Prevalence of antibiotic resistance and genetic relatedness of Escherichia coli isolates in HIV and thalassemia patients in southeastern Iran.

The present study was carried out to evaluate the prevalence of antibiotic resistance genes in Escherichia coli isolates from HIV and thalassemia patients and to determine the phylogenetic group distribution and to genotype the isolates in southeastern Iran. This cross-sectional study was performed in E. coli isolates taken from fecal and urine samples of 43 HIV and 62 thalassemia patients. The E. coli isolates were examined for 13 antibiotic resistance genes and determine the phylogroups. The Rep-PCR DNA fingerprinting method was utilized to determine the genotype of the isolates. Among the 105 E. coli isolates, 66.7% isolates were positive for qnrS, 55.2% for dhfrI, 40.9% for sulI, 33.3% for sulII and 31.4% for blaTEM genes. A blaCTX-M-15 gene was detected in 20.9% isolates, aac(3)-I in 14.3% isolates and aadA in 12.4% isolates, whereas blaSHV and qnrB genes were identified in 10.5% and 8.6% isolates, respectively. Out of the isolates, only 2.8% isolates possessed the blaOXA-1 gene, and no IMP and VIM genes were detected. The significant phylogroup was A (37.2%), B2 (15.3%), B1 and unknown (each 14.3%), D (13.4%) and C, F and clade I (each 2%). Phylogroup A accounted for the highest antibiotic resistance. The results of Rep-PCR indicated that the isolates were closely related. These results showed a high prevalence of genes encoding antibiotic resistance in the E. coli isolates. The majority of E. coli isolates distributed among phylogroup A, whereas positive isolates for antibiotic resistance genes were disseminated among various phylogroups (A, B2, and D).

Antibiotic resistance profile and virulence genes of uropathogenic Escherichia coli isolates in relation to phylogeny.

Escherichia coli (E. coli) strains are the major cause of urinary tract infections (UTI) and belong to the large group of extra-intestinal pathogenic E. coli. The purposes of this study were to determine the antibiotic resistance profile, virulence genes and phylogenetic background of E. coli isolates from UTI cases. A total of 137 E. coli isolates were obtained from UTI samples. The antimicrobial susceptibility of confirmed isolates was determined by disk diffusion method against eight antibiotics. The isolates were examined to determine the presence and prevalence of selected virulence genes including iucD, sfa/focDE, papEF and hly. ECOR phylo-groups of isolates were determined by detection of yjaA and chuA genes and fragment TspE4.C2. The antibiogram results showed that 71% of the isolates were resistant to cefazolin, 60.42% to co-trimoxazole, 54.16% to nalidixic acid, 36.45% to gentamicin, 29.18% to ciprofloxacin, 14.58% to cefepime, 6.25% to nitrofurantoin and 0.00% to imipenem. Twenty-two antibiotic resistance patterns were observed among the isolates. Virulence genotyping of isolates revealed that 58.39% isolates had at least one of the four virulence genes. The iucD gene was the most prevalent gene (43.06%). The other genes including sfa/focDE, papEF and hly genes were detected in 35.76%, 18.97% and 2.18% isolates, respectively. Nine combination patterns of the virulence genes were detected in isolates. Phylotyping of 137 isolates revealed that the isolates fell into A (45.99%), B1 (13.14%), B2 (19.71%) and D (21.16%) groups. Phylotyping of multidrug resistant isolates indicated that these isolates are mostly in A (60.34%) and D (20.38%) groups. In conclusion, the isolates that possessed the iucD, sfa/focDE, papEF and hly virulence genes mostly belonged to A and B2 groups, whereas antibiotic resistant isolates were in groups A and D. Escherichia coli strains carrying virulence factors and antibiotic resistance are distributed in specific phylogenetic background.

Virulence genotyping of Escherichia coli isolates from diarrheic and urinary tract infections in relation to phylogeny in southeast of Iran.

The purpose of this study was to determine the prevalence of virulence genes and phylogenetic groups/subgroups of Escherichia coli (E. coli) isolates from diarrheic and urinary tract infections (UTI) cases in Rigan area, southeast of Iran. One hundred thirty five E. coli were isolated from diarrheic (90 isolates) and urinary tract infections (45 isolates) samples. The confirmed isolates were examined to detect the phylogenetic group/subgroups and a selection of virulence genes including iucD, sfa/focDE, afaIBC, papEF, hly, cnfI and cdtI by PCR. The examined isolates belonged to four phylogenetic groups A (42.2%), B1 (14.1%), B2 (10.4%), and D (33.3%). Among 135 tested bacteria, 62.22% of diarrheic and 30.37% of UTI isolates had at least one of the virulence genes. In the diarrheic isolates iucD (47.77%) was the most prevalent gene. The other genes including sfa/focDE, afaIBC, papEF and cnfI/cdtI genes were detected in 15, 13, 11 and one diarrheic isolates respectively. None of the diarrheic isolates were positive for hly gene. Out of 45 UTI isolates 28.88% were positive for iucD, 13.33% for cnfI, 11.11% for afaIBC, 11.11% for papEF, 6.66% for sfa/focDE and 4.44% for cdtI genes. Several combination patterns of the virulence genes were detected in diarrheic and UTI isolates. In conclusion, the prevalence of virulence genes in diarrheic and UTI isolates differ according to phylogenetic groups, although B2 and D phylotypes have an accumulation of virulence associated genes.

Identification of DREB homologous genes in bread wheat via CODEHOP PCR primer design.

In this study, we exploit the useful described CODEHOP primer design and RT-PCR strategy for targeted isolation of homologues in large gene families. The method was tested with two different objectives. The first was to apply CODEHOP strategy for design degenerate oligonucleotide primers in a broad range of plant species. The second was to isolate an orthologus of the transcription factor of dehydration-responsive element binding protein (DREB) and to determine the complexity of gene family in bread wheat. We used a new primer design strategy for PCR amplification of unknown targets that are related to multiply-aligned protein sequences. Each primer consists of a short 3' degenerate core region and a longer 5' consensus clamp region. Only 3-4 highly conserved amino acid residues are necessary for design of the core, which is stabilized by the clamp annealing to templates molecules. This provides the possibility of isolating numerous additional DREB genes by Polymerase Chain Reaction (PCR) with degenerate oligonucleotide primers. The relationship of the amplified products to DREB genes was evaluated by several sequence and genetic criteria. Present data show that expression of DREB and its homologues, is induced by low temperature stress. Towards this step, it found that the expression of DRE-regulated genes increased freezing tolerance in plants.

The effects of Fusarium oxysporum on broomrape (Orobanche egyptiaca) seed germination.

Broomrape (Orobanche aegyptiaca L.), one of the most important parasitic weeds in Iran, is a root parasitic plant that can attack several crops such as tobacco, sunflower, tomato and etc. Several methods were used for Orobanche control, however these methods are inefficient and very costly. Biological control is an additional recent tool for the control of parasitic weeds. In order to study of the fungus Fusarium oxysporum (biocontrol agent) effects on broomrape seed germination, two laboratory studies were conducted in Tehran University. In the first experiment, different concentration of GR60 (0, 1, 2 and 5 ppm) as stimulation factor for Orobanche seeds germination were experimented. Results showed that concentrations of GR60 had a significant effect on seed germination. The highest seed germination percent was obtained in 1 ppm. In the second experiment, the effect of Fusarium oxysporum was tested on O. aegyptiaca seeds germination. The fungus Fusarium oxysporum were isolated from infested and juvenile O. aegyptiaca ower stalks in tomato field in karaj. Fungus spores suspension in different concentrations (0 (Control), 10(5) (T1), 10(6) (T2), 10(7) (T3) and 3 x 10(7) (T4)) from potato dextrose agar (PDA) prepared and together with 1ppm of GR60 concentration were tested on O. aegyptiaca seeds. Results show that the highest inhibition of seed germination obtained in 10(5) spores/ml. With increasing of suspension concentrations, inhibition percent was reduced and mortality of seeds germ tube was increased. In this investigation, Fusarium oxysporum can be used to inhibit seed germination, stimulate the "suicidal germination" of seeds and reduce the Orobanche seed bank.