Microbial susceptibility, virulence factors, and plasmid profiles of uropathogenic Escherichia coli strains isolated from children in Jahrom, Iran.

BACKGROUND: Urinary tract infections (UTIs), including cystitis and pyelonephritis, are the most common infectious diseases in childhood. Escherichia coli (E. coli) accounts for as much as 90% of the community-acquired and 50% of nosocomial UTIs. Therefore, identification of E. coli strains is important for both clinical and epidemiological implications. Understanding antibiotic resistance patterns and molecular characterization of plasmids and other genetic elements is also epidemiologically useful. METHODS: To characterize uropathogenic strains of E. coli, we studied 96 E. coli strains recovered from urine samples of children aged 1 month to 14 years with community-acquired UTIs in Jahrom, Iran. We assessed virulence factors (VFs), drug sensitivities, and plasmid profiles. RESULTS: Drug sensitivities of the isolates were: 19.8% (ampicillin), 24% (trimethoprim-sulfamethoxazole), 29.2% ( tetracycline), 75.5% (nalidixic acid), 80.4% (cefixime), 84.6% (gentamicin), 91.4% (ciprofloxacin), 96.8% (nitrofurantoin), 96.8% (amikacin) and 100% (imipenem). Totally, 76 isolates harbored plasmids with an average of 5.5 plasmids (range: 1-10) in each strain. Plasmid profiling distinguished 22 different E. coli genotypes in all isolates that ranged in similarity from 50% to 100%. PCR showed that the prevalence of virulence genes ranged from 15.62% for hly to 30.2% for pap. CONCLUSION: These data mandate local monitoring of drug resistance and its consideration in empirical therapy of E. coli infections. Plasmid analysis of representative E. coli isolates also demonstrates the presence of a wide range of plasmid sizes, with no consistent relationship between plasmid profiles and resistance phenotypes. Plasmid profiles distinguished more strains than did the antimicrobial susceptibility pattern.

Site-specific chemical labeling of long RNA molecules.

Site-specific labeling of RNA molecules is a valuable tool for studying their structure and function. Here, we describe a new site-specific RNA labeling method, which utilizes a DNA-templated chemical reaction to attach a label at a specific internal nucleotide in an RNA molecule. The method is nonenzymatic and based on the formation of a four-way junction, where a donor strand is chemically coupled to an acceptor strand at a specific position via an activated chemical group. A disulfide bond in the linker is subsequently cleaved under mild conditions leaving a thiol group attached to the acceptor-RNA strand. The site-specific thiol-modified target RNA can then be chemically labeled with an optional group, here demonstrated by coupling of a maleimide-functionalized fluorophore. The method is rapid and allows site specific labeling of both in vitro and in vivo synthesized RNA with a broad range of functional groups.

Variations in Serratia marcescens differentiation using different primers.

OBJECTIVE: To study primer sequences (1060, 1247, 1254, 1281, 1283, and 1290) for random amplified polymorphic DNA polymerase chain reaction (RAPD-PCR). METHODS: Twenty-four clinical Serratia marcescens (S. marcescens) isolates were obtained over a 6-month period from April 2002 to September 2002 from hospitals in the Fars province of Iran. Six primers were used due to S. marcescens genome properties, and RAPD-PCR was carried out. The results were subjected to unweighted pair-group method analysis using NTSYSpc 2.02. The primers were blasted with the S. marcescens genome, and the primers efficiency was estimated. RESULTS: The results of blast primers with S. marcescens genome sequence showed that primer 1283 had the highest homology and primer 1290 had the lowest homology. Comparing the resulted dendrograms showed that the pattern of the primers to separate isolates was closely related to their sequence homology with the genome and their amount of guanine and cytosine nucleotide content. CONCLUSION: There are clear differences in RAPD-PCR results when different primers are used, and it is recommended to consider genomic properties of an organism to design a primer for RAPD-PCR.

Computational comparison of T-cell epitopes of gp120 of Iranian HIV-1 with different subtypes of the virus.

In the present study, T-cell epitopes of gp120 of an Iranian isolate have been compared to different subtypes of HIV-1. At first, the amino acid sequences of gp120 were fetched from data banks. Then T-cell epitopes, disulfide bonding states, protein kinase C phosphorylation sites, cAMP-dependent protein kinase phosphorylation sites, casein kinase II phosphorylation sites, N-myristoylation sites and amidation sites were predicted using different soft wares. According to this computational analysis 6 good disulfide binding states in Iranian gp120 were predicted. From the viewpoint of cAMP-dependent protein kinase phosphorylation site (1 site) Iranian isolate was similar to clades B and F. Like subtype C 1 amidation site was predicted in the Iranian subtype. In the Iranian isolate 7 sites protein kinase C phosphorylation sites and 4 N-myristoylation sites were predicted. Since the number of individuals infected with HIV-1 in Iran, like many other countries is increasing, study of similarities and differences between the Iranian samples and different clades of HIV-1 can help us in identification of the origin and understanding the changes in the virus.