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

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Musicha, Patrick, Feasey, Nicholas ORCID: https://orcid.org/0000-0003-4041-1405, Cain, Amy, Kallonen, Teemu, Chaguza, Chrispin, Peno, Chikondi, Khonga, Margaret, Thompson, Sarah, Gray, Katherine J, Mather, Alison E, Heyderman, Robert S, Everett, Dean B, Thomson, Nicholas R and Msefula, Chisomo L (2017) 'Genomic landscape of extended-spectrum β-lactamase resistance in Escherichia coli from an urban African setting.'. The Journal of Antimicrobial Chemotherapy, Vol 72, Issue 6, pp. 1602-1609.

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Abstract

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. 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. 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 bla CTX-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]. 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.

Item Type: Article
Subjects: QU Biochemistry > Genetics > QU 460 Genomics. Proteomics
QU Biochemistry > Genetics > QU 500 Genetic phenomena
QW Microbiology and Immunology > QW 45 Microbial drug resistance. General or not elsewhere classified.
WC Communicable Diseases > Infection. Bacterial Infections > Enteric Infections > WC 290 Escherichia coli infections
Faculty: Department: Clinical Sciences & International Health > Clinical Sciences Department
Clinical Sciences & International Health > International Public Health Department
Digital Object Identifer (DOI): https://doi.org/10.1093/jac/dkx058
SWORD Depositor: JISC Pubrouter
Depositing User: JISC Pubrouter
Date Deposited: 20 Apr 2017 11:23
Last Modified: 06 Feb 2018 13:14
URI: http://archive.lstmed.ac.uk/id/eprint/6982

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