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Title: Extensive within-host diversity in fecally carried extended-spectrum-beta-lactamase-producing Escherichia coli Isolates: Implications for transmission analyses
Authors: N. Stoesser
A. E. Sheppard
C. E. Moore
T. Golubchik
C. M. Parry
P. Nget
M. Saroeun
N. P.J. Day
A. Giess
J. R. Johnson
T. E.A. Peto
D. W. Crook
A. S. Walker
Nuffield Department of Clinical Medicine
University of Oxford
London School of Hygiene & Tropical Medicine
Nagasaki University
Mahidol University
Angkor Hospital for Children
Minneapolis Veterans Affairs Health Care System
University of Minnesota Twin Cities
Keywords: Medicine
Issue Date: 1-Jul-2015
Citation: Journal of Clinical Microbiology. Vol.53, No.7 (2015), 2122-2131
Abstract: © 2015, Stoesser et al. Studies of the transmission epidemiology of antimicrobial-resistant Escherichia coli, such as strains harboring extended-spectrum beta-lactamase (ESBL) genes, frequently use selective culture of rectal surveillance swabs to identify isolates for molecular epidemiological investigation. Typically, only single colonies are evaluated, which risks underestimating species diversity and transmission events. We sequenced the genomes of 16 E. coli colonies from each of eight fecal samples (n = 127 genomes; one failure), taken from different individuals in Cambodia, a region of high ESBL-producing E. coli prevalence. Sequence data were used to characterize both the core chromosomal diversity of E. coli isolates and their resistance/virulence gene content as a proxy measure of accessory genome diversity. The 127 E. coli genomes represented 31 distinct sequence types (STs). Seven (88%) of eight subjects carried ESBL-positive isolates, all containing blaCTX-M variants. Diversity was substantial, with a median of four STs/individual (range, 1 to 10) and wide genetic divergence at the nucleotide level within some STs. In 2/8 (25%) individuals, the same blaCTX-M variant occurred in different clones, and/or different blaCTX-M variants occurred in the same clone. Patterns of other resistance genes and common virulence factors, representing differences in the accessory genome, were also diverse within and between clones. The substantial diversity among intestinally carried ESBL-positive E. coli bacteria suggests that fecal surveillance, particularly if based on single-colony subcultures, will likely underestimate transmission events, especially in high-prevalence settings.
ISSN: 1098660X
Appears in Collections:Scopus 2011-2015

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