title: Extensive Within-Host Diversity in Fecally Carried Extended-Spectrum-Beta-Lactamase-Producing Escherichia coli Isolates: Implications for Transmission Analyses.
abstract: 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.
authors.affiliation: 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.
authors.forename: N
authors.initials: N
authors.lastname: Stoesser
authors.affiliation: NIHR Biomedical Research Center, University of Oxford/Oxford University Hospitals NHS Trust, Oxford, United Kingdom.
authors.forename: A E
authors.initials: AE
authors.lastname: Sheppard
authors.affiliation: NIHR Biomedical Research Center, University of Oxford/Oxford University Hospitals NHS Trust, Oxford, United Kingdom.
authors.forename: C E
authors.initials: CE
authors.lastname: Moore
authors.affiliation: NIHR Biomedical Research Center, University of Oxford/Oxford University Hospitals NHS Trust, Oxford, United Kingdom.
authors.forename: T
authors.initials: T
authors.lastname: Golubchik
authors.affiliation: Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, United Kingdom School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand.
authors.forename: C M
authors.initials: CM
authors.lastname: Parry
authors.affiliation: Angkor Hospital for Children, Siem Reap, Cambodia.
authors.forename: P
authors.initials: P
authors.lastname: Nget
authors.affiliation: Angkor Hospital for Children, Siem Reap, Cambodia.
authors.forename: M
authors.initials: M
authors.lastname: Saroeun
authors.affiliation: Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand.
authors.forename: N P J
authors.initials: NP
authors.lastname: Day
authors.affiliation: NIHR Biomedical Research Center, University of Oxford/Oxford University Hospitals NHS Trust, Oxford, United Kingdom.
authors.forename: A
authors.initials: A
authors.lastname: Giess
authors.affiliation: Minneapolis Veterans Affairs Health Care System, Minneapolis, Minnesota, USA Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA.
authors.forename: J R
authors.initials: JR
authors.lastname: Johnson
authors.affiliation: 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.
authors.forename: T E A
authors.initials: TE
authors.lastname: Peto
authors.affiliation: 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.
authors.forename: D W
authors.initials: DW
authors.lastname: Crook
authors.affiliation: NIHR Biomedical Research Center, University of Oxford/Oxford University Hospitals NHS Trust, Oxford, United Kingdom.
authors.forename: A S
authors.initials: AS
authors.lastname: Walker
mesh_terms: D000293:Adolescent; D002160:Cambodia; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D024881:Drug Resistance, Bacterial; D004926:Escherichia coli / Q000145:classification* / Q000201:enzymology* / Q000302:isolation & purification; D005243:Feces / Q000382:microbiology*; D005260:Female; D005798:Genes, Bacterial; D014644:Genetic Variation; D016680:Genome, Bacterial; D005838:Genotype; D006801:Humans; D008297:Male; D017422:Sequence Analysis, DNA; D037521:Virulence Factors / Q000235:genetics; D001618:beta-Lactamases / Q000378:metabolism*
chemical_list: D004269:DNA, Bacterial; D037521:Virulence Factors; D001618:beta-Lactamases