutants or linked to environmental resistome, and demonstrates the potential importance of these animals as reservoirs and disseminators of such determinants in marine environmental.

Spread of Enterococcal Surface Protein in Antibiotic Resistant Entero-coccus faecium and Enterococcus faecalis isolates from Urinary Tract Infections

Enterococci rank among leading cause of nosocomial bacteremia and urinary tract infection in hospital and community acquired infections. Several traits that may contribute to enhanced virulence have been identified in Enterococci. Extracellular surface protein (Esp) is a virulence factor that contributes in biofilm formation and resistance to environmental stresses. In this study we aimed to determine occurrence of esp in E. faecium and E. faecalis isolates isolated from urinary tract infections and to investigate whether there is any correlation between presence of esp and antibiotic resistance. One hundred and sixty six isolates were collected from patients with UTI and after identification by biochemical and PCR, antibiotic resistances were examined. The presence of esp was investigated by primer-specific PCR. 43.3% of isolates identified as E. faecium and 56.7% as E. faecalis. The esp gene was found in 76.1% of E. faecium isolates and 77.9% of E. faecalis isolate. There were significant correlation between esp positive E. faecium and resistance to Vancomycin (p<0.01), also in E.faecalis we found correlation between esp positive and resistance to Ampicillin, Chloramphenicol and Tetracycline (p<0.01, p<0.01, p<0.01 respectively). Occurrence of esp in our isolates from urinary tract infection was high that indicates importance of this gene in urinary tract infections and shows importance of ability to forming biofilm and hydrophobicity of surface of Enterococci for causing urinary infection by Enterococci. Also, our finding showed significant correlation between resistance to antibiotics and presence of esp in Enterococci.

The anti-Candida activity by Ancillary Proteins of an Enterococcus faecium strain

An antimycotic activity toward seven strains of Candida albicans was demonstrated erstwhile by a wild-type Enterococcus faecium isolated from a penguin rookery of the Antarctic region. In the present study the antimicrobial principle was purified by ion exchange and gel permeation chromatography and further was analyzed by LC-ESI-MS/MS. In the purification steps, the dialyzed concentrate and ion exchange fractions inhibited C. albicans MTCC 3958, 183, and SC 5314. However, the gel filtration purified fractions inhibited MTCC 3958 and 183. The data obtained from the LC-ESI-MS/MS indicate that the antimicrobial activity of the anti-Candida protein produced by E. faecium is facilitated by Sag A/Bb for the binding of the indicator organism's cell membrane. Partial N-terminal sequence revealed 12 N-terminal amino acid residues and its analysis shown that it belongs to the LysM motif. The nucleotide sequence of PCR-amplified product could detect 574 nucleotides of the LysM gene responsible for binding to chitin of the cell wall of Candida sp.

Molecular characteristics of vancomycin-resistant Enterococcus faecium from a tertiary care hospital in Chengdu, China: molecular characteristics of VRE in China

The aim of this study was to characterize vancomycin-resistant Enterococcus faecium (VREfm) isolates phenotypically and molecularly, and investigate associations between the virulence factors enterococcal surface protein (esp), hyaluronidase (hyl), and collagen adhesin (acm) and colonization/infection. A total of 126 E. faecium [66 VREfm and 60 vancomycin-susceptible (VSEfm)] were collected in West China Hospital. Nine E. faecium isolates (7 VREfm and 2 VSEfm) were selected at random for comparative study in a large region from China. Minimum inhibitory concentrations (MICs) were measured by Etest and agar dilution, vancomycin resistance genes (vanA, vanB, and vanC) and virulence genes (esp, acm, and hyl) were detected by polymerase chain reaction (PCR). Thirty-four VREfm underwent repetitive sequence-based PCR (rep-PCR) and multi-locus sequence typing (MLST). One linezolid-resistant isolate (MIC = 8 μg/ml) was found; none were tigecycline resistant. All 73 VREfm (28 infective strains and 45 intestinal colonizers) had the vanA gene and VanA phenotype. Positivity for esp, hyl, and acm in VREfm was 79.5, 46.6, and 86.3%, respectively, which was higher than in VSEfm (54.8, 27.4, and 56.5%, respectively). Among VSEfm, positivity for acm in isolates from pleural or cerebrospinal fluid (84.6%) was higher than that from blood (32.4%). There were 11 rep-PCR types (similarity >95%) and MLST revealed nine sequence types (STs) among the selected isolates. Most VREfm and all VSEfm belonged to clonal complex 17. A new ST was found, with allele sequence (15, 1, 38, 1, 1, 1, 1). In China, most VREfm seem to belong to the classical nosocomial CC17 clone, and many of them have acquired virulence genes, further strengthening a hospital-adapted type.

Mortality in kittens is associated with a shift in ileum mucosa-associated enterococci from Enterococcus hirae to biofilm-forming Enterococcus faecalis and adherent Escherichia coli

Approximately 15% of foster kittens die before 8 weeks of age, with most of these kittens demonstrating clinical signs or postmortem evidence of enteritis. While a specific cause of enteritis is not determined in most cases, these kittens are often empirically administered probiotics that contain enterococci. The enterococci are members of the commensal intestinal microbiota but also can function as opportunistic pathogens. Given the complicated role of enterococci in health and disease, it would be valuable to better understand what constitutes a "healthy" enterococcal community in these kittens and how this microbiota is impacted by severe illness. In this study, we characterized the ileum mucosa-associated enterococcal community of 50 apparently healthy and 50 terminally ill foster kittens. In healthy kittens, Enterococcus hirae was the most common species of ileum mucosa-associated enterococci and was often observed to adhere extensively to the small intestinal epithelium. These E. hirae isolates generally lacked virulence traits. In contrast, non-E. hirae enterococci, notably Enterococcus faecalis, were more commonly isolated from the ileum mucosa of kittens with terminal illness. Isolates of E. faecalis had numerous virulence traits and multiple antimicrobial resistances. Moreover, the attachment of Escherichia coli to the intestinal epithelium was significantly associated with terminal illness and was not observed in any kitten with adherent E. hirae. These findings identify a significant difference in the species of enterococci cultured from the ileum mucosa of kittens with terminal illness compared to the species cultured from healthy kittens. In contrast to prior case studies that associated enteroadherent E. hirae with diarrhea in young animals, these controlled studies identified E. hirae as more often isolated from healthy kittens and adherence of E. hirae as more common and extensive in healthy kittens than in sick kittens.

Avaliação da microbiota bacteriana do queijo de coalho artesanal produzido na região Agreste do estado de Pernambuco

O objetivo desta pesquisa foi avaliar a qualidade microbiológica e o perfil ácido-láctico do queijo de coalho artesanal. Todas as amostras de queijo apresentaram coliformes totais, termotolerantes e presença de Escherichia coli, porém com os valores dentro dos padrões estabelecidos pela legislação vigente no país. O perfil ácido-láctico estudado mostrou uma microbiota heterogênea, constituída por lactobacilos, lactococos, estreptococos e enterococos, confirmadas as espécies Enterococcus faecalis, Enterococcus faecium, Streptococcus thermophilus e Lactococcus lactis.

Characterization and risk factors of vancomycin-resistant Enterococci (VRE) among animal-affiliated workers in Malaysia

AIMS

This study determined the risk factors and characteristics of vancomycin-resistant Enterococci (VRE) among individuals working with animals in Malaysia.

METHODS AND RESULTS

Targeted cross-sectional studies accompanied with laboratory analysis for the identification and characterization of resistance and virulence genes and with genotype of VRE were performed. VRE were detected in 9·4% (95% CI: 6·46-13·12) of the sampled populations. Enterococcus faecium, Enterococcus faecalis and Enterococcus gallinarum were isolated, and vanA was detected in 70% of the isolates. Enterococcus faecalis with vanB was obtained from one foreign poultry worker. At least one virulence gene was detected in >50% of Ent. faecium and Ent. faecalis isolates. The esp and gelE genes were common among Ent. faecium (58·3%) and Ent. faecalis (78%), respectively. The VRE species showed diverse RAPD profiles with some clustering of strains based on the individual's background. However, the risk factors found to be significantly associated with the prevalence of VRE were age (OR: 5·39, 95% CI: 1·98-14·61) and previous hospitalization (OR: 4·06, 95% CI: 1·33-12·35).

CONCLUSION

VRE species isolated from individuals in this study have high level of vancomycin resistance, were genetically diverse and possessed the virulence traits. Age of individuals and history of hospitalization rather than occupational background determined VRE colonization.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study provides comprehensive findings on the epidemiological and molecular features of VRE among healthy individuals working with animals.

Biochemical characterization of an anti-Candida factor produced by Enterococcus faecalis

Background

Because Candida albicans is resistant to several antifungal antibiotics, there is a need to identify other less toxic natural products, particularly antimicrobial proteins, peptides or bacteriocin like inhibitory substances. An attempt has been made to purify and characterise an anti-Candida compound produced by Enterococcus faecalis.

Results

An anti-Candida protein (ACP) produced by E. faecalis active against 8 C. albicans strains was characterised and partially purified. The ACP showed a broad-spectrum activity against multidrug resistant C. albicans MTCC 183, MTCC 7315, MTCC 3958, NCIM 3557, NCIM 3471 and DI. It was completely inactivated by treatment with proteinase K and partially by pronase E.

The ACP retained biological stability after heat-treatment at 90°C for 20 min, maintained activity over a pH range 6–10, and remained active after treatment with α-amylase, lipase, organic solvents, and detergents. The antimicrobial activity of the E. faecalis strain was found exclusively in the extracellular filtrate produced in the late logarithmic growth phase. The highest activity (1600 AU mL^-1) against C. albicans MTCC 183 was recorded at 48 h of incubation, and activity decreased thereafter. The peptide showed very low haemagglutination and haemolytic activities against human red blood cells. The antimicrobial substance was purified by salt-fractionation and chromatography.

Partially purified ACP had a molecular weight of approximately 43 KDa in Tricine-PAGE analysis. The 12 amino acid N terminal sequence was obtained by Edman degradation. The peptide was de novo sequenced by ESI-MS, and the deduced combined sequence when compared to other bacteriocins and antimicrobial peptide had no significant sequence similarity.

Conclusions

The inhibitory activity of the test strain is due to the synthesis of an antimicrobial protein. To our knowledge, this is the first report on the isolation of a promising non-haemolytic anti-Candida protein from E. faecalis that might be used to treat candidiasis especially in immunocompromised patients.

Detection of an unusual van genotype in a vancomycin-resistant Enterococcus faecium hospital isolate

We highlight the detection of a rare vanM genotype in Enterococcus faecium. This isolate exhibited a VanB phenotype, with high levels of resistance to vancomycin (MIC, >256 mg/liter) and susceptibility to teicoplanin (MIC, 1 mg/liter). It was, however, vanB negative by PCR. Further screening for other van loci revealed the presence of a complete vanM operon.

Multiple-antibiotic resistance of Enterococcus faecalis and Enterococcus faecium from cecal contents in broiler chicken and turkey flocks slaughtered in Canada and plasmid colocalization of tetO and ermB genes

This study was conducted to characterize the antimicrobial resistance determinants and investigate plasmid colocalization of tetracycline and macrolide genes in Enterococcus faecalis and Enterococcus faecium from broiler chicken and turkey flocks in Canada. A total of 387 E. faecalis and E. faecium isolates were recovered from poultry cecal contents from five processing plants. The percentages of resistant E. faecalis and E. faecium isolates, respectively, were 88.1 and 94% to bacitracin, 0 and 0.9% to chloramphenicol, 0.7 and 14.5% to ciprofloxacin, 72.6 and 80.3% to erythromycin, 3.7 and 41% to flavomycin, 9.6 and 4.3% (high-level resistance) to gentamicin, 25.2 and 17.1% (high-level resistance) to kanamycin, 100 and 94% to lincomycin, 0 and 0% to linezolid, 2.6 and 20.5% to nitrofurantoin, 3 and 27.4% to penicillin, 98.5 and 89.7% to quinupristin-dalfopristin, 7 and 12.8% to salinomycin, 46.7 and 38.5% (high-level resistance) to streptomycin, 95.6 and 89.7% to tetracycline, 73 and 75.2% to tylosin, and 0 and 0% to vancomycin. One predominant multidrug-resistant phenotypic pattern was identified in both E. faecalis and E. faecium (bacitracin, erythromycin, lincomycin, quinupristin-dalfopristin, tetracycline, and tylosin). These isolates were further examined by PCR and sequencing for the genes encoding their antimicrobial resistance. Various combinations of vatD, vatE, bcrR, bcrA, bcrB, bcrD, ermB, msrC, linB, tetM, and tetO genes were detected, and ermB, tetM, and bcrB were the most common antimicrobial resistance genes identified. For the first time, plasmid extraction and hybridization revealed colocalization of tetO and ermB genes on a ca. 11-kb plasmid in E. faecalis isolates, and filter mating experiments demonstrated its transferability. Results indicate that the intestinal enterococci of healthy poultry, which can contaminate poultry meat at slaughter, could be a reservoir for quinupristin-dalfopristin, bacitracin, tetracycline, and macrolide resistance genes.

Antibiotic resistance and adhesion properties of oral Enterococci associated to dental caries

BACKGROUND

Enterococci are increasingly associated with opportunistic infections in Humans but the role of the oral cavity as a reservoir for this species is unclear. This study aimed to explore the carriage rate of Enterococci in the oral cavity of Tunisian children and their antimicrobial susceptibility to a broad range of antibiotics together with their adherence ability to abiotic and biotic surfaces.

RESULTS

In this study, 17 E. faecalis (27.5%) and 4 E. faecium (6.5%) were detected. The identified strains showed resistance to commonly used antibiotics. Among the 17 isolated E. faecalis, 12 strains (71%) were slime producers and 5 strains were non-producers. Among the 4 E. faecium, 2 strains were slime producers. All the tested strains were able to adhere to at least one of the two tested cell lines. Our result showed that 11 E. faecalis and 2 E. faecium strains adhered strongly to Hep-2 as well as to A549 cells.

CONCLUSIONS

Drugs resistance and strong biofilm production abilities together with a high phenotypic adhesion to host cells are important equipment in E. faecalis and E. faecium which lead to their oral cavity colonization and focal infections.

Genotypic analysis of Enterococci isolated from fecal-polluted water from different sources by pulsed-field gel electrophoresis (PFGE) for application to microbial source tracking

PFGE has potential applications in the source tracking of fecal pollution in aquatic environments. We tried to distinguish the genotypes of Enterococcus faecium collected from fecal-contaminated water using PFGE. Well identified 115 strains of E. faecium were classified into 25 PFGE patterns, and characteristics distinctive to each genotype were recognized. Analysis of the characteristics of genotypes using PFGE can be used to track source of fecal pollution.

Microbiota associated with chronic osteomyelitis of the jaws

Chronic osteomyelitis of maxilla and mandible is rare in industrialized countries and its occurrence in developing countries is associated with trauma and surgery, and its microbial etiology has not been studied thoroughly. The aim of this investigation was to evaluate the microbiota associated with osteomyelitis of mandible or maxilla from some Brazilian patients. After clinical and radiographic evaluation, samples of bone sequestra, purulent secretion, and biopsies of granulomatous tissues from twenty-two patients with chronic osteomyelitis of mandible and maxilla were cultivated and submitted for pathogen detection by using a PCR method. Each patient harbored a single lesion. Bacterial isolation was performed on fastidious anaerobe agar supplemented with hemin, menadione and horse blood for anaerobes; and on tryptic soy agar supplemented with yeast extract and horse blood for facultative bacteria and aerobes. Plates were incubated in anaerobiosis and aerobiosis, at 37(o)C for 14 and 3 days, respectively. Bacteria were cultivated from twelve patient samples; and genera Actinomyces, Fusobacterium, Parvimonas, and Staphylococcus were the most frequent. By PCR, bacterial DNA was detected from sixteen patient samples. The results suggest that cases of chronic osteomyelitis of the jaws are usually mixed anaerobic infections, reinforcing the concept that osteomyelitis of the jaws are mainly related to microorganisms from the oral environment, and periapical and periodontal infections may act as predisposing factors.

Purification and characterization of enterocin FH 99 produced by a faecal isolate Enterococcus faecium FH 99

Enterococcus faecium FH 99 was isolated from human faeces and selected because of its broad spectrum of inhibitory activity against several Gram-positive foodborne spoilage and pathogenic bacteria. Ent. faecium FH 99 accumulates enterocin in large number in early stationary phase of the growth. The enterocin FH 99 was stable over a wide pH range (2-10) and recovered activity even after treatment at high temperatures (10 min at 100°C). The enterocin was subjected to different purification techniques viz., gel filteration, cation exchange chromatography and reverse-phase high-performance liquid chromatography. The activity was eluted as one individual active fraction. SDSPAGE revealed a molecular weight of less than 6.5 kDa. Studies carried out to identify the genetic determinants for bacteriocin production showed that this trait may be plasmid encoded as loss in both of the plasmids (size>chromosomal DNA) led to loss in bacteriocin production by Ent. faecium FH 99. Ent. faecium strain FH 99 is a newly discovered high bacteriocin producer with Activity Units 1.8 × 10(5) AU ml(-1) and its characteristics indicate that it may have strong potential for application as a protective agent against pathogens and spoilage bacteria in foods.

Ecological characterization of the colonic microbiota of normal and diarrheic dogs

We used terminal restriction fragment polymorphism (T-RFLP) analysis to assess (1) stability of the fecal microbiota in dogs living in environments characterized by varying degrees of exposure to factors that might alter the microbiota and (2) changes in the microbiota associated with acute episodes of diarrhea. Results showed that the healthy canine GI tract harbors potential enteric pathogens. Dogs living in an environment providing minimal exposure to factors that might alter the microbiota had similar microbiotas; the microbiotas of dogs kept in more variable environments were more variable. Substantial changes in the microbiota occurred during diarrheic episodes, including increased levels of Clostridium perfringens, Enterococcus faecalis, and Enterococcus faecium. When diet and medications of a dog having a previously stable microbiota were changed repeatedly, the microbiota also changed repeatedly. Temporal trend analysis showed directional changes in the microbiota after perturbation, a return to the starting condition, and then fluctuating changes over time.

Phenotypic and genotypic heterogeneity of Enterococcus species isolated from food in Southern Brazil

Enterococcus is an important group of lactic acid bacteria (LAB), which inhabits the gastrointestinal tract of humans and animals. These microorganisms can also be found in large groups of foods where they can play a beneficial role during food maturation processes or, conversely, can be used as a food contamination indicator. These microorganisms have an additional importance in various aspects of clinical microbiology. The aim of this study was to investigate and determine the phenotypic and genetic diversity in 55 enterococci isolated from different food sources. Phenotypic characteristics based upon substrate hydrolysis differences were used to identify different Enterococcus species. Analysis of the resultant data divided these species into eight Enterococcus phenotype groups. E. faecalis was the food isolate species with the greatest phenotypic variability. Fifty-five previously isolated Enterococcus strains were re-confirmed as belonging to this genus by PCR techniques. Randomly amplified polymorphic DNA (RAPD-PCR) was used to study the genetic variability using M13 primers and the resultant DNA fragments produced a database of different fingerprints. After statistical analyses of the RAPD-PCR profiles, 42 patterns were obtained and 6 different Enterococcus RAPD clusters (ERC) were identified. Genetic diversity was highest in ERC I, which grouped together approximately 40% of the E. faecium and E. faecalis isolates obtained from dairy products. Samples isolated from meat and vegetables offered the greatest genotype variability. Results of the present study suggest the presence of both phenotypic and genotypic variability within enterococci strains isolated from diverse sources of food common to Southern Brazil.