Survey of Genomic Diversity among Enterococcus faecalis Strains by Microarray-Based Comparative Genomic Hybridization

ABSTRACT We have compared nine Enterococcus faecalis strains with E. faecalis V583 by comparative genomic hybridization using microarrays (CGH). The strains used in this study (the “test” strains) originated from various environments. CGH is a powerful and promising tool for obtaining novel information on genome diversity in bacteria. By CGH, one obtains clues about which genes are present or divergent in the strains, compared to a reference strain (here, V583). The information obtained by CGH is important from both ecological and systematic points of view. CGH of E. faecalis showed considerable diversity in gene content: Compared to V583, the percentage of divergent genes in the test strains varied from 15% to 23%, and 154 genes were divergent in all strains. The main variation was found in regions corresponding to exogenously acquired or mobile DNA in V583. Antibiotic resistance genes, virulence factors, and integrated plasmid genes dominated among the divergent genes. The strains examined showed various contents of genes corresponding to the pTEF1, pTEF2, and pTEF3 genes in V583. The extensive transport and metabolic capabilities of V583 appeared similar in the test strains; CGH indicated that the ability to transport and metabolize various carbohydrates was similar in the test strains (verified by API 50 CH assays). The contents of genes related to stress tolerance appeared similar in V583 and the nine test strains, supporting the view of E. faecalis as an organism able to resist harsh conditions.

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Faculty Opinions recommendation of Comparative genomic hybridization analysis of Enterococcus faecalis: identification of genes absent from food strains.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1046262.496195 ◽

2006 ◽

Author(s):

Claire Shearman

Keyword(s):

Enterococcus Faecalis ◽

Comparative Genomic Hybridization ◽

Hybridization Analysis ◽

Comparative Genomic ◽

Comparative Genomic Hybridization Analysis ◽

Genomic Hybridization

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Investigating the role of pneumococcal neuraminidase A activity in isolates from pneumococcal haemolytic uraemic syndrome

Journal of Medical Microbiology ◽

10.1099/jmm.0.063479-0 ◽

2013 ◽

Vol 62 (11) ◽

pp. 1735-1742 ◽

Cited By ~ 15

Author(s):

Andrew Smith ◽

Calum Johnston ◽

Donald Inverarity ◽

Mary Slack ◽

Gavin K. Paterson ◽

...

Keyword(s):

Gene Expression ◽

Young Children ◽

Comparative Genomic Hybridization ◽

Haemolytic Uraemic Syndrome ◽

Genomic Diversity ◽

Comparative Genomic ◽

Genomic Hybridization ◽

Neuraminidase Activity ◽

Atypical Haemolytic Uraemic Syndrome ◽

Significant Difference

Streptococcus pneumoniae diseases are a rare but increasingly recognized trigger of atypical haemolytic uraemic syndrome (HUS) in young children and associated with a higher mortality rate than diarrhoea-associated HUS. This study aimed to determine the importance of neuraminidase A (NanA) and genomic diversity in the pathogenesis of pneumococcal HUS (pHUS). We investigated the nanA gene sequence, gene expression, neuraminidase activity and comparative genomic hybridization of invasive pneumococcal disease (IPD) isolates from patients with pHUS and control strains matched by serotype and sequence type (ST), isolated from patients with IPD but not pHUS. The nanA sequence of 33 isolates was determined and mutations at 142 aa positions were identified. High levels of diversity were observed within the NanA protein, with mosaic blocks, insertions and repeat regions present. When comparing nanA allelic diversity with ST and disease profile in the isolates tested, nanA alleles clustered mostly by ST. No particular nanA allele was associated with pHUS. There was no significant difference in overall neuraminidase activity between pHUS isolates and controls when induced/uninduced with N-acetylneuraminic acid. Comparative genomic hybridization showed little difference in genetic content between the pHUS isolates and the controls. Results of gene expression studies identified 12 genes differentially regulated in all pHUS isolates compared with the control. Although neuraminidase enzyme activity may be important in pHUS progression and contribute to pathogenesis, the lack of a distinction between pHUS isolates and controls suggests that host factors, such as acquired abnormalities of the alternative complement cascade in young children, may play a more significant role in the outcome of pHUS.

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Extensive Genomic Diversity in Pathogenic Escherichia coli and Shigella Strains Revealed by Comparative Genomic Hybridization Microarray

Journal of Bacteriology ◽

10.1128/jb.186.12.3911-3921.2004 ◽

2004 ◽

Vol 186 (12) ◽

pp. 3911-3921 ◽

Cited By ~ 104

Author(s):

Satoru Fukiya ◽

Hiroshi Mizoguchi ◽

Toru Tobe ◽

Hideo Mori

Keyword(s):

Escherichia Coli ◽

Comparative Genomic Hybridization ◽

Cell Envelope ◽

Genome Structure ◽

Genomic Diversity ◽

Comparative Genomic ◽

Genomic Hybridization ◽

Phylogenic Tree ◽

E Coli ◽

K 12

ABSTRACT Escherichia coli, including the closely related genus Shigella, is a highly diverse species in terms of genome structure. Comparative genomic hybridization (CGH) microarray analysis was used to compare the gene content of E. coli K-12 with the gene contents of pathogenic strains. Missing genes in a pathogen were detected on a microarray slide spotted with 4,071 open reading frames (ORFs) of W3110, a commonly used wild-type K-12 strain. For 22 strains subjected to the CGH microarray analyses 1,424 ORFs were found to be absent in at least one strain. The common backbone of the E. coli genome was estimated to contain about 2,800 ORFs. The mosaic distribution of absent regions indicated that the genomes of pathogenic strains were highly diversified becasue of insertions and deletions. Prophages, cell envelope genes, transporter genes, and regulator genes in the K-12 genome often were not present in pathogens. The gene contents of the strains tested were recognized as a matrix for a neighbor-joining analysis. The phylogenic tree obtained was consistent with the results of previous studies. However, unique relationships between enteroinvasive strains and Shigella, uropathogenic, and some enteropathogenic strains were suggested by the results of this study. The data demonstrated that the CGH microarray technique is useful not only for genomic comparisons but also for phylogenic analysis of E. coli at the strain level.

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Comparative Genomic Hybridization Analysis of Enterococcus faecalis: Identification of Genes Absent from Food Strains

Journal of Bacteriology ◽

10.1128/jb.00421-06 ◽

2006 ◽

Vol 188 (19) ◽

pp. 6858-6868 ◽

Cited By ~ 40

Author(s):

E. Lepage ◽

S. Brinster ◽

C. Caron ◽

Céline Ducroix-Crepy ◽

L. Rigottier-Gois ◽

...

Keyword(s):

Enterococcus Faecalis ◽

Comparative Genomic Hybridization ◽

Comparative Genomic ◽

Fermented Foods ◽

Genomic Hybridization ◽

Component Mixture ◽

Dairy Food ◽

Gene Group ◽

Specific Pcr ◽

Variable Genes

ABSTRACT Enterococcus faecalis, a member of the natural microbiota of animal and human intestinal tracts, is also present as a natural contaminant in a variety of fermented foods. Over the last decade, E. faecalis has emerged as a major cause of nosocomial infections. We investigated the genetic diversity in 30 clinical and food isolates, including strains V583 and MMH594, in order to determine whether clinical and food isolates could be distinguished. Data were obtained using comparative genomic hybridization and specific PCR with a total of 202 probes of E. faecalis, selected using the available V583 genome sequence and part of the MMH594 pathogenicity island. The cognate genes encoded mainly exported proteins. Hybridization data were analyzed by a two-component mixture model that estimates the probability of any given gene to be either present or absent in the strains. A total of 78 genes were found to be variable, as they were absent in at least one isolate. Most of the variable genes were clustered in regions that, in the published V583 sequence, related to prophages or mobile genetic elements. The variable genes were distributed in three main groups: (i) genes equally distributed between clinical and dairy food isolates, (ii) genes absent from dairy food-related isolates, and (iii) genes present in MMH594 and V583 strains only. Further analysis of the distribution of the last gene group in 70 other isolates confirmed that six of the probed genes were always absent in dairy food-related isolates, whereas they were detected in clinical and/or commensal isolates. Two of them corresponded to prophages that were not detected in the cognate isolates, thus possibly extending the number of genes absent from dairy food isolates. Genes specifically detected in clinical isolates may prove valuable for the development of new risk assessment markers for food safety studies and for identification of new factors that may contribute to host colonization or infection.

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Leptospire Genomic Diversity Revealed by Microarray-Based Comparative Genomic Hybridization

Applied and Environmental Microbiology ◽

10.1128/aem.07465-11 ◽

2012 ◽

Vol 78 (9) ◽

pp. 3045-3050 ◽

Cited By ~ 1

Author(s):

Broderick Eribo ◽

Sirima Mingmongkolchai ◽

Tingfen Yan ◽

Padunsri Dubbs ◽

Karen E. Nelson

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Comparative Genomic Hybridization ◽

Virulence Factors ◽

Genomic Diversity ◽

Comparative Genomic ◽

Leptospira Interrogans ◽

Genomic Hybridization ◽

Content Type ◽

Reference Genomes

ABSTRACTComparative genomic hybridization was used to compare genetic diversity of five strains ofLeptospira(Leptospira interrogansserovars Bratislava, Canicola, and Hebdomadis andLeptospira kirschneriserovars Cynopteri and Grippotyphosa). The array was designed based on two available sequencedLeptospirareference genomes, those ofL. interrogansserovar Copenhageni andL. interrogansserovar Lai. A comparison of genetic contents showed thatL. interrogansserovar Bratislava was closest to the reference genomes whileL. kirschneriserovar Grippotyphosa had the least similarity to the reference genomes. Cluster analysis indicated thatL. interrogansserovars Bratislava and Hebdomadis clustered together first, followed byL. interrogansserovar Canicola, before the twoL. kirschneristrains. Confirmed/potential virulence factors identified in previous research were also detected in the tested strains.

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