title: Development of a multiplex real-time PCR assay for phylogenetic analysis of Uropathogenic Escherichia coli.
abstract: Uropathogenic Escherichia coli (UPEC) is among major pathogens causing 80-90% of all episodes of urinary tract infections (UTIs). Recently, E. coli strains are divided into eight main phylogenetic groups including A, B1, B2, C, D, E, F, and clade I. This study was aimed to develop a rapid, sensitive, and specific multiplex real time PCR method capable of detecting phylogenetic groups of E. coli strains. This study was carried out on E. coli strains (isolated from the patient with UTI) in which the presence of all seven target genes had been confirmed in our previous phylogenetic study. An EvaGreen-based singleplex and multiplex real-time PCR with melting curve analysis was designed for simultaneous detection and differentiation of these genes. The primers were selected mainly based on the production of amplicons with melting temperatures (Tm) ranging from 82°C to 93°C and temperature difference of more than 1.5°C between each peak.The multiplex real-time PCR assays that have been developed in the present study were successful in detecting the eight main phylogenetic groups. Seven distinct melting peaks were discriminated, with Tm value of 93±0.8 for arpA, 89.2±0.1for chuA, 86.5±0.1 for yjaA, 82.3±0.2 for TspE4C2, 87.8±0.1for trpAgpC, 85.4±0.6 for arpAgpE genes, and 91±0.5 for the internal control. To our knowledge, this study is the first melting curve-based real-time PCR assay developed for simultaneous and discrete detection of these seven target genes. Our findings showed that this assay has the potential to be a rapid, reliable and cost-effective alternative for routine phylotyping of E. coli strains.
authors.affiliation: The Persian Gulf Marine Biotechnology Research Center, Bushehr University of Medical Sciences, Bushehr, Iran. Electronic address: m.hasanpour@hotmail.com.
authors.forename: Mojtaba
authors.initials: M
authors.lastname: Hasanpour
authors.affiliation: The Persian Gulf Marine Biotechnology Research Center, Bushehr University of Medical Sciences, Bushehr, Iran. Electronic address: akna85@gmail.com.
authors.forename: Akram
authors.initials: A
authors.lastname: Najafi
mesh_terms: D001425:Bacterial Outer Membrane Proteins / Q000235:genetics; D017931:DNA Primers; D004269:DNA, Bacterial / Q000235:genetics; D004927:Escherichia coli Infections / Q000382:microbiology; D029968:Escherichia coli Proteins / Q000235:genetics; D006801:Humans; D060885:Multiplex Polymerase Chain Reaction / Q000191:economics / Q000379:methods*; D010802:Phylogeny; D011956:Receptors, Cell Surface / Q000235:genetics; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D044366:Transition Temperature; D014552:Urinary Tract Infections / Q000382:microbiology; D056689:Uropathogenic Escherichia coli / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification
chemical_list: D001425:Bacterial Outer Membrane Proteins; C423457:ChuA protein, E coli; D017931:DNA Primers; D004269:DNA, Bacterial; D029968:Escherichia coli Proteins; D011956:Receptors, Cell Surface
keywords: Escherichia coli; EvaGreen real-time PCR; Melting curve; Phylogenetic groups