Herein, we report the pathogenic and phylogenetic characteristics of seven Shiga toxin (Stx)-producing Escherichia coli (STEC) isolates from 434 retail meats collected in Korea during 2006 to 2012. The experimental analyses revealed that all isolates (i) were identified as non-O157 STEC, including O91:H14 (3 isolates), O121:H10 (2 isolates), O91:H21 (1 isolate), and O18:H20 (1 isolate), (ii) carried diverse Stx subtype genes (stx₁, stx(2c), stx(2e), or stx₁ + stx(2b)) whose expression levels varied strain by strain, and (iii) lacked the locus of enterocyte effacement (LEE) pathogenicity island, a major virulence factor of STEC, but they possessed one or more alternative virulence genes encoding cytotoxins (Cdt and SubAB) and/or adhesins (Saa, Iha, and EcpA). Notably, a significant heterogeneity in glutamate-induced acid resistance was observed among the STEC isolates (p < 0.05). In addition, phylogenetic analyses demonstrated that all three STEC O91:H14 isolates were categorized into sequence type (ST) 33, of which two beef isolates were identical in their pulsotypes. Similar results were observed with two O121:H10 pork isolates (ST641; 88.2% similarity). Interestingly, 96.0% of the 100 human STEC isolates collected in Korea during 2003 to 2014 were serotyped as O91:H14, and the ST33 lineage was confirmed in approximately 72.2% (13/18 isolates) of human STEC O91:H14 isolates from diarrheal patients.
Cytotoxins ; Enterocytes ; Escherichia coli ; Genomic Islands ; Humans ; Korea ; Meat ; Population Characteristics ; Red Meat ; Shiga Toxin ; Shiga-Toxigenic Escherichia coli ; Virulence ; Virulence Factors

PURPOSE: Escherichia coli O157:H7 is one of the most important pathogens which create hemorrhagic colitis and hemolytic uremic syndrome in human. It is one of the most prevalent causes of diarrhea leading to death of many people every year. The first diagnosed gene in the locus of enterocyte effacement pathogenicity island is eae gene. The product of this gene is a binding protein called intimin belonging to the group of external membrane proteins regarded as a good stimulants of the immune system. Chitosan with its lipophilic property is an environmentally friendly agent able to return to the environment. MATERIALS AND METHODS: Intimin recombinant protein was expressed in pET28a vector with eae gene and purification was performed using Ni-NTA and finally the recombinant protein was approved through western blotting. This protein was encapsulated using chitosan nanoparticles and the size of nanoparticles was measured by Zetasizer. Intimin encapsulated was prescribed for three sessions among three groups of oral, injection, and oral-injection using Chitosan nanoparticles. Challenge was performed for all three groups with 108 E. coli O157:H7 bacteria. RESULTS: Intimin produced by chitosan nanoparticles improves immunological responses through the adjuvant nature of chitosan nanoparticles. Chitosan may be used as a carrier for transportation of the prescribed vaccine. Among the mice, encapsulated intimin could be able to provide suitable titers of IgG and IgA by the aid of chitosan nanoparticles. Results of mice challenge showed that decreased the bacterial shedding significantly. CONCLUSION: Results showed that the chitosan nanovaccine with intimin protein may be used as a suitable candidate vaccine against E. coli O157:H7.
Animals ; Bacteria ; Bacterial Shedding ; Blotting, Western ; Carrier Proteins ; Chitosan ; Colitis ; Diarrhea ; Enterocytes ; Escherichia coli ; Genomic Islands ; Hemolytic-Uremic Syndrome ; Humans ; Immune System ; Immunoglobulin A ; Immunoglobulin G ; Membrane Proteins ; Mice ; Nanoparticles ; Transportation

OBJECTIVES: An atypical Shigella flexneri strain with a plural agglutination pattern [i.e., reacting not only with serum samples containing type antigen II but also with serum samples containing group antigens (3)4 and 7(8)] was selected for genome sequencing, with the aim of obtaining additional comparative information about such strains. METHODS: The genomic DNA of atypical S. flexneri strain NCCP 15744 was sequenced using an Ion Torrent PGM sequencing machine (Life Technologies, USA). The raw sequence data were preprocessed and reference-assembled in the CLC Assembly Cell software (version 4.0.6; CLC bio, USA). RESULTS: Ion Torrent sequencing produced 1,450,025 single reads with an average length of 144 bp, totaling ~209 Mbp. The NCCP 15744 genome is composed of one chromosome and four plasmids and contains a gtrX gene. Among the published genome sequences of S. flexneri strains, including 2457T, Sf301, and 2002017, strain NCCP 15744 showed high similarity with strain 2002017. The differences between NCCP 15744 and 2002017 are as follows: i) NCCP 15744 carries four plasmids whereas 2002017 carries five; ii) 19 genes (including CI, CII, and cro) were lost in the SHI-O genomic island of NCCP 15744 and six genes were gained as compared with strain 2002017. CONCLUSION: Strain NCCP 15744 is genetically similar to 2002017, but these two strains have different multilocus sequence types and serotypes. The exact reason is unclear, but the 19 lost genes may be responsible for the atypical seroconversion of strain NCCP 15744.
Agglutination ; DNA ; Genome* ; Genomic Islands ; Genomics ; Korea* ; Plasmids ; Sequence Analysis ; Seroconversion ; Serogroup ; Shigella flexneri* ; Shigella*

HilA is a central regulator of Salmonella pathogenicity island 1 (SPI1), which is necessary for host invasion by Salmonella and induction of gastroenteritis. The iagB lies downstream of hilA and is thought to be co-transcribed with hilA, but iagB expression has not yet been analyzed directly. In this study, iagB expression in various mutant strains was measured to determine whether the expression pattern was similar to that of hilA. A β-galactosidase assay revealed that iagB expression was greater under shaking than standing culture condition. iagB expression was decreased in relA/spoT and ihfB mutants but not in luxS mutant, in line with previous reports on hilA expression. The hilA and iagB mRNA levels decreased by approximately 2-fold in arcA mutant grown aerobically and increased by approximately 10-fold in fnr mutant grown anaerobically. Although the fold changes in hilA and iagB mRNA level differed in hfq mutant strain, the patterns of time- and Hfq-dependent regulation were similar for both genes. Thus, iagB and hilA exhibited similar expression patterns in various mutational backgrounds and under different growth condition.
Gastroenteritis ; Genomic Islands* ; RNA, Messenger ; Salmonella typhimurium ; Salmonella* ; Virulence*

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