BACKGROUND: We investigated the whole genome sequence (WGS) of a carbapenem-resistant Acinetobacter baumannii isolate belonging to the global clone 2 (GC2) and predicted resistance islands using a software tool. METHODS: A. baumannii strain YU-R612 was isolated from the sputum of a 61-yr-old man with sepsis. The WGS of the YU-R612 strain was obtained by using the PacBio RS II Sequencing System (Pacific Biosciences Inc., USA). Antimicrobial resistance genes and resistance islands were analyzed by using ResFinder and Genomic Island Prediction software (GIPSy), respectively. RESULTS: The YU-R612 genome consisted of a circular chromosome (ca. 4,075 kb) and two plasmids (ca. 74 kb and 5 kb). Its sequence type (ST) under the Oxford scheme was ST191, consistent with assignment to GC2. ResFinder analysis showed that YU-R612 possessed the following resistance genes: four β-lactamase genes bla(ADC-30), bla(OXA-66), bla(OXA-23), and bla(TEM-1); armA, aadA1, and aacA4 as aminoglycoside resistance-encoding genes; aac(6')Ib-cr for fluoroquinolone resistance; msr(E) for macrolide, lincosamide, and streptogramin B resistance; catB8 for phenicol resistance; and sul1 for sulfonamide resistance. By GIPSy analysis, six putative resistant islands (PRIs) were determined on the YU-R612 chromosome. Among them, PRI1 possessed two copies of Tn2009 carrying bla(OXA-23), and PRI5 carried two copies of a class I integron carrying sul1 and armA genes. CONCLUSIONS: By prediction of resistance islands in the carbapenem-resistant A. baumannii YU-R612 GC2 strain isolated in Korea, PRIs were detected on the chromosome that possessed Tn2009 and class I integrons. The prediction of resistance islands using software tools was useful for analysis of the WGS.
Acinetobacter Infections/*drug therapy/microbiology ; Acinetobacter baumannii/drug effects/*genetics/isolation & purification ; Anti-Bacterial Agents/pharmacology/*therapeutic use ; Bacterial Proteins/genetics ; Carbapenems/*therapeutic use ; DNA, Bacterial/chemistry/*genetics/metabolism ; Drug Resistance, Bacterial ; Genomic Islands/genetics ; Humans ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Plasmids/genetics/metabolism ; Polymerase Chain Reaction ; Sequence Analysis, DNA

BACKGROUND/AIMS: The cytosolic host protein nucleotide binding oligomerization domain 1 (Nod1) has emerged as a key pathogen recognition molecule for innate immune responses in epithelial cells. The purpose of the study was to elucidate the mechanism by which Helicobacter pylori infection leads to transepithelial neutrophil migration in a Nod1-mediated manner. METHODS: Human epithelial cell lines AGS and Caco-2 were grown and infected with H. pylori. Interleukin (IL)-8 mRNA expression and IL-8 secretion were assessed, and nuclear factor kappaB (NF-kappaB) activation was determined. Stable transfections of AGS and Caco-2 cells with dominant negative Nod1 were generated. Neutrophil migration across the monolayer was quantified. RESULTS: Cytotoxin-associated gene pathogenicity island (cagPAI)(+) H. pylori infection upregulated IL-8 mRNA expression and IL-8 secretion in AGS and Caco-2 cells compared with controls. NF-kappaB activation, IL-8 mRNA expression and IL-8 secretion by cagPAI knockdown strains were reduced compared with those infected with the wild-type strain. NF-kappaB activation, IL-8 mRNA expression and IL-8 secretion in dominant-negative (DN)-Nod1 stably transfected cells were reduced compared with the controls. The transepithelial migration of neutrophils in DN-Nod1 stably transfected cells was reduced compared with that in controls. CONCLUSIONS: Signaling through Nod1 plays an essential role in neutrophil migration induced by the upregulated NF-kappaB activation and IL-8 expression in H. pylori-infected human epithelial cells.
Adult Stem Cells/physiology ; Caco-2 Cells ; Cell Line ; Epithelial Cells/*metabolism/microbiology ; Gene Expression ; Genomic Islands ; Helicobacter Infections/*genetics ; *Helicobacter pylori ; Humans ; Interleukin-8/genetics/secretion ; NF-kappa B/metabolism ; Neutrophils/*physiology ; Nod1 Signaling Adaptor Protein/*physiology ; RNA, Messenger/metabolism ; Signal Transduction ; Transendothelial and Transepithelial Migration/*physiology ; Up-Regulation

Epigenetic changes frequently occur in human colorectal cancer. Genomic global hypomethylation, gene promoter region hypermethylation, histone modifications, and alteration of miRNA patterns are major epigenetic changes in colorectal cancer. Loss of imprinting(LOI) is associated with colorectal neoplasia. Folate deficiency may cause colorectal carcinogenesis by inducing gene-specific hypermethylation and genomic global hypomethylation. HDAC inhibitors and demethylating agents have been approved by the FDA for myelodysplastic syndrome and leukemia treatment. Non-coding RNA is regarded as another kind of epigenetic marker in colorectal cancer. This review is mainly focused on DNA methylation, histone modification, and microRNA changes in colorectal cancer.
Colorectal Neoplasms ; genetics ; metabolism ; CpG Islands ; genetics ; DNA Methylation ; Epigenesis, Genetic ; Folic Acid Deficiency ; genetics ; Genomic Imprinting ; Histone Deacetylase Inhibitors ; metabolism ; Histone Deacetylases ; metabolism ; Histones ; metabolism ; Humans ; MicroRNAs ; genetics ; metabolism ; Promoter Regions, Genetic ; genetics ; RNA, Untranslated ; genetics ; metabolism

OBJECTIVE: To establish two methods by denaturing gradient gel electrophoresis (DGGE) and pyrosequencing for genotyping rs220030 (a SNP in the promoter region of small nuclear ribonucleoprotein polypeptide N, SNRPN). To establish an analytical technique for detecting CpG methylation status by pyrosequencing and to further investigate the feasibility of applying rs220030 to the determination of parental origin allele. METHODS: The rs220030 of 97 blood samples from individuals of Shanghai Han population were genotyped by DGGE, meanwhile the rs220030 of 25 blood samples of them were genotyped by pyrosequencing to compare the two methods in genotyping SNP. Pyrosequencing united bisulfite conversion method was applied to detect CpG methylation status of region upstream rs220030 of two random blood genealogical samples and investigate whether the methylation status was parental related. RESULTS: The rs220030 genotyping results of 97 blood samples detected by DGGE were 20 C homozygote, 29 T homozygote, and 48 C/T heterozygote. Twenty-five blood samples genotyped by pyrosequencing showed the same result with DGGE. The CpG methylation status of region upstream rs220030 of the child was similar to the mother. CONCLUSION Compared with DGGE, pyrosequencing is more accurate, convenient, and suitable for large samples and high throughput SNP genotyping. Pyrosequencing united bisulfite conversion can be used to detect CpG methylation status precisely. It is feasible to apply rs220030 to parental origin allele determination.
Asian People/genetics* ; CpG Islands ; DNA/genetics* ; DNA Methylation ; DNA Primers ; Genomic Imprinting ; Genotype ; Heterozygote ; Humans ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; Sulfites/metabolism* ; snRNP Core Proteins/genetics*

OBJECTIVETo study the characteristics of the strains of Salmonella enterica (S. enterica) serovar Senftenberg lacking Salmonella pathogenicity island 1 (SPI-1).

METHODSA total of 10 strains of S. enterica serovar Senftenberg were isolated from 10 cases of diarrhea patients. Pulsed field gel electrophoresis (PFGE), PCR, sequencing techniques and cell invasion test were adapted to study the molecular types and invasiveness of the genes and cells; and made a comparison between the 10 strains and the strains (C02013) isolated in Shenzhen in 2002.

RESULTSThe 10 Senftenberg isolated (S09007-S09012, S09014-S09017) in Shanghai showed three PFGE patterns, which were significantly different from the strains isolated in Shenzhen. PCR-amplified results indicated the invasion gene (invA), secreted effector protein gene (sipA) and gene fragments as fhlA-hilA, hilA-spaP and spaP-invH in the 10 strains of SPI-1 were all negative. The sequencing results revealed that the 10 strains isolated in Shanghai lacked most parts of SPI-1 genes, as fragments from orgA to invH and parts of orgA gene itself; however, compared with strains isolated in Shenzhen, the sprB-orgC gene existed. The missing parts of genes were replaced by a simple insertion sequence (IS) of 1000 bp in the strains isolated both in Shenzhen in 2002 and in Shanghai in 2006. The invasiveness rates of the 10 strains (S09007-S09012, S09014-S09017) towards Hela cells were (0.0053 ± 0.0024)%, (0.0046 ± 0.0006)%, (0.0047 ± 0.0003)%, (0.0064 ± 0.0012)%, (0.0065 ± 0.0011)%, (0.0070 ± 0.0020)%, (0.0115 ± 0.0030)%, (0.0099 ± 0.0039)%, (0.0180 ± 0.0135)% and (0.0031 ± 0.0012)%, respectively; which were all significantly lower than the rate of invA-positive control strain STM1344 ((5.0800 ± 0.6333)%); lower or close to the rate of invA-lacked artificial-mutated strain STMinvA-((0.0193 ± 0.0045)%).

CONCLUSIONSPI-1 genes are not essential for the diarrhea caused by S. enterica serovar Senftenberg.

Adult ; Aged ; Bacterial Typing Techniques ; Diarrhea ; microbiology ; Feces ; microbiology ; Female ; Genes, Bacterial ; Genomic Islands ; HeLa Cells ; Humans ; Male ; Middle Aged ; Salmonella enterica ; genetics ; isolation & purification ; pathogenicity

The aberrant epigenetic reprogramme is an important cause for abnormal development of nuclear transfer embryos. The objective of this study was to investigate the CpG island methylation profiles and relative expression levels of H19 gene in different tissues of cloned goat fetus. We detected liver, placenta, kidney, lung and heart in the dead cloned goat fetus and the age-matched normal goat fetus (control) by using bisulfite sequencing and real time PCR. Results indicated that methylation levels of the fifth CpG island of H19 gene in dead cloned goat fetus was significant high compared with that in the control in placenta (70% vs 49.41%, P < 0.05), and relative expression levels of H19 gene was significant low compared with that in the control (883.3 vs 1 264.5, P < 0.05). Reversely, the methylation levels was significant low compared with that in the control in lung (63.53% vs 88.24%, P < 0.05), and relative expression levels was significant high compared with that in the control (1 003.4 vs 515.5, P < 0.05). The differences of others groups were insignificant (P > 0.05). Results showed the abnormal DNA methylation proflies of H19 gene occurred in some tissues of cloned goat fetus, which affected normal expression levels of H19 gene, indicating that aberrant DNA methylation reprogramme may be one of the important factors for the death of cloned animals.
Animals ; Cloning, Organism ; veterinary ; CpG Islands ; DNA Methylation ; Epigenesis, Genetic ; Female ; Fetus ; metabolism ; Genomic Imprinting ; Goats ; Kidney ; embryology ; metabolism ; Liver ; embryology ; metabolism ; Lung ; embryology ; metabolism ; Nuclear Transfer Techniques ; RNA, Long Noncoding ; RNA, Untranslated ; genetics ; metabolism

Bacteria ; genetics ; pathogenicity ; Dental Research ; Genomic Islands ; Periodontitis ; microbiology

OBJECTIVETo investigate the presence of pathogenicity island (PAI)-associated genes in the enterococcal isolates.

METHODSUsing PCR and hybridization methods, PAI-associated genes were detected in 155 enteococcal strains isolated from clinical patients and healthy individuals.

RESULTSAmong the 155 enterococcal isolates, 137 (88.39%) carried at least one of PAI-associated genes, namely hyd (positivity rate of 81.94%), psaA (78.06%), nuc (57.42%), esp (53.55%), cylB (52.90%), and gls24-like (38.06%) genes. Expect for esp gene, the other 5 genes showed higher positivity rates in the E. faecalis strains than in the E. faecium strains, and this difference was statistically significant for the genes nuc, cylB, and gls24-like. The positivity rates and the number of these genes in the E. faecalis from clinical isolates were both significantly higher than those in the strains isolated from healthy individuals.

CONCLUSIONThe data show a wide distribution of the PAI-associated genes among the enterococcal strains, and E. faecalis strains are more likely than E. faecium strains to be positive for the 6 genes, which are present at significant higher rates in the clinically isolated samples than in that from healthy individuals.

Bacterial Proteins ; chemistry ; genetics ; Enterococcus ; genetics ; isolation & purification ; pathogenicity ; Enterococcus faecalis ; genetics ; isolation & purification ; pathogenicity ; Genomic Islands ; genetics ; Gram-Positive Bacterial Infections ; microbiology ; Humans ; Membrane Proteins ; genetics ; Virulence ; genetics

Enterohemorrhagic Escherichia coli (EHEC) O157:H7 is an important pathogen. One of the important virulence traits of EHEC O157:H7 is the capacity to produce attaching and effacing (A/E) lesions on enterocyte. This property encoded by a pathogenicity island termed the locus of enterocyte effacement (LEE). LEE contains ler (LEE-encoded regulator) gene. The product of ler is a central up-regulator of many virulence genes of the LEE. Another important virulence factor of EHEC O157: H7 is Shiga toxin (Stx), encoded by a prophage integrated into the chromosome of O157:H7. In order to obtain an attenuated vaccine candidate, a ler deletion mutant of O157: H7 was constructed by use of suicide vector pCVD442. Meanwhile, due to potential instability of the prophage carrying the stx gene, the prophage was cured with serial passages of bacteria and confirmed by PCR and DNA sequencing. A ler/stx deletion mutant of EHEC O157:H7 was constructed, termed as O157:H7(deltaler/deltastx). The cultural supernatant of O157 ler/stx deletion mutant was inoculated in vero cell culture, and the result indicating that O157 ler/stx deletion mutant lost the toxigenicity to vero cell. Test group and control group of mice were orogstrically inoculated with the O157 ler/stx deletion mutant and the virulent strain O157:H7 EDL933, respectively. Mice were observed daily for clinical signs and weight changes. After inoculation of the deletion mutant, test group of mice (inoculated with O157:H7(deltaler/deltastx)) gained weight normally and experienced no clinical signs. In contrast, control group of mice (inoculated with O157: H7) exhibited weight loss and all died in four days. In another experiment, pregnant mice were orally vaccinated by O157:H7(deltaler/ deltastx) twice at interval of 14 days. Subsequently, the suckling mice were orally challenged with O157:H7 EDL933 at 7 days of age. The results showed that 78.34% of the sucking mice born by vaccinated mice were survival and 12.73% of the sucking mice born by non-vaccinated mice were survival. This study demonstrated that O157 ler/stx deletion mutant lost the toxigenicity to vero cell and to be safety to mice. Oral immunization can induce specific immune responses, and this mutant strain could be used as an attenuated vaccine candidate against EHEC O157.
Administration, Oral ; Animals ; Animals, Suckling ; Antibodies, Bacterial ; blood ; immunology ; Cercopithecus aethiops ; Escherichia coli Infections ; immunology ; mortality ; prevention & control ; Escherichia coli O157 ; genetics ; immunology ; pathogenicity ; Escherichia coli Proteins ; genetics ; Escherichia coli Vaccines ; administration & dosage ; genetics ; immunology ; Female ; Gene Deletion ; Genetic Vectors ; genetics ; Genomic Islands ; genetics ; Immunization ; Lactation ; immunology ; Male ; Mice ; Mutation ; Pregnancy ; Shiga Toxin ; genetics ; Survival Rate ; Trans-Activators ; genetics ; Vaccines, Attenuated ; administration & dosage ; genetics ; immunology ; Vero Cells ; Virulence ; genetics

The extent of unilateral chromosomal losses and the presence of microsatellite instability (MSI) have been classified into high-risk (high- and baseline-level loss) and low-risk (low-level loss and MSI) stem-line genotypes in gastric carcinomas. A unilateral genome-dosage reduction might stimulate compensation mechanism, which maintains the genomic dosage via CpG hypomethylation. A total of 120 tumor sites from 40 gastric carcinomas were examined by chromosomal loss analysis using 40 microsatellite markers on 8 chromosomes and methylation analysis in the 13 CpG (island/non-island) regions near the 10 genes using the bisulfite-modified DNAs. The high-level-loss tumor (four or more losses) showed a tendency toward unmethylation in the Maspin, CAGE, MAGE-A2 and RABGEF1 genes, and the other microsatellite-genotype (three or fewer losses and MSI) toward methylation in the p16, hMLH1, RASSF1A, and Cyclin D2 genes (p<0.05). The non-island CpGs of the p16 and hMLH1 genes were hypomethylated in the high-level-loss and hypermethylated in the non-high-level-loss sites (p<0.05). Consequently, hypomethylation changes were related to a high-level loss, whereas the hypermethylation changes were accompanied by a baseline-level loss, a low-level loss, or a MSI. This indicates that hypomethylation compensates the chromosomal losses in the process of tumor progression.
Chromosome Aberrations/*statistics and numerical data ; Chromosome Mapping/*methods ; CpG Islands/*genetics ; *DNA Methylation ; DNA Mutational Analysis/methods ; France/epidemiology ; Genetic Predisposition to Disease/epidemiology/genetics ; Genetic Screening/methods ; Genomic Instability/genetics ; Humans ; Incidence ; Korea/epidemiology ; Microsatellite Repeats/genetics ; Polymorphism, Genetic ; Research Support, Non-U.S. Gov't ; Risk Assessment/*methods ; Risk Factors ; Statistics ; Stomach Neoplasms/*enzymology/*genetics