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

Patrick Musicha*, Nicholas A. Feasey, Amy K. Cain, Teemu Kallonen, Chrispin Chaguza, Chikondi Peno, Margaret Khonga, Sarah Thompson, Katherine J. Gray, Alison E. Mather, Robert S. Heyderman, Dean B. Everett, Nicholas R. Thomson, Chisomo L. Msefula

*Corresponding author for this work

Research output: Contribution to journalArticle

16 Citations (Scopus)
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Abstract

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 fromMalawi. 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.

Original languageEnglish
Pages (from-to)1602-1609
Number of pages8
JournalJournal of Antimicrobial Chemotherapy
Volume72
Issue number6
DOIs
Publication statusPublished - Jun 2017
Externally publishedYes

Bibliographical note

Copyright The Author 2017. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

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