TY - JOUR
T1 - Rapid and specific detection of the Escherichia coli sequence type 648 complex within phylogroup F
AU - Johnson, James R.
AU - Johnston, Brian D.
AU - Gordon, David M.
PY - 2017/4
Y1 - 2017/4
N2 - 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.
AB - 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.
KW - Antimicrobial resistance
KW - Diagnostics
KW - Escherichia coli
KW - Molecular epidemiology
KW - Polymerase chain reaction
KW - Sequence type
KW - Strain typing
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UR - http://www.scopus.com/inward/citedby.url?scp=85016124463&partnerID=8YFLogxK
U2 - 10.1128/JCM.01949-16
DO - 10.1128/JCM.01949-16
M3 - Article
C2 - 28100599
AN - SCOPUS:85016124463
SN - 0095-1137
VL - 55
SP - 1116
EP - 1121
JO - Journal of clinical microbiology
JF - Journal of clinical microbiology
IS - 4
ER -