title: Rapid and Specific Detection of the Escherichia coli Sequence Type 648 Complex within Phylogroup F.
abstract: TheEscherichia colisequence type 648 complex (STc648) is an emerging lineage within phylogroup F-formerly included within phylogroup D-that is associated with multidrug resistance. Here, we designed and validated a novel multiplex PCR-based assay for STc648 that took advantage of (i) four distinctive single-nucleotide polymorphisms inicdallele 96 andgyrBallele 87, two of the multilocus sequence typing alleles that define ST648; and (ii) the typical absence within STc648 ofuidA, anE. coli-specific gene encoding β-glucuronidase. Within a diverse 212-strain validation set that included 109 STs other than STc648, from phylogroups A, B1, B2, C, D, E, and F, the assay exhibited 100% sensitivity (95% confidence interval [CI], 82% to 100%) and specificity (95% CI, 98% to 100%). It functioned similarly well in two distant laboratories that used boiled lysates or DNAzol-purified DNA as the template DNA. Thus, this novel multiplex PCR-based assay should enable any laboratory equipped for diagnostic PCR to rapidly, accurately, and economically screenE. coliisolates for membership in STc648.
authors.affiliation: Minneapolis VA Medical Center, Minneapolis, Minnesota, USA johns007@umn.edu.|University of Minnesota, Minneapolis, Minnesota, USA.
authors.forename: James R
authors.initials: JR
authors.lastname: Johnson
authors.affiliation: Minneapolis VA Medical Center, Minneapolis, Minnesota, USA.|University of Minnesota, Minneapolis, Minnesota, USA.
authors.forename: Brian D
authors.initials: BD
authors.lastname: Johnston
authors.affiliation: Australian National University, Canberra, Australia.
authors.forename: David M
authors.initials: DM
authors.lastname: Gordon
mesh_terms: D004926:Escherichia coli / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D004927:Escherichia coli Infections / Q000175:diagnosis* / Q000382:microbiology*; D005838:Genotype; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D060885:Multiplex Polymerase Chain Reaction / Q000379:methods*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D013997:Time Factors
keywords: Escherichia coli; antimicrobial resistance; diagnostics; molecular epidemiology; polymerase chain reaction; sequence type; strain typing