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Genomic landscape of extended-spectrum β-lactamase resistance in Escherichia coli from an urban African setting

Musicha, P; Feasey, NA; Cain, AK; Kallonen, T; Chaguza, C; Peno, C; Khonga, M; ... Msefula, CL; + view all (2017) Genomic landscape of extended-spectrum β-lactamase resistance in Escherichia coli from an urban African setting. Journal of Antimicrobial Chemotherapy 10.1093/jac/dkx058. (In press). Green open access

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OBJECTIVES: Efforts to treat Escherichia coli infections are increasingly being compromised by the rapid, global spread of antimicrobial resistance (AMR). Whilst AMR in E. coli has been extensively investigated in resource-rich settings, in sub-Saharan Africa molecular patterns of AMR are not well described. In this study, we have begun to explore the population structure and molecular determinants of AMR amongst E. coli isolates from Malawi. METHODS: Ninety-four E. coli isolates from patients admitted to Queen’s Hospital, Malawi, were whole-genome sequenced. The isolates were selected on the basis of diversity of phenotypic resistance profiles and clinical source of isolation (blood, CSF and rectal swab). Sequence data were analysed using comparative genomics and phylogenetics. RESULTS: Our results revealed the presence of five clades, which were strongly associated with E. coli phylogroups A, B1, B2, D and F. We identified 43 multilocus STs, of which ST131 (14.9%) and ST12 (9.6%) were the most common. We identified 25 AMR genes. The most common ESBL gene was blaCTX-M-15 and it was present in all five phylogroups and 11 STs, and most commonly detected in ST391 (4/4 isolates), ST648 (3/3 isolates) and ST131 [3/14 (21.4%) isolates]. CONCLUSIONS: This study has revealed a high diversity of lineages associated with AMR, including ESBL and fluoroquinolone resistance, in Malawi. The data highlight the value of longitudinal bacteraemia surveillance coupled with detailed molecular epidemiology in all settings, including low-income settings, in describing the global epidemiology of ESBL resistance.

Type: Article
Title: Genomic landscape of extended-spectrum β-lactamase resistance in Escherichia coli from an urban African setting
Location: England
Open access status: An open access version is available from UCL Discovery
DOI: 10.1093/jac/dkx058
Publisher version: https://doi.org/10.1093/jac/dkx058
Language: English
Additional information: Copyright © The Author 2017. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Keywords: phenotype, bacteremia, drug resistance, microbial, fluoroquinolones, genes, genome, ichthyosis, x-linked, malawi, sequence tagged sites, escherichia coli, sodium thiosulfate, surveillance, medical, extended-spectrum beta lactamases, rectal swab
URI: http://discovery.ucl.ac.uk/id/eprint/1549787
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