Cookies on this website
We use cookies to ensure that we give you the best experience on our website. If you click 'Continue' we'll assume that you are happy to receive all cookies and you won't see this message again. Click 'Find out more' for information on how to change your cookie settings.

<jats:p>Studies of the transmission epidemiology of antimicrobial-resistant<jats:named-content content-type="genus-species">Escherichia coli</jats:named-content>, 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<jats:named-content content-type="genus-species">E. coli</jats:named-content>colonies from each of eight fecal samples (<jats:italic>n =</jats:italic>127 genomes; one failure), taken from different individuals in Cambodia, a region of high ESBL-producing<jats:named-content content-type="genus-species">E. coli</jats:named-content>prevalence. Sequence data were used to characterize both the core chromosomal diversity of<jats:named-content content-type="genus-species">E. coli</jats:named-content>isolates and their resistance/virulence gene content as a proxy measure of accessory genome diversity. The 127<jats:named-content content-type="genus-species">E. coli</jats:named-content>genomes represented 31 distinct sequence types (STs). Seven (88%) of eight subjects carried ESBL-positive isolates, all containing<jats:italic>bla</jats:italic><jats:sub>CTX-M</jats:sub>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<jats:italic>bla</jats:italic><jats:sub>CTX-M</jats:sub>variant occurred in different clones, and/or different<jats:italic>bla</jats:italic><jats:sub>CTX-M</jats:sub>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<jats:named-content content-type="genus-species">E. coli</jats:named-content>bacteria suggests that fecal surveillance, particularly if based on single-colony subcultures, will likely underestimate transmission events, especially in high-prevalence settings.</jats:p>

Original publication





Journal of Clinical Microbiology


American Society for Microbiology

Publication Date





2122 - 2131