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J Clin Microbiol. 2015 Jan;53(1):160-6. doi: 10.1128/JCM.02562-14. Epub 2014 Oct 29.

Rapid identification of major Escherichia coli sequence types causing urinary tract and bloodstream infections.

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Public Health England, London, United Kingdom
Public Health England, London, United Kingdom.
Public Health England, London, United Kingdom Antimicrobial Research Group, Centre for Immunology and Infectious Disease, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary, University of London, London, United Kingdom.
Department of Medical Microbiology, Southmead Hospital, Bristol, United Kingdom.
Norwich Medical School, University of East Anglia, Norwich, United Kingdom.
Public Health England, London, United Kingdom Norwich Medical School, University of East Anglia, Norwich, United Kingdom.


Escherichia coli sequence types (STs) 69, 73, 95, and 131 are collectively responsible for a large proportion of E. coli urinary tract and bloodstream infections, and they differ markedly in their antibiotic susceptibilities. Here, we describe a novel PCR method to rapidly detect and distinguish these lineages. Three hundred eighteen published E. coli genomes were compared in order to identify signature sequences unique to each of the four major STs. The specificities of these sequences were assessed in silico by seeking them in an additional 98 genomes. A PCR assay was designed to amplify size-distinguishable fragments unique to the four lineages and was validated using 515 E. coli isolates of known STs. Genome comparisons identified 22 regions ranging in size from 335 bp to 26.5 kb that are unique to one or more of the four predominant E. coli STs, with two to 10 specific regions per ST. These regions predominantly harbor genes encoding hypothetical proteins and are within or adjacent to prophage sequences. Most (13/22) were highly conserved (>96.5% identity) in the genomes of their respective ST. The new assay correctly identified all 142 representatives of the four major STs in the validation set (n = 515), with only two ST12 isolates misidentified as ST95. Compared with MLST, the assay has 100% sensitivity and 99.5% specificity. The rapid identification of major extraintestinal E. coli STs will benefit future epidemiological studies and could be developed to tailor antibiotic therapy to the different susceptibilities of these dominant lineages.

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