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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.

Original publication

DOI

10.1128/jcm.00378-15

Type

Journal article

Journal

Journal of clinical microbiology

Publication Date

07/2015

Volume

53

Pages

2122 - 2131

Addresses

Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom NIHR Biomedical Research Center, University of Oxford/Oxford University Hospitals NHS Trust, Oxford, United Kingdom nicole.stoesser@ndm.ox.ac.uk.

Keywords

Modernizing Medical Microbiology Informatics Group, Feces, Humans, Escherichia coli, beta-Lactamases, DNA, Bacterial, Virulence Factors, Sequence Analysis, DNA, Drug Resistance, Bacterial, Genotype, Genes, Bacterial, Genome, Bacterial, Adolescent, Cambodia, Female, Male, Genetic Variation