Tetsuya Hayashi

Diversification of Escherichia coli genomes: are bacteriophages the major contributors?

Determination of the genome sequence of enterohemorrhagic Escherichia coli O157 Sakai and genomic comparison with the laboratory strain K-12 has revealed that the two strains share a highly conserved 4.1-Mb sequence and that each also contains a large amount of strain-specific sequence. The analysis also revealed the presence of a surprisingly large number of prophages in O157, most of which are lambda-like phages that resemble each other. Based on these results, we discuss how the E. coli strains have diverged from a common ancestral strain, and how bacteriophages contributed to this process. We also describe possible mechanisms by which O157 acquired many closely related phages, and raise the possibility that such bacteria might function as phage factories, releasing a variety of chimeric or mosaic phages into the environment.

Genomic diversity of enterohemorrhagic Escherichia coli O157 revealed by whole genome PCR scanning

Enterohemorrhagic Escherichia coli O157 is one of the leading worldwide public health concerns, causing large outbreaks of hemorrhagic colitis as well as numerous small outbreaks and sporadic cases. The variability of restriction enzyme-digestion patterns of O157 genomes, which is widely used to distinguish strains in the molecular epidemiology of O157 infections, suggests the presence of some genomic diversity among the strains. Based on the complete genome sequence of O157 Sakai, we analyzed the whole genome structures of eight O157 strains displaying diverse XbaI-digestion patterns by a systematic PCR analysis that we have named whole genome PCR scanning. This analysis identified not only the O157-specific sequences that are highly conserved among the strains, but also revealed an unexpectedly high degree of genomic diversity. In particular, prophages, including Shiga toxin-transducing phages, exhibited extensive structural and positional diversity, implying that variation of bacteriophages is a major factor in generating genomic diversity among the O157 lineage.

Complete Nucleotide Sequence of a Staphylococcus aureus Exfoliative Toxin B Plasmid and Identification of a Novel ADP-Ribosyltransferase, EDIN-C

ABSTRACT The complete nucleotide sequence of pETB, a 38.2-kbStaphylococcus aureus plasmid encoding the exfoliative toxin B (ETB), was determined. A total of 50 open reading frames were identified on the plasmid genome and, among these, 32 showed sequence similarity to known proteins. pETB contains three copies of IS257, which divide the pETB genome into three regions: (i) a cadmium resistance operon-containing region, (ii) a lantibiotic production gene-containing region, and (iii) the remaining part where genes for plasmid replication and/or maintenance are dispersed. In the third region, genes of various kinds of functions are present among the replication- and maintenance-related genes. They include two virulence-related genes, the etb gene and a gene encoding a novel ADP-ribosyltransferase closely related to EDIN, which belongs to the C3 family of ADP-ribosyltransferases modifying Rho GTPases. They also include genes for a cell wall-anchoring surface protein and a phage resistance protein. Based on the determined sequence of pETB, the genome structures of etb-bearing plasmids (ETB plasmids) from various clinical isolates were analyzed by the PCR scanning method. The data indicate that, although the ETB plasmids are highly heterogeneous in genome size, the fundamental genome organization is well conserved. The size variation of the plasmid is mainly attributed to defined regions which may be hot spots for gene shuffling.

Clonal association of Staphylococcus aureus causing bullous impetigo and the emergence of new methicillin-resistant clonal groups in Kansai district in Japan

A molecular epidemiological analysis was performed to reveal the clonal association of Staphylococcus aureus strains isolated from patients with bullous impetigo. Pulsed-field gel electrophoresis with cluster analysis, genetic and phenotypic characterizations, and antimicrobial susceptibility profiling of 88 S. aureus strains isolated from outpatients at 4 hospitals in the Kansai district in Japan were undertaken. Three distinct clonal groups were identified: 2 of them carried the exfoliative toxin (ET) A gene (eta), and the other carried the ETB gene (etb). The former groups represent 2 eta-positive clonal groups that have not been described previously. All the strains in the more dominant eta-positive clonal group and some of the strains in the etb-positive clonal group were methicillin-resistant S. aureus (MRSA) showing borderline-to-moderate resistance to beta-lactams. These MRSA strains appear to be emerging clonal groups that have not been considered in previous epidemiological studies of ET-producing S. aureus in Japan and thus pose a significant threat for future treatment of patients with bullous impetigo and/or staphylococcal scalded-skin syndrome.

Association of the Urease Gene with Enterohemorrhagic Escherichia coli Strains Irrespective of Their Serogroups

ABSTRACT Among various diarrheagenic Escherichia coli strains from clinical sources, we found that the urease gene was specifically associated with enterohemorrhagic E. coli (EHEC) strains irrespective of their serogroups. The results suggest that the urease gene can be a useful genetic marker for the detection of EHEC strains and for the diagnosis of infections caused by EHEC strains in the clinical situation.

Two-Dimensional Partial Response Maximum Likelihood with Constant-Weight Constraint for Holographic Data Storage

The areal density of holographic memory can be increased by decreasing the aperture size of the optical system; however, this causes the deterioration of a reproduced image due to the elimination of the high-frequency components of the image. We have developed two-dimensional partial response maximum likelihood (2D PRML), which is based on the previously proposed decision feedback Viterbi algorithm and added the new idea of the constant-weight constraint (CW constraint) and the amplitude PR method. We have confirmed the improvement in error rate using 2D PRML compared with the conventional differential detection method in a high-density holographic memory system by simulation.

New Equalizer Optimization Method for Partial Response Maximum Likelihood Systems Using Normal Equation with Sequenced Amplitude Margin

A new equalizer optimization method was proposed for partial response maximum likelihood systems. It provides a wider tangential tilt margin and defocus margin in an optical disk system that uses a blue laser (406 nm) and has a numerical aperture of 0.85.

Bit-Error-Rate-Based Evaluation of Energy-Gap-Induced Super-Resolution Read-Only-Memory Disc in Blu-ray Disc Optics

Bit error rate (bER) of an energy-gap-induced super-resolution (EG-SR) read-only-memory (ROM) disc with a zinc oxide (ZnO) film was measured in Blu-ray Disc (BD) optics by the partial response maximum likelihood (PRML) detection method. The experimental capacity was 40 GB in a single-layered 120 mm disc, which was about 1.6 times as high as the commercially available BD with 25 GB capacity. BER near 1 ×10-5 was obtained in an EG-SR ROM disc with a tantalum (Ta) reflective film. Practically available characteristics, including readout power margin, readout cyclability, environmental resistance, tilt margins, and focus offset margin, were also confirmed in the EG-SR ROM disc with 40 GB capacity.

Bit-Error-Rate Evaluation of Energy-Gap-Induced Super-Resolution Read-Only-Memory Disc with Dual-Layer Structure

Practically available readout characteristics were obtained in a dual-layer energy-gap-induced super-resolution (EG-SR) read-only-memory (ROM) disc with an 80 gigabytes (GB) capacity. One of the dual layers consisted of zinc oxide and titanium films and the other layer consisted of zinc oxide and tantalum films. Bit error rates better than 3.0×10-4 were obtained with a minimum readout power of approximately 1.6 mW in both layers using a Blu-ray Disc tester by a partial response maximum likelihood (PRML) detection method. The dual-layer disc showed good tolerances in disc tilts and focus offset and also showed good readout cyclability in both layers.