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    Enterococcus faecium
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    baa-472
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    ATCC e faecium do
    Growth curves of Enterococcus faecalis OG1RF and Enterococcus <t>faecium</t> 64/3 and their optrA transconjugants

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    e faecium do - by Bioz Stars, 2020-04
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    Images

    1) Product Images from "Linezolid-resistant enterococci in Polish hospitals: species, clonality and determinants of linezolid resistance"

    Article Title: Linezolid-resistant enterococci in Polish hospitals: species, clonality and determinants of linezolid resistance

    Journal: European Journal of Clinical Microbiology & Infectious Diseases

    doi: 10.1007/s10096-017-2934-7

    Growth curves of Enterococcus faecalis OG1RF and Enterococcus faecium 64/3 and their optrA transconjugants
    Figure Legend Snippet: Growth curves of Enterococcus faecalis OG1RF and Enterococcus faecium 64/3 and their optrA transconjugants

    Techniques Used:

    2) Product Images from "Core Genome Multilocus Sequence Typing Scheme for High-Resolution Typing of Enterococcus faecium"

    Article Title: Core Genome Multilocus Sequence Typing Scheme for High-Resolution Typing of Enterococcus faecium

    Journal: Journal of Clinical Microbiology

    doi: 10.1128/JCM.01946-15

    NeighborNet phylogenetic network to visualize the relationships between 176 E. faecium isolates. The distance matrix underlying the network was built from all pairwise allelic profile comparisons. Allelic profiles were extracted from SeqSphere+. E. faecium
    Figure Legend Snippet: NeighborNet phylogenetic network to visualize the relationships between 176 E. faecium isolates. The distance matrix underlying the network was built from all pairwise allelic profile comparisons. Allelic profiles were extracted from SeqSphere+. E. faecium

    Techniques Used:

    Minimum spanning network built from the core genome allelic profiles of 103 clinical E. faecium isolates. The core genome allelic profiles were determined by loading de novo assemblies into the E. faecium cgMLST scheme developed in this study using the
    Figure Legend Snippet: Minimum spanning network built from the core genome allelic profiles of 103 clinical E. faecium isolates. The core genome allelic profiles were determined by loading de novo assemblies into the E. faecium cgMLST scheme developed in this study using the

    Techniques Used:

    Allele-based neighbor-joining (NJ) and SNP-based maximum likelihood (ML) trees of 103 clinical E. faecium isolates. The allele-based NJ tree (left) was built using the E. faecium cgMLST scheme developed in this study using the SeqSphere+ software. The
    Figure Legend Snippet: Allele-based neighbor-joining (NJ) and SNP-based maximum likelihood (ML) trees of 103 clinical E. faecium isolates. The allele-based NJ tree (left) was built using the E. faecium cgMLST scheme developed in this study using the SeqSphere+ software. The

    Techniques Used: Software

    Distribution of allele differences (A) and recombination-filtered SNPs (B) for pairs of E. faecium isolates with the same ST and isolated from the same hospital. The distributions represent 1,073 pairwise comparisons. Allelic profiles were extracted from
    Figure Legend Snippet: Distribution of allele differences (A) and recombination-filtered SNPs (B) for pairs of E. faecium isolates with the same ST and isolated from the same hospital. The distributions represent 1,073 pairwise comparisons. Allelic profiles were extracted from

    Techniques Used: Isolation

    3) Product Images from "Mechanisms of Resistance to Daptomycin in Enterococcus faecium ▿"

    Article Title: Mechanisms of Resistance to Daptomycin in Enterococcus faecium ▿

    Journal: Antimicrobial Agents and Chemotherapy

    doi: 10.1128/AAC.00774-07

    PFGE analysis of E. faecium isolates evaluated in this study. Analysis was performed using BioNumerics software. Dendrograms were generated using the unweighted-pair group method using average linkages and band-based Dice similarity coefficients. The optimization parameter for this evaluation was set to 0.5 and band position tolerance to 1.0%. Isolate 5 results are not shown in this figure, but that isolate exhibited a restriction pattern identical to that of isolate 4.
    Figure Legend Snippet: PFGE analysis of E. faecium isolates evaluated in this study. Analysis was performed using BioNumerics software. Dendrograms were generated using the unweighted-pair group method using average linkages and band-based Dice similarity coefficients. The optimization parameter for this evaluation was set to 0.5 and band position tolerance to 1.0%. Isolate 5 results are not shown in this figure, but that isolate exhibited a restriction pattern identical to that of isolate 4.

    Techniques Used: Software, Generated

    Diameter of zone of inhibition as a function of incubation time with different E. faecium strains. No significant difference was observed between the strains tested and the control solution with daptomycin and tryptic soy broth. For isolate 1, the daptomycin MIC was 4 μg/ml; for isolate 8, the MIC was 16 μg/ml; and for E. faecium ATCC 35667, the MIC was 1 μg/ml).
    Figure Legend Snippet: Diameter of zone of inhibition as a function of incubation time with different E. faecium strains. No significant difference was observed between the strains tested and the control solution with daptomycin and tryptic soy broth. For isolate 1, the daptomycin MIC was 4 μg/ml; for isolate 8, the MIC was 16 μg/ml; and for E. faecium ATCC 35667, the MIC was 1 μg/ml).

    Techniques Used: Inhibition, Incubation

    4) Product Images from "Complete Genome Sequence of Enterococcus mundtii QU 25, an Efficient l-(+)-Lactic Acid-Producing Bacterium"

    Article Title: Complete Genome Sequence of Enterococcus mundtii QU 25, an Efficient l-(+)-Lactic Acid-Producing Bacterium

    Journal: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes

    doi: 10.1093/dnares/dsu003

    Analysis of the Enterococcus mundtii QU 25 complete genome. (A) Linearized Nco I-digested whole-genome optical map of QU 25 compared with the in silico -derived Nco I-digest map, demonstrating correct chromosome assembly. (B) Genome map of the QU 25 strain. In the outermost circle, three prophages of phiEmqu1, phiEmqu2, and phiEmqu3, replication origin ( dnaA ), and terminus ( dif ) are shown. In the second circle, the ORFs transcribed in a clockwise manner are shown as bars. The third circle shows ORFS transcribed in a counter-clockwise manner. The fourth to ninth circles depict the results of ortholog analyses (BLASTP E -value ≤1 × 10 −10 ) with E. mundtii ATCC 882, E. faecium DO, E. faecium Aus0004, E. hirae ATCC 9790, E. casseliflavus EC20, and E. faecalis V583, respectively. The extent of homology relative to QU 25 is depicted using a heat map of arbitrarily chosen bins. The colour scheme and percentage identity for orthologs are as follows: red, orthologs with > 90% identity; green, 70–90% identity; blue, 50–70% identity; and black,
    Figure Legend Snippet: Analysis of the Enterococcus mundtii QU 25 complete genome. (A) Linearized Nco I-digested whole-genome optical map of QU 25 compared with the in silico -derived Nco I-digest map, demonstrating correct chromosome assembly. (B) Genome map of the QU 25 strain. In the outermost circle, three prophages of phiEmqu1, phiEmqu2, and phiEmqu3, replication origin ( dnaA ), and terminus ( dif ) are shown. In the second circle, the ORFs transcribed in a clockwise manner are shown as bars. The third circle shows ORFS transcribed in a counter-clockwise manner. The fourth to ninth circles depict the results of ortholog analyses (BLASTP E -value ≤1 × 10 −10 ) with E. mundtii ATCC 882, E. faecium DO, E. faecium Aus0004, E. hirae ATCC 9790, E. casseliflavus EC20, and E. faecalis V583, respectively. The extent of homology relative to QU 25 is depicted using a heat map of arbitrarily chosen bins. The colour scheme and percentage identity for orthologs are as follows: red, orthologs with > 90% identity; green, 70–90% identity; blue, 50–70% identity; and black,

    Techniques Used: In Silico, Derivative Assay

    5) Product Images from "Genomic insights into the pathogenicity and environmental adaptability of Enterococcus hirae R17 isolated from pork offered for retail sale, et al. Genomic insights into the pathogenicity and environmental adaptability of Enterococcus hirae R17 isolated from pork offered for retail sale"

    Article Title: Genomic insights into the pathogenicity and environmental adaptability of Enterococcus hirae R17 isolated from pork offered for retail sale, et al. Genomic insights into the pathogenicity and environmental adaptability of Enterococcus hirae R17 isolated from pork offered for retail sale

    Journal: MicrobiologyOpen

    doi: 10.1002/mbo3.514

    Circular map of the Enterococcus hirae R17 genome. Circles from outside to inside are as follows: (1) scale marks of the E. hirae R17 genome. The blue rectangles represent genomic islands ( GI 1 through GI 12), gray rectangles represent genomic regions unique in E. hirae R17 compared to E. hirae ATCC ™ 9790 (R1 through R9), and red rectangles represent genomic regions unique in E. hirae R17 compared to E. hirae ATCC ™ 9790, Enterococcus faecium DO , and Enterococcus faecalis V583 (R#1 through R#5); (2) and (3) predicted proteins encoded by genes on the forward and reverse strands; (4), (5), and (6): common genes shared by E. hirae R17 with those of reference genomes E. hirae ATCC ™ 9790, E. faecium DO , and E. faecalis V583, respectively; (7) GC content percentage, above median GC content (red), less than median (blue); (8) GC skew [(G‐C)/(G+C)], values > 0 (red), values
    Figure Legend Snippet: Circular map of the Enterococcus hirae R17 genome. Circles from outside to inside are as follows: (1) scale marks of the E. hirae R17 genome. The blue rectangles represent genomic islands ( GI 1 through GI 12), gray rectangles represent genomic regions unique in E. hirae R17 compared to E. hirae ATCC ™ 9790 (R1 through R9), and red rectangles represent genomic regions unique in E. hirae R17 compared to E. hirae ATCC ™ 9790, Enterococcus faecium DO , and Enterococcus faecalis V583 (R#1 through R#5); (2) and (3) predicted proteins encoded by genes on the forward and reverse strands; (4), (5), and (6): common genes shared by E. hirae R17 with those of reference genomes E. hirae ATCC ™ 9790, E. faecium DO , and E. faecalis V583, respectively; (7) GC content percentage, above median GC content (red), less than median (blue); (8) GC skew [(G‐C)/(G+C)], values > 0 (red), values

    Techniques Used:

    6) Product Images from "Complete Genome Sequence of Enterococcus mundtii QU 25, an Efficient l-(+)-Lactic Acid-Producing Bacterium"

    Article Title: Complete Genome Sequence of Enterococcus mundtii QU 25, an Efficient l-(+)-Lactic Acid-Producing Bacterium

    Journal: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes

    doi: 10.1093/dnares/dsu003

    Analysis of the Enterococcus mundtii QU 25 complete genome. (A) Linearized Nco I-digested whole-genome optical map of QU 25 compared with the in silico -derived Nco I-digest map, demonstrating correct chromosome assembly. (B) Genome map of the QU 25 strain. In the outermost circle, three prophages of phiEmqu1, phiEmqu2, and phiEmqu3, replication origin ( dnaA ), and terminus ( dif ) are shown. In the second circle, the ORFs transcribed in a clockwise manner are shown as bars. The third circle shows ORFS transcribed in a counter-clockwise manner. The fourth to ninth circles depict the results of ortholog analyses (BLASTP E -value ≤1 × 10 −10 ) with E. mundtii ATCC 882, E. faecium DO, E. faecium Aus0004, E. hirae ATCC 9790, E. casseliflavus EC20, and E. faecalis V583, respectively. The extent of homology relative to QU 25 is depicted using a heat map of arbitrarily chosen bins. The colour scheme and percentage identity for orthologs are as follows: red, orthologs with > 90% identity; green, 70–90% identity; blue, 50–70% identity; and black,
    Figure Legend Snippet: Analysis of the Enterococcus mundtii QU 25 complete genome. (A) Linearized Nco I-digested whole-genome optical map of QU 25 compared with the in silico -derived Nco I-digest map, demonstrating correct chromosome assembly. (B) Genome map of the QU 25 strain. In the outermost circle, three prophages of phiEmqu1, phiEmqu2, and phiEmqu3, replication origin ( dnaA ), and terminus ( dif ) are shown. In the second circle, the ORFs transcribed in a clockwise manner are shown as bars. The third circle shows ORFS transcribed in a counter-clockwise manner. The fourth to ninth circles depict the results of ortholog analyses (BLASTP E -value ≤1 × 10 −10 ) with E. mundtii ATCC 882, E. faecium DO, E. faecium Aus0004, E. hirae ATCC 9790, E. casseliflavus EC20, and E. faecalis V583, respectively. The extent of homology relative to QU 25 is depicted using a heat map of arbitrarily chosen bins. The colour scheme and percentage identity for orthologs are as follows: red, orthologs with > 90% identity; green, 70–90% identity; blue, 50–70% identity; and black,

    Techniques Used: In Silico, Derivative Assay

    7) Product Images from "Comparative genome analysis reveals key genetic factors associated with probiotic property in Enterococcus faecium strains"

    Article Title: Comparative genome analysis reveals key genetic factors associated with probiotic property in Enterococcus faecium strains

    Journal: BMC Genomics

    doi: 10.1186/s12864-018-5043-9

    Summarizes properties which can help in delineating probiotic, pathogenic and NPNP strains of E. faecium . ✓ indicates presence of a property, X indicates absence of property and ✓ / X indicates either presence or absence of a property
    Figure Legend Snippet: Summarizes properties which can help in delineating probiotic, pathogenic and NPNP strains of E. faecium . ✓ indicates presence of a property, X indicates absence of property and ✓ / X indicates either presence or absence of a property

    Techniques Used:

    Core Genome Phylogeny. Phylogenetic tree of 10 Enterococcus faecium strains using the Maximum Likelihood method based on the GTR + G substitution model. The tree with the highest log likelihood (− 17,644.1414) is shown. Evolutionary analyses were conducted in MEGA6. A concatenated tree of core 1945 genes common in all the strains were considered in the final dataset
    Figure Legend Snippet: Core Genome Phylogeny. Phylogenetic tree of 10 Enterococcus faecium strains using the Maximum Likelihood method based on the GTR + G substitution model. The tree with the highest log likelihood (− 17,644.1414) is shown. Evolutionary analyses were conducted in MEGA6. A concatenated tree of core 1945 genes common in all the strains were considered in the final dataset

    Techniques Used:

    Core and pan genome of E. faecium strains. The number of shared genes was plotted as a function of number of strains (n) added sequentially. 1935 genes were shared by all 10 genomes. The orange line represents the least-squares fit to the power law function f(x) = a.x^b where a = 2577.54, b = 0.222602. The red line represents the least-squares fit to the exponential decay function f1(x) = c.e^(d.x) where c = 2293.44, d = − 0.0232013
    Figure Legend Snippet: Core and pan genome of E. faecium strains. The number of shared genes was plotted as a function of number of strains (n) added sequentially. 1935 genes were shared by all 10 genomes. The orange line represents the least-squares fit to the power law function f(x) = a.x^b where a = 2577.54, b = 0.222602. The red line represents the least-squares fit to the exponential decay function f1(x) = c.e^(d.x) where c = 2293.44, d = − 0.0232013

    Techniques Used:

    Number of core, accessory and unique gene families of E. faecium genomes. The inner circle represents core genome consisting of 1935 genes. The outer red circle represents accessory genomes for all ten strains adding to a sum of 5718 genes, while the outer petals represent unique genes associated with all the strains. Green color indicate probiotic strains, brown are NPNP and black are pathogenic
    Figure Legend Snippet: Number of core, accessory and unique gene families of E. faecium genomes. The inner circle represents core genome consisting of 1935 genes. The outer red circle represents accessory genomes for all ten strains adding to a sum of 5718 genes, while the outer petals represent unique genes associated with all the strains. Green color indicate probiotic strains, brown are NPNP and black are pathogenic

    Techniques Used:

    8) Product Images from "Comparative genome analysis reveals key genetic factors associated with probiotic property in Enterococcus faecium strains"

    Article Title: Comparative genome analysis reveals key genetic factors associated with probiotic property in Enterococcus faecium strains

    Journal: BMC Genomics

    doi: 10.1186/s12864-018-5043-9

    Summarizes properties which can help in delineating probiotic, pathogenic and NPNP strains of E. faecium . ✓ indicates presence of a property, X indicates absence of property and ✓ / X indicates either presence or absence of a property
    Figure Legend Snippet: Summarizes properties which can help in delineating probiotic, pathogenic and NPNP strains of E. faecium . ✓ indicates presence of a property, X indicates absence of property and ✓ / X indicates either presence or absence of a property

    Techniques Used:

    Core Genome Phylogeny. Phylogenetic tree of 10 Enterococcus faecium strains using the Maximum Likelihood method based on the GTR + G substitution model. The tree with the highest log likelihood (− 17,644.1414) is shown. Evolutionary analyses were conducted in MEGA6. A concatenated tree of core 1945 genes common in all the strains were considered in the final dataset
    Figure Legend Snippet: Core Genome Phylogeny. Phylogenetic tree of 10 Enterococcus faecium strains using the Maximum Likelihood method based on the GTR + G substitution model. The tree with the highest log likelihood (− 17,644.1414) is shown. Evolutionary analyses were conducted in MEGA6. A concatenated tree of core 1945 genes common in all the strains were considered in the final dataset

    Techniques Used:

    Core and pan genome of E. faecium strains. The number of shared genes was plotted as a function of number of strains (n) added sequentially. 1935 genes were shared by all 10 genomes. The orange line represents the least-squares fit to the power law function f(x) = a.x^b where a = 2577.54, b = 0.222602. The red line represents the least-squares fit to the exponential decay function f1(x) = c.e^(d.x) where c = 2293.44, d = − 0.0232013
    Figure Legend Snippet: Core and pan genome of E. faecium strains. The number of shared genes was plotted as a function of number of strains (n) added sequentially. 1935 genes were shared by all 10 genomes. The orange line represents the least-squares fit to the power law function f(x) = a.x^b where a = 2577.54, b = 0.222602. The red line represents the least-squares fit to the exponential decay function f1(x) = c.e^(d.x) where c = 2293.44, d = − 0.0232013

    Techniques Used:

    Number of core, accessory and unique gene families of E. faecium genomes. The inner circle represents core genome consisting of 1935 genes. The outer red circle represents accessory genomes for all ten strains adding to a sum of 5718 genes, while the outer petals represent unique genes associated with all the strains. Green color indicate probiotic strains, brown are NPNP and black are pathogenic
    Figure Legend Snippet: Number of core, accessory and unique gene families of E. faecium genomes. The inner circle represents core genome consisting of 1935 genes. The outer red circle represents accessory genomes for all ten strains adding to a sum of 5718 genes, while the outer petals represent unique genes associated with all the strains. Green color indicate probiotic strains, brown are NPNP and black are pathogenic

    Techniques Used:

    Related Articles

    Negative Control:

    Article Title: The Genus Enterococcus: Between Probiotic Potential and Safety Concerns—An Update
    Article Snippet: .. Both analysis should contain positive E. faecium ATCC BAA-472 (TX16) or E. faecium DSMZ 25390) and negative control ( E. faecium DSMZ 25389) strains (EFSA, ). .. For instance, the determination of antibiotic's (mainly ampicillin) minimum inhibitory concentration (MIC) should be performed according to internationally recognized standards such as European Union Committee on Antimicrobial Susceptibility Testing (EUCAST), the Clinical and Laboratory Standard Institute (CLSI), ISO standard or similar.

    Article Title: The Genus Enterococcus: Between Probiotic Potential and Safety Concerns—An Update
    Article Snippet: .. Both analysis should contain positive E. faecium ATCC BAA-472 (TX16) or E. faecium DSMZ 25390) and negative control (E. faecium DSMZ 25389) strains (EFSA, ). .. For instance, the determination of antibiotic's (mainly ampicillin) minimum inhibitory concentration (MIC) should be performed according to internationally recognized standards such as European Union Committee on Antimicrobial Susceptibility Testing (EUCAST), the Clinical and Laboratory Standard Institute (CLSI), ISO standard or similar.

    Amplification:

    Article Title: The Genus Enterococcus: Between Probiotic Potential and Safety Concerns—An Update
    Article Snippet: The amplification of the IS 16 gene by PCR as described by Werner et al. ( ) is recommended, while the hybridization technique described by Rice et al. ( ) is used for detection of esp and hyl Efm. .. Both analysis should contain positive E. faecium ATCC BAA-472 (TX16) or E. faecium DSMZ 25390) and negative control ( E. faecium DSMZ 25389) strains (EFSA, ).

    Article Title: The Genus Enterococcus: Between Probiotic Potential and Safety Concerns—An Update
    Article Snippet: The amplification of the IS16 gene by PCR as described by Werner et al. ( ) is recommended, while the hybridization technique described by Rice et al. ( ) is used for detection of esp and hyl Efm. .. Both analysis should contain positive E. faecium ATCC BAA-472 (TX16) or E. faecium DSMZ 25390) and negative control (E. faecium DSMZ 25389) strains (EFSA, ).

    Concentration Assay:

    Article Title: The Genus Enterococcus: Between Probiotic Potential and Safety Concerns—An Update
    Article Snippet: Both analysis should contain positive E. faecium ATCC BAA-472 (TX16) or E. faecium DSMZ 25390) and negative control ( E. faecium DSMZ 25389) strains (EFSA, ). .. For instance, the determination of antibiotic's (mainly ampicillin) minimum inhibitory concentration (MIC) should be performed according to internationally recognized standards such as European Union Committee on Antimicrobial Susceptibility Testing (EUCAST), the Clinical and Laboratory Standard Institute (CLSI), ISO standard or similar.

    Article Title: The Genus Enterococcus: Between Probiotic Potential and Safety Concerns—An Update
    Article Snippet: Both analysis should contain positive E. faecium ATCC BAA-472 (TX16) or E. faecium DSMZ 25390) and negative control (E. faecium DSMZ 25389) strains (EFSA, ). .. For instance, the determination of antibiotic's (mainly ampicillin) minimum inhibitory concentration (MIC) should be performed according to internationally recognized standards such as European Union Committee on Antimicrobial Susceptibility Testing (EUCAST), the Clinical and Laboratory Standard Institute (CLSI), ISO standard or similar.

    Infection:

    Article Title: The Genus Enterococcus: Between Probiotic Potential and Safety Concerns—An Update
    Article Snippet: Finally, an assessment of lack of infectivity by the candidate strain in immunocompromised animals would add a measure of confidence in the safety (FAO/WHO, ). .. Both analysis should contain positive E. faecium ATCC BAA-472 (TX16) or E. faecium DSMZ 25390) and negative control ( E. faecium DSMZ 25389) strains (EFSA, ).

    Article Title: The Genus Enterococcus: Between Probiotic Potential and Safety Concerns—An Update
    Article Snippet: Finally, an assessment of lack of infectivity by the candidate strain in immunocompromised animals would add a measure of confidence in the safety (FAO/WHO, ). .. Both analysis should contain positive E. faecium ATCC BAA-472 (TX16) or E. faecium DSMZ 25390) and negative control (E. faecium DSMZ 25389) strains (EFSA, ).

    End-sequence Profiling:

    Article Title: The Genus Enterococcus: Between Probiotic Potential and Safety Concerns—An Update
    Article Snippet: The amplification of the IS 16 gene by PCR as described by Werner et al. ( ) is recommended, while the hybridization technique described by Rice et al. ( ) is used for detection of esp and hyl Efm. .. Both analysis should contain positive E. faecium ATCC BAA-472 (TX16) or E. faecium DSMZ 25390) and negative control ( E. faecium DSMZ 25389) strains (EFSA, ).

    Article Title: The Genus Enterococcus: Between Probiotic Potential and Safety Concerns—An Update
    Article Snippet: The amplification of the IS16 gene by PCR as described by Werner et al. ( ) is recommended, while the hybridization technique described by Rice et al. ( ) is used for detection of esp and hyl Efm. .. Both analysis should contain positive E. faecium ATCC BAA-472 (TX16) or E. faecium DSMZ 25390) and negative control (E. faecium DSMZ 25389) strains (EFSA, ).

    Produced:

    Article Title: Selection of Amine-Oxidizing Dairy Lactic Acid Bacteria and Identification of the Enzyme and Gene Involved in the Decrease of Biogenic Amines
    Article Snippet: Since putrescine may be produced not only from ornithine but also from agmatine , the amine-degrading strains identified were further tested using two pairs of primers (AgmSq1/AgmSq2 and AgD1/AgD2; ) targeting genes ( agu and agdA , respectively) involved in the agmatine deiminase pathway. .. Lactobacillus brevis ATCC 367 and E. faecium ATCC BAA-472, capable of producing putrescine and cadaverine from agmatine and Lys , respectively, were used as positive controls.

    Sequencing:

    Article Title: The N-Terminal GYPSY Motif Is Required for Pilin-Specific Sortase SrtC1 Functionality in Lactobacillus rhamnosus Strain GG
    Article Snippet: Paragraph title: Bioinformatics sequence analysis ... Lactobacillus rhamnosus GG [ ], Corynebacterium glutamicum R [ ], Enterococcus faecium TX0016 [ – ], Bacillus cereus ATCC 14579 [ , ], Streptococcus agalactiae 2603V/R [ – ], Streptococcus pneumoniae TIGR4 [ – ], Enterococcus faecalis V583 [ , ], Corynebacterium diphtheriae NCTC 13129 [ – ] and Lactococcus lactis IL1403 [ , ].

    Article Title: Mechanisms of Resistance to Daptomycin in Enterococcus faecium ▿
    Article Snippet: .. Sequences from these two strains were identical to each other and to the genome sequence of E. faecium DO (ATCC BAA-472), suggesting an alternative resistance mechanism. ..

    Generated:

    Article Title: The N-Terminal GYPSY Motif Is Required for Pilin-Specific Sortase SrtC1 Functionality in Lactobacillus rhamnosus Strain GG
    Article Snippet: Lactobacillus rhamnosus GG [ ], Corynebacterium glutamicum R [ ], Enterococcus faecium TX0016 [ – ], Bacillus cereus ATCC 14579 [ , ], Streptococcus agalactiae 2603V/R [ – ], Streptococcus pneumoniae TIGR4 [ – ], Enterococcus faecalis V583 [ , ], Corynebacterium diphtheriae NCTC 13129 [ – ] and Lactococcus lactis IL1403 [ , ]. .. The sequence alignment of pilin-specific sortases was generated using MUSCLE [ ].

    Polymerase Chain Reaction:

    Article Title: The Genus Enterococcus: Between Probiotic Potential and Safety Concerns—An Update
    Article Snippet: The amplification of the IS 16 gene by PCR as described by Werner et al. ( ) is recommended, while the hybridization technique described by Rice et al. ( ) is used for detection of esp and hyl Efm. .. Both analysis should contain positive E. faecium ATCC BAA-472 (TX16) or E. faecium DSMZ 25390) and negative control ( E. faecium DSMZ 25389) strains (EFSA, ).

    Article Title: The Genus Enterococcus: Between Probiotic Potential and Safety Concerns—An Update
    Article Snippet: The amplification of the IS16 gene by PCR as described by Werner et al. ( ) is recommended, while the hybridization technique described by Rice et al. ( ) is used for detection of esp and hyl Efm. .. Both analysis should contain positive E. faecium ATCC BAA-472 (TX16) or E. faecium DSMZ 25390) and negative control (E. faecium DSMZ 25389) strains (EFSA, ).

    Article Title: Mechanisms of Resistance to Daptomycin in Enterococcus faecium ▿
    Article Snippet: Sequencing was performed as previously described ( ) using PCR products from the closest homologs in E. faecium to regions within rpoC , rpoB , mprF , and yycG associated with daptomycin-resistant S. aureus strains ( ). .. Sequences from these two strains were identical to each other and to the genome sequence of E. faecium DO (ATCC BAA-472), suggesting an alternative resistance mechanism.

    Activity Assay:

    Article Title: Mechanisms of Resistance to Daptomycin in Enterococcus faecium ▿
    Article Snippet: Sequences from these two strains were identical to each other and to the genome sequence of E. faecium DO (ATCC BAA-472), suggesting an alternative resistance mechanism. .. Reduction of antimicrobial activity of the filtered solutions was evaluated by a modified bioassay ( ) by adding 10 μl (25 μg) of the filtered solution to tryptic soy agar plates with 5% sheep blood previously inoculated with S. aureus ATCC 29213 (daptomycin MIC, 0.25 μg/ml).

    Modification:

    Article Title: Mechanisms of Resistance to Daptomycin in Enterococcus faecium ▿
    Article Snippet: Sequences from these two strains were identical to each other and to the genome sequence of E. faecium DO (ATCC BAA-472), suggesting an alternative resistance mechanism. .. Reduction of antimicrobial activity of the filtered solutions was evaluated by a modified bioassay ( ) by adding 10 μl (25 μg) of the filtered solution to tryptic soy agar plates with 5% sheep blood previously inoculated with S. aureus ATCC 29213 (daptomycin MIC, 0.25 μg/ml).

    Hybridization:

    Article Title: The Genus Enterococcus: Between Probiotic Potential and Safety Concerns—An Update
    Article Snippet: As an alternative method, hybridization to colony lysates or Southern blots can be used. .. Both analysis should contain positive E. faecium ATCC BAA-472 (TX16) or E. faecium DSMZ 25390) and negative control ( E. faecium DSMZ 25389) strains (EFSA, ).

    Article Title: The Genus Enterococcus: Between Probiotic Potential and Safety Concerns—An Update
    Article Snippet: As an alternative method, hybridization to colony lysates or Southern blots can be used. .. Both analysis should contain positive E. faecium ATCC BAA-472 (TX16) or E. faecium DSMZ 25390) and negative control (E. faecium DSMZ 25389) strains (EFSA, ).

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    ATCC e faecium do
    Growth curves of Enterococcus faecalis OG1RF and Enterococcus <t>faecium</t> 64/3 and their optrA transconjugants
    E Faecium Do, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Growth curves of Enterococcus faecalis OG1RF and Enterococcus faecium 64/3 and their optrA transconjugants

    Journal: European Journal of Clinical Microbiology & Infectious Diseases

    Article Title: Linezolid-resistant enterococci in Polish hospitals: species, clonality and determinants of linezolid resistance

    doi: 10.1007/s10096-017-2934-7

    Figure Lengend Snippet: Growth curves of Enterococcus faecalis OG1RF and Enterococcus faecium 64/3 and their optrA transconjugants

    Article Snippet: The rplC and rplD genes encoding ribosomal proteins L3 and L4, respectively, were sequenced [ ] and compared to the wild-type sequences from E. faecalis ATCC 29212 (CP008816.1), E. faecium DO (CP003583.1) and E. avium ATCC 14025 (ASWL01000001.1) strains.

    Techniques:

    NeighborNet phylogenetic network to visualize the relationships between 176 E. faecium isolates. The distance matrix underlying the network was built from all pairwise allelic profile comparisons. Allelic profiles were extracted from SeqSphere+. E. faecium

    Journal: Journal of Clinical Microbiology

    Article Title: Core Genome Multilocus Sequence Typing Scheme for High-Resolution Typing of Enterococcus faecium

    doi: 10.1128/JCM.01946-15

    Figure Lengend Snippet: NeighborNet phylogenetic network to visualize the relationships between 176 E. faecium isolates. The distance matrix underlying the network was built from all pairwise allelic profile comparisons. Allelic profiles were extracted from SeqSphere+. E. faecium

    Article Snippet: These plasmids came from the following strains (with GenBank accession numbers): Enterococcus faecalis D32 ( and ), E. faecalis V583 ( , , and ), E. faecium Aus0004 ( , , and ), E. faecium Aus0085 ( , , , , , and ), E. faecium DO ( , , and ), E. faecium NRRL B-2354 , Enterococcus hirae ATCC 9790 , and Enterococcus mundtii QU 25 ( , , , , and ).

    Techniques:

    Minimum spanning network built from the core genome allelic profiles of 103 clinical E. faecium isolates. The core genome allelic profiles were determined by loading de novo assemblies into the E. faecium cgMLST scheme developed in this study using the

    Journal: Journal of Clinical Microbiology

    Article Title: Core Genome Multilocus Sequence Typing Scheme for High-Resolution Typing of Enterococcus faecium

    doi: 10.1128/JCM.01946-15

    Figure Lengend Snippet: Minimum spanning network built from the core genome allelic profiles of 103 clinical E. faecium isolates. The core genome allelic profiles were determined by loading de novo assemblies into the E. faecium cgMLST scheme developed in this study using the

    Article Snippet: These plasmids came from the following strains (with GenBank accession numbers): Enterococcus faecalis D32 ( and ), E. faecalis V583 ( , , and ), E. faecium Aus0004 ( , , and ), E. faecium Aus0085 ( , , , , , and ), E. faecium DO ( , , and ), E. faecium NRRL B-2354 , Enterococcus hirae ATCC 9790 , and Enterococcus mundtii QU 25 ( , , , , and ).

    Techniques:

    Allele-based neighbor-joining (NJ) and SNP-based maximum likelihood (ML) trees of 103 clinical E. faecium isolates. The allele-based NJ tree (left) was built using the E. faecium cgMLST scheme developed in this study using the SeqSphere+ software. The

    Journal: Journal of Clinical Microbiology

    Article Title: Core Genome Multilocus Sequence Typing Scheme for High-Resolution Typing of Enterococcus faecium

    doi: 10.1128/JCM.01946-15

    Figure Lengend Snippet: Allele-based neighbor-joining (NJ) and SNP-based maximum likelihood (ML) trees of 103 clinical E. faecium isolates. The allele-based NJ tree (left) was built using the E. faecium cgMLST scheme developed in this study using the SeqSphere+ software. The

    Article Snippet: These plasmids came from the following strains (with GenBank accession numbers): Enterococcus faecalis D32 ( and ), E. faecalis V583 ( , , and ), E. faecium Aus0004 ( , , and ), E. faecium Aus0085 ( , , , , , and ), E. faecium DO ( , , and ), E. faecium NRRL B-2354 , Enterococcus hirae ATCC 9790 , and Enterococcus mundtii QU 25 ( , , , , and ).

    Techniques: Software

    Distribution of allele differences (A) and recombination-filtered SNPs (B) for pairs of E. faecium isolates with the same ST and isolated from the same hospital. The distributions represent 1,073 pairwise comparisons. Allelic profiles were extracted from

    Journal: Journal of Clinical Microbiology

    Article Title: Core Genome Multilocus Sequence Typing Scheme for High-Resolution Typing of Enterococcus faecium

    doi: 10.1128/JCM.01946-15

    Figure Lengend Snippet: Distribution of allele differences (A) and recombination-filtered SNPs (B) for pairs of E. faecium isolates with the same ST and isolated from the same hospital. The distributions represent 1,073 pairwise comparisons. Allelic profiles were extracted from

    Article Snippet: These plasmids came from the following strains (with GenBank accession numbers): Enterococcus faecalis D32 ( and ), E. faecalis V583 ( , , and ), E. faecium Aus0004 ( , , and ), E. faecium Aus0085 ( , , , , , and ), E. faecium DO ( , , and ), E. faecium NRRL B-2354 , Enterococcus hirae ATCC 9790 , and Enterococcus mundtii QU 25 ( , , , , and ).

    Techniques: Isolation

    PFGE analysis of E. faecium isolates evaluated in this study. Analysis was performed using BioNumerics software. Dendrograms were generated using the unweighted-pair group method using average linkages and band-based Dice similarity coefficients. The optimization parameter for this evaluation was set to 0.5 and band position tolerance to 1.0%. Isolate 5 results are not shown in this figure, but that isolate exhibited a restriction pattern identical to that of isolate 4.

    Journal: Antimicrobial Agents and Chemotherapy

    Article Title: Mechanisms of Resistance to Daptomycin in Enterococcus faecium ▿

    doi: 10.1128/AAC.00774-07

    Figure Lengend Snippet: PFGE analysis of E. faecium isolates evaluated in this study. Analysis was performed using BioNumerics software. Dendrograms were generated using the unweighted-pair group method using average linkages and band-based Dice similarity coefficients. The optimization parameter for this evaluation was set to 0.5 and band position tolerance to 1.0%. Isolate 5 results are not shown in this figure, but that isolate exhibited a restriction pattern identical to that of isolate 4.

    Article Snippet: Sequences from these two strains were identical to each other and to the genome sequence of E. faecium DO (ATCC BAA-472), suggesting an alternative resistance mechanism.

    Techniques: Software, Generated

    Diameter of zone of inhibition as a function of incubation time with different E. faecium strains. No significant difference was observed between the strains tested and the control solution with daptomycin and tryptic soy broth. For isolate 1, the daptomycin MIC was 4 μg/ml; for isolate 8, the MIC was 16 μg/ml; and for E. faecium ATCC 35667, the MIC was 1 μg/ml).

    Journal: Antimicrobial Agents and Chemotherapy

    Article Title: Mechanisms of Resistance to Daptomycin in Enterococcus faecium ▿

    doi: 10.1128/AAC.00774-07

    Figure Lengend Snippet: Diameter of zone of inhibition as a function of incubation time with different E. faecium strains. No significant difference was observed between the strains tested and the control solution with daptomycin and tryptic soy broth. For isolate 1, the daptomycin MIC was 4 μg/ml; for isolate 8, the MIC was 16 μg/ml; and for E. faecium ATCC 35667, the MIC was 1 μg/ml).

    Article Snippet: Sequences from these two strains were identical to each other and to the genome sequence of E. faecium DO (ATCC BAA-472), suggesting an alternative resistance mechanism.

    Techniques: Inhibition, Incubation

    Analysis of the Enterococcus mundtii QU 25 complete genome. (A) Linearized Nco I-digested whole-genome optical map of QU 25 compared with the in silico -derived Nco I-digest map, demonstrating correct chromosome assembly. (B) Genome map of the QU 25 strain. In the outermost circle, three prophages of phiEmqu1, phiEmqu2, and phiEmqu3, replication origin ( dnaA ), and terminus ( dif ) are shown. In the second circle, the ORFs transcribed in a clockwise manner are shown as bars. The third circle shows ORFS transcribed in a counter-clockwise manner. The fourth to ninth circles depict the results of ortholog analyses (BLASTP E -value ≤1 × 10 −10 ) with E. mundtii ATCC 882, E. faecium DO, E. faecium Aus0004, E. hirae ATCC 9790, E. casseliflavus EC20, and E. faecalis V583, respectively. The extent of homology relative to QU 25 is depicted using a heat map of arbitrarily chosen bins. The colour scheme and percentage identity for orthologs are as follows: red, orthologs with > 90% identity; green, 70–90% identity; blue, 50–70% identity; and black,

    Journal: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes

    Article Title: Complete Genome Sequence of Enterococcus mundtii QU 25, an Efficient l-(+)-Lactic Acid-Producing Bacterium

    doi: 10.1093/dnares/dsu003

    Figure Lengend Snippet: Analysis of the Enterococcus mundtii QU 25 complete genome. (A) Linearized Nco I-digested whole-genome optical map of QU 25 compared with the in silico -derived Nco I-digest map, demonstrating correct chromosome assembly. (B) Genome map of the QU 25 strain. In the outermost circle, three prophages of phiEmqu1, phiEmqu2, and phiEmqu3, replication origin ( dnaA ), and terminus ( dif ) are shown. In the second circle, the ORFs transcribed in a clockwise manner are shown as bars. The third circle shows ORFS transcribed in a counter-clockwise manner. The fourth to ninth circles depict the results of ortholog analyses (BLASTP E -value ≤1 × 10 −10 ) with E. mundtii ATCC 882, E. faecium DO, E. faecium Aus0004, E. hirae ATCC 9790, E. casseliflavus EC20, and E. faecalis V583, respectively. The extent of homology relative to QU 25 is depicted using a heat map of arbitrarily chosen bins. The colour scheme and percentage identity for orthologs are as follows: red, orthologs with > 90% identity; green, 70–90% identity; blue, 50–70% identity; and black,

    Article Snippet: The relatively closed species, such as E. mundtii ATCC 882, E. faecium DO and Aus0004 strains, and E. hirae ATCC 9790, have 21, 180, 76, and 14 ISEs and transposase-related genes, respectively.

    Techniques: In Silico, Derivative Assay