Quantitative analysis of the three gut microbiota in UC and non-UC patients using real-time PCR.

BACKGROUND: and study aims: Gastrointestinal microbiota are closely related to the pathogenesis of ulcerative colitis (UC). This study aimed at quantification of F. prausnitzii, Provetella, and Peptostreptococcus in UC and non-UC patients using Real-Time PCR and a new set of primers were also validated for this purpose. MATERIALS AND METHODS: In this study, the relative abundance of microbial populations between the UC and non-UC subjects were evaluated by quantitative real-time polymerase chain reaction (qRT-PCR). DNA extraction from biopsies and polymerase chain reaction (PCR) amplification of bacterial 16S rRNA gene-targeted species-specific primers was performed to detect the anaerobic bacterial species. The qRT-PCR was used to show the relative change in the bacterial populations of F. prausnitzii, Provetella, and Peptostreptococcus in the UC and non-UC subjects. RESULTS: Our data for detection of the anaerobic intestinal flora showed Faecalibacterium prausnitzii, Provetella and Peptostreptococcus were the predominant microflora in the controls and showed significant differences (p = 0.002, 0.025 and 0.039, respectively). The qRT-PCR analyses of F. prausnitzii, Provetella and Peptostreptococcus were 8.69-, 9.38- and 5.77-higher, respectively, in the control group than in the UC group. CONCLUSION: The results of this study showed decreased abundance of F. prausnitzii, Provetella and Peptostreptococcus in the intestine of UC patients in comparison to non-UC patients. Quantitative RT-PCR, as a progressive and sensitive method, could be useful for evaluation of bacterial populations in patients with inflammatory bowel diseases to attain appropriate therapeutic strategies.

Antibacterial and anti-biofilm properties of carvacrol alone and in combination with cefixime against Escherichia coli.

BACKGROUND: Plant-derived compounds can be used as antimicrobial agents in medicines and as food preservatives. These compounds can be applied along with other antimicrobial agents to strengthen the effect and/or reduce the required treatment dose. RESULTS: In the present study, the antibacterial, anti-biofilm and quorum sensing inhibitory activity of carvacrol alone and in combination with the antibiotic cefixime against Escherichia coli was investigated. The MIC and MBC values for carvacrol were 250 µg/mL. In the checkerboard test, carvacrol showed a synergistic interaction with cefixime against E. coli (FIC index = 0.5). Carvacrol and cefixime significantly inhibited biofilm formation at MIC/2 (125 and 62.5 µg/mL), MIC/4 (62.5 and 31.25 µg/mL) and MIC/8 (31.25 and 15.625 µg/mL) for carvacrol and cefixime, respectively. The antibacterial and anti-biofilm potential effect of carvacrol confirmed by the scanning electron microscopy. Real-time quantitative reverse transcription PCR revealed significant down-regulation of the luxS and pfs genes following treatment with a MIC/2 (125 µg/mL) concentration of carvacrol alone and of only pfs gene following treatment with MIC/2 of carvacrol in combination with MIC/2 of cefixime (p < 0.05). CONCLUSIONS: Because of the significant antibacterial and anti-biofilm activity of carvacrol, the present study examines this agent as an antibacterial drug of natural origin. The results indicate that in this study the best antibacterial and anti-biofilm properties are for the combined use of cefixime and carvacrol.

Investigation of the target genes of BLV miRNAs and the expression levels of miR-B4-3p and miR-B2-5p in cattle infected with Bovine Leukemia Virus.

Bovine Leukemia Virus (BLV) is an oncogenic retrovirus of the genus Deltaretrovirus. The genome of BLV encodes a cluster of 10 mature microRNAs (miRNAs). Considering the importance of miRNAs in regulating gene expression, it seems that each of the miRNAs of BLV plays a vital role in the process of pathogenesis and tumorigenesis of the virus. First, sequences of each of the miRNAs of BLV were selected and downloaded from the miRBase database. The sequences were then investigated using TargetScan and miRWalk to identify target genes of each of the mature miRNAs of the virus. Second, the expression levels of the two miRNAs with the highest number of target genes in B lymphocytes and lymphoid tissues were evaluated using qPCR and were compared between cattle with different forms of BLV infection: PL form was compared to aleukemic (AL) form (Group 1) and BLV+ with normal lymph nodes were compared to lymphosarcoma form (Group 2). We identified a total of 1595 target genes of the micro RNAs. The miRNAs with the highest target genes included miR-B4-3p with 760 and B2-5p with 102 target genes. In the second phase, miRNA expression in BLV-infected animals was investigated. The Fold Change (FC) values for miR-B4-3p and miR-B2-5p in group 1 were 22 and 67, respectively. In the second group, the FCs for miR-B4-3p and miR-B2-5p were 47 and 133, respectively. The expression was significantly higher in persistent lymphocytosis (PL) cattle in group one and lymphosarcoma cattle in group two.

In-silico design and production of a novel antigenic chimeric Shigella IpaB fused to C-terminal of Clostridium perfringens enterotoxin.

The emergence of antibiotic-resistant phenotypes in Shigella serotypes and the high mortality rate, approximately one million dead annually, in affected patients announce a global demand for an effective serotype-independent vaccine against Shigella. This study aims to design, express, and purify a novel chimeric protein, as a serotype-independent vaccine candidate against Shigella containing full-length Shigella invasion plasmid antigen B (IpaB) and a C-terminal fragment (residues 194-319) of Clostridium perfringens enterotoxin (C-CPE) as a mucosal adjuvant. Several online databases and bioinformatics software were utilized to design the chimeric protein and the relative recombinant gene. The recombinant gene encoding IpaB-CPE194-319 was synthesized, cloned into pACYCDuet-1 expression vector, and transferred to E. coli Bl21 (DE3) cells. IpaB-CPE194-319 was then expressed in auto-induction medium, purified and characterized using MALDI-TOF-TOF mass spectrometry. Followed by subcutaneous injection of the purified IpaB-CPE194-319 to BALB/c mice, antigenicity of this chimeric protein was determined through performing dot-blot immunoassay on nitrocellulose membrane using mice sera. The outcomes of this study show the successful design, efficient expression, and purification of IpaB-CPE194-319 divalent chimeric protein under mentioned conditions. The obtained results also demonstrate the intrinsic antigenic property of IpaB-CPE194-319.

Induction of specific cell-mediated immune responses and protection in BALB/c mice by vaccination with outer membrane vesicles from a Brucella melitensis human isolate.

Brucellosis is a worldwide bacterial zoonosis caused by Brucella spp. No approved vaccine is available for human use against the disease. In this study, outer membrane vesicles (OMVs) from a Brucella melitensis biovar 1 human isolate obtained in Iran were used to immunize BALB/c mice (n = 12) by 2 intramuscular injections with a 2-week interval. Another group of 12 mice was used as non-vaccinated controls. Two weeks after the last vaccination, six mice of each group were sacrificed, and proliferation and interferon gamma (IFNγ) production responses of their splenocytes were evaluated following in vitro stimulation with killed Brucella cells. The other mice were challenged with the virulent B. melitensis isolate. Two weeks later, mice were killed and spleens were cultured to determine the number of the challenge strain. The results showed proliferative response and IFNγ production of splenocytes from vaccinated mice (stimulation index: 2.18 ± 0.57, and 1519.35 ± 10.70 pg/mL, respectively) were significantly higher than those of control mice (stimulation index: 1.02 ± 0.02, and 210.01 ± 17.58 pg/mL, respectively). Numbers of the challenge strain in spleens of vaccinated mice were also significantly less than those in the controls with 1.6 units of protection. Our study revealed vaccination with OMVs of the B. melitensis isolate could induce specific immune responses and protection against infection in the mouse model suggesting their potential application for active immunization against brucellosis.

Prevalence and characterization of multidrug resistance and variant Salmonella genomic island 1 in Salmonella isolates from cattle, poultry and humans in Iran.

Salmonella enterica is a common food-borne pathogen with occasional multidrug resistance (MDR). Salmonella genomic island (SGI1) is a horizontally transmissible genomic island, containing an MDR gene cluster. All Salmonella serotypes are public health concern, although there is an additional concern associated with those that harbour SGI1. In Iran, there are no data on the presence of SGI1 variants in Salmonella isolates. The present study was conducted to identify MDR- and SGI1-carrying Salmonella strains isolated from various sources and to compare their genetic relatedness between human and animal sources. In total, 242 Salmonella isolates collected from chicken, cattle, and humans from 2008 through 2014 were studied. The isolates were tested for resistance to 14 antimicrobials via the disc diffusion method. They were also tested for the presence of SGI1 variants via PCR, and genetic relatedness was evaluated based on pulsed-field gel electrophoresis (PFGE). Resistance to at least one antimicrobial agent was observed in 132 (54%) Salmonella isolates (n = 242), while more than 40% of the isolates showed MDR. Based on PCR analysis, eight variants of SGI1, including SGI1, SGI1-B, SGI1-C, SGI1-D, SGI1-F, SGI1-I, SGI1-J and SGI1-O, were found in both human and animal isolates. Statistical analysis revealed no significant difference in the prevalence of SGI1 variants between human and animal isolates (p > 0.05). Macrorestriction PFGE analysis of the isolates with the same SGI1 variant and resistance patterns revealed genetic relatedness ranging from 70% to 100% among human and animal isolates. According to our review, this is the first documentation of SGI1 in Salmonella isolates in Iran. The presence of similar SGI1 variants in both humans and animals, along with their related PFGE patterns, suggests that food-producing animals may be a source of MDR Salmonella isolates in Iran.

New Brucella abortus S19 Mutant to Improve Distinction Between Infected and Vaccinated Animals.

BACKGROUND: Using Brucella abortus Strain 19 (S19) to control bovine brucellosis is restricted due to induce antibodies to the O-side chain of the smooth lipopolysaccharide (LPS) which may be difficult to differentiate vaccinated and infected animals. Furthermore, it is virulent for humans and can induce abortion to cattle. OBJECTIVES: The aim of this study was to employ gene knockout B. abortus S19 for the first time to eliminate diagnostic defects and obtain the attenuated mutant strain. MATERIAL AND METHODS: The wbkA gene, which is one of the LPS O-chain coding genes, was knocked out in vaccinal Brucella abortus S19. The proliferative response and immunoglobulin M production were analyzed in wbkA deletion strain-infected BALB/c mice. RESULTS: The loss of wbkA gene function resulted in induction of the splenocyte proliferative response in mice infected by the mutant S19 strain compare to those induced by parental S19 and RB51 strains. Moreover, wbkA mutant did not induce any IgM antibody response using the enzyme-linked immunosorbent assay. CONCLUSIONS: As a result, the new mutant S19 strain had deficiency in its LPS O-chain structure, besides cannot induce IgM response then, reduce mistakes to discriminate between vaccinated and infected animal, and also can be considered as a new vaccine candidate.

Complete genome analysis of Iranian IS-1494 like avian infectious bronchitis virus.

The nephropathogenic infectious bronchitis virus (IBV) strain IS-1494 like (variant-2; GI-23) was first isolated in the Middle East (1998). Despite intensive vaccinations, IS-1494 like IBVs are still circulating in Iran (the dominant genotype) and spread to other countries. Here, the full-length genome of this Iranian IS-1494 like IBV was (Mahed) determined to understand its evolutionary relationships. The genome consists of 27,652 nucleotides, with mutations in most of the structural genes. Thirteen open reading frames (ORFs) were predicted in the Mahed isolate (5' UTR-1a-1b-S-3a-3b-E-M-4b-4c-5a-5b-N-6b-3' UTR). ORFs 4b, 4c, and 6b, which has rarely been reported, were present in the Mahed genome. According to phylogenetic analysis of the full-length genome, 1a, S2, M, E, N protein, Mahed isolate clustered with the QX type strain. Based on the partial 1b, S1, Mahed clustered with the Q1 strain. The full-length genome of Mahed isolate shared the highest sequence homology with Gray and JMK (90.06-90.07%) and was least related to the Vic-s (86.21%). These data show that evolutionary variation because of recombination in IBV plays a major role in the adaptation and origin of IBV leading to new genetic and types of the virus strain.

In silico design of a novel chimeric shigella IpaB fused to C terminal of clostridium perfringens enterotoxin as a vaccine candidate.

This study aimed to design a novel chimeric protein in silico to serve as a serotype-independent vaccine candidate against Shigella. The chimera contains amino acid residues 240-460 of Shigella invasion plasmid antigen B (IpaB) and the C-terminus of Clostridium perfringens enterotoxin (C-CPE). Amino acid sequences of 537 peptide linkers were obtained from two protein linker databases. 3D structures of IpaB-CPE290-319, IpaB-CPE184-319, IpaB-CPE194-319 and 537 newly designed IpaB-linker-CPE290-319 constructs with varying linker regions were predicted. These predicted 3D structures were merged with the 3D structures of native IpaB240-460, CPE194-319, CPE184-319 and CPE290-319 to select the structure most similar to native IpaB and C-CPE. Several in silico tools were used to determine the suitability of the selected IpaB-C-CPE structure as a vaccine candidate. None of the 537 linkers was capable of preserving the native structure of CPE290-319 within the IpaB-linker-CPE290-319 structure. In silico analysis determined that the IpaB-CPE194-319 3D structure was the most similar to the 3D structure of the respective native CPE domain and that it was a stable chimeric protein exposing multiple B-cell epitopes. IpaB-CPE194-319 was designed for its capability to bind to human intestinal epithelial and M cells and to accumulate on these cells. The predicted B-cell epitopes are likely to be capable of inducing a mucosal antibody response in the human intestine against Shigella IpaB. This study also showed that the higher binding affinities of CPE184-319 and CPE194-319 to claudin molecules than those of CPE290-319 is the result of preserving the 3D structures of CPE184-319 and CPE194-319 when they are linked to the C-termini of other proteins.

Longitudinal Analyses of Gut-Associated Bacterial Microbiota in Ulcerative Colitis Patients.

BACKGROUND: The normal colonic microbiota is associated with the etiology of ulcerative colitis (UC). Several bacterial species are associated with the initiation and amplification of disease process. However, the etiology and mechanism of UC are poorly understood. The present study aimed to investigate, characterize, and compare the main composition of the mucosa-associated intestinal microflora in colonoscopic biopsy specimens of UC and non-UC patients. METHODS: Aerobic and facultative-anaerobic mucosa-associated bacteria were isolated and diagnosed from colonoscopic biopsy specimens of 40 UC patients and 40 patients without UC. Patients were selected as control from the same centers and colonoscopy was carried out for other reasons (mainly colorectal screening). Isolation and characterization for aerobic and facultative-anaerobic intestinal bacteria were carried out by conventional culture techniques. DNA extraction from biopsies and polymerase chain reaction (PCR) amplification of bacterial 16S rRNA with gene-targeted and species-specific primers was performed for detection of anaerobic bacterial species. RESULTS: Several species of mucosa-associated aerobic and facultative anaerobic bacteria were found in biopsy specimens and there were no significant differences between UC patients and non-UC patients. Our investigation for detection of the anaerobic intestinal flora showed Faecalibacterium prausnitzii, Prevotella, and Peptostreptococcus productus were the predominant microflora in controls and have significant differences (P = 0.002, 0.025 and 0.039, respectively). CONCLUSION: This is the first investigation of the intestinal mucosa-associated microflora in patients with UC in Iran. These results, although limited by sample size, allow a better understanding of changes in mucosa-associated bacterial flora in these patients, showing that decrease of Faecalibacterium prausnitzii, Provetella, and Peptostreptococcus productus in the intestinal tract may translate into a reduction in the important role of this beneficial bacterial species, which can lead to reduced protection of the gut mucosa and UC development.

Isolation of atypical enteropathogenic and shiga toxin encoding Escherichia coli strains from poultry in Tehran, Iran.

AIM: The purpose of this study was to investigate the prevalence of enteropathogenic Escherichia coli (EPEC) and shiga toxin producing E. coli (STEC) strains in healthy broilers in Iran. BACKGROUND: STEC and EPEC strains as diarrheagenic E. coli are among the most prevalent causative agents in acute diarrhea. Domestic animals, mainly cattle and sheep, have been implicated as the principal reservoirs of these pathotypes; however their prevalence among the broilers is varied among different countries. PATIENTS AND METHODS: A total of 500 cloacal swab samples from broilers of five different poultry houses (A-E) were collected to investigate the presence of stx1, stx2, hly, eae, and bfp virulence genes among the E. coli isolates by polymerase chain reaction. The shiga toxin encoding strains were evaluated serologically to detect their interaction with a commercial antiserum against O157 antigen. RESULTS: Out of the 500 collected samples, 444 E. coli strains were isolated. Three strains (0.67%) presented at least one of the studied virulence genes (stx2, hly and eae), two strains were identified as STEC (stx2 (+), O157:nonH7) and one as an atypical EPEC strains (eae (+) bfp (-)). CONCLUSION: The study established the presence of STEC and atypical EPEC in healthy broilers in Iran. Poultry might serve as vectors for transmission of pathogenic E. coli to human populations.

Purification of the Immunogenic Fractions and Determination of Toxicity in Mesobuthus eupeus (Scorpionida: Buthidae) Venom.

BACKGROUND: Scorpions stings are a health problem in many parts of the world. Mesobuthus eupeus (Buthidae) is the most prevalent species in the Middle East and Central Asia. Definition of toxicogenic and immunogenic characteristics of the venom is necessary to produce antidote. In this study, the noted properties of M. eupeus venom were evaluated. METHODS: Venom was obtained by milking M. eupeus scorpions for lyophilization. Toxicity was determined after injecting the venom to albino mice and calculating LD50. Polyclonal antibodies against M. eupeus venom were obtained from immunized rabbits. The CH-Sepharose 4B column was used for isolating the specific antibodies. 10 mg of the affinity-purified antibodies were conjugated with a CH-Sepharose 4B column and M. eupeus venom was applied to the column. The bound fragments were eluted using hydrogen chloride (pH: 2.5). Crude venom and affinity-purified fractions of the venom were analyzed by SDS-PAGE technique. RESULTS: Lethal dose (LD) was 8.75, 11.5 and 4.5 mg/kg for IP, SC and IV respectively. The LD50 of M. eupeus venom was 6.95 mg/kg. The crude venom had 12 detectable bands with molecular weights of 140, 70, 50, 33, 30, 27, 22, 18, 14, 10 kDa and two bands less than 5 kDa. The affinity-purified venom presented eight bands. The 27 kDa band was clearly sharper than other bands but 70, 18, 10 and one of the less than 5 kDa bands were not observed. CONCLUSIONS: Contrary to popular belief, which know scorpion venom as non-immunogenic composition, the current study was shown that the most fractions of the M. eupeus are immunogenic.