Rapid and specific detection of the Escherichia coli sequence type 648 complex within phylogroup F

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Abstract

The Escherichia coli sequence 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 in icd allele 96 and gyrB allele 87, two of the multilocus sequence typing alleles that define ST648; and (ii) the typical absence within STc648 of uidA, an E. 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 screen E. Coli isolates for membership in STc648.

Original languageEnglish (US)
Pages (from-to)1116-1121
Number of pages6
JournalJournal of clinical microbiology
Volume55
Issue number4
DOIs
StatePublished - Apr 2017

Keywords

  • Antimicrobial resistance
  • Diagnostics
  • Escherichia coli
  • Molecular epidemiology
  • Polymerase chain reaction
  • Sequence type
  • Strain typing

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