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Please use this identifier to cite or link to this item: http://repository.li.mahidol.ac.th/dspace/handle/123456789/41785
Title: Whole genome sequencing of ESBL-producing Escherichia coli isolated from patients, farm waste and canals in Thailand
Authors: Chakkaphan Runcharoen
Kathy E. Raven
Sandra Reuter
Teemu Kallonen
Suporn Paksanont
Jeeranan Thammachote
Suthatip Anun
Beth Blane
Julian Parkhill
Sharon J. Peacock
Narisara Chantratita
Mahidol University
University of Cambridge
Bhuddhasothon Hospital
Wellcome Trust Sanger Institute
London School of Hygiene & Tropical Medicine
Keywords: Biochemistry, Genetics and Molecular Biology
Issue Date: 6-Sep-2017
Citation: Genome Medicine. Vol.9, No.1 (2017)
Abstract: © 2017 The Author(s). Background: Tackling multidrug-resistant Escherichia coli requires evidence from One Health studies that capture numerous potential reservoirs in circumscribed geographic areas. Methods: We conducted a survey of extended β-lactamase (ESBL)-producing E. coli isolated from patients, canals and livestock wastewater in eastern Thailand between 2014 and 2015, and analyzed isolates using whole genome sequencing. Results: The bacterial collection of 149 isolates consisted of 84 isolates from a single hospital and 65 from the hospital sewer, canals and farm wastewater within a 20 km radius. E. coli ST131 predominated the clinical collection (28.6%), but was uncommon in the environment. Genome-based comparison of E. coli from infected patients and their immediate environment indicated low genetic similarity overall between the two, although three clinical-environmental isolate pairs differed by ≤ 5 single nucleotide polymorphisms. Thai E. coli isolates were dispersed throughout a phylogenetic tree containing a global E. coli collection. All Thai ESBL-positive E. coli isolates were multidrug resistant, including high rates of resistance to tobramycin (77.2%), gentamicin (77.2%), ciprofloxacin (67.8%) and trimethoprim (68.5%). ESBL was encoded by six different CTX-M elements and SHV-12. Three isolates from clinical samples (n = 2) or a hospital sewer (n = 1) were resistant to the carbapenem drugs (encoded by NDM-1, NDM-5 or GES-5), and three isolates (clinical (n = 1) and canal water (n = 2)) were resistant to colistin (encoded by mcr-1); no isolates were resistant to both carbapenems and colistin. Conclusions: Tackling ESBL-producing E. coli in this setting will be challenging based on widespread distribution, but the low prevalence of resistance to carbapenems and colistin suggests that efforts are now required to prevent these from becoming ubiquitous.
URI: https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85028945128&origin=inward
http://repository.li.mahidol.ac.th/dspace/handle/123456789/41785
ISSN: 1756994X
Appears in Collections:Scopus 2016-2017

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