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    Dynamics of antimicrobial resistance in intestinal Escherichia coli from children in community settings in South Asia and sub-Saharan Africa

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    Author
    Ingle, Danielle J.
    Levine, Myron M.
    Kotloff, Karen L.
    Date
    2018-09-01
    Journal
    Nature Microbiology
    Publisher
    Nature Publishing Group
    Type
    Article
    
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    See at
    https://10.1038/s41564-018-0217-4
    Abstract
    The dynamics of antimicrobial resistance (AMR) in developing countries are poorly understood, especially in community settings, due to a sparsity of data on AMR prevalence and genetics. We used a combination of phenotyping, genomics and antimicrobial usage data to investigate patterns of AMR amongst atypical enteropathogenic Escherichia coli (aEPEC) strains isolated from children younger than five years old in seven developing countries (four in sub-Saharan Africa and three in South Asia) over a three-year period. We detected high rates of AMR, with 65% of isolates displaying resistance to three or more drug classes. Whole-genome sequencing revealed a diversity of known genetic mechanisms for AMR that accounted for >95% of phenotypic resistance, with comparable rates amongst aEPEC strains associated with diarrhoea or asymptomatic carriage. Genetic determinants of AMR were associated with the geographic location of isolates, not E. coli lineage, and AMR genes were frequently co-located, potentially enabling the acquisition of multi-drug resistance in a single step. Comparison of AMR with antimicrobial usage data showed that the prevalence of resistance to fluoroquinolones and third-generation cephalosporins was correlated with usage, which was higher in South Asia than in Africa. This study provides much-needed insights into the frequency and mechanisms of AMR in intestinal E. coli in children living in community settings in developing countries. © 2018, The Author(s).
    Sponsors
    This work was supported by the NHMRC of Australia (Project Grants 1043830 to K.E.H., and 1009296 and 1067428 to R.M.R-B.; Fellowship 1061409 to K.E.H.) and the Bill & Melinda Gates Foundation (Grant 38874 to M.M.L.).
    Keyword
    antibiotic resistance
    bacterial genome
    controlled study
    developing country
    enteropathogenic Escherichia coli
    diarrhea
    intestine flora
    multidrug resistance
    whole genome sequencing
    Identifier to cite or link to this item
    https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85052381939&origin=inward; http://hdl.handle.net/10713/9858
    ae974a485f413a2113503eed53cd6c53
    10.1038/s41564-018-0217-4
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