Dissemination of extended-spectrum beta-lactamase-producing Escherichia coli in poultry in Zimbabwe

TL;DR

This study found high prevalence of antibiotic-resistant E. coli in Zimbabwean poultry farms and markets, highlighting the spread through clonal expansion and plasmid transfer.

Contribution

The study provides molecular genetic evidence for clonal expansion and plasmid transfer as key mechanisms for ESBL-E. coli dissemination in Zimbabwean poultry.

Findings

ESBL-E. coli were detected at 42% of farms and all markets surveyed in Zimbabwe.

Eight distinct blaCTX-M variants and multidrug-resistant isolates were identified through genomic analysis.

Clonal expansion and plasmid-mediated gene transfer were found to drive the spread of ESBL-E. coli.

Abstract

Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli are resistant to the critically important third- and fourth-generation cephalosporin antibiotics and present a risk to animal and human health. In Zimbabwe, there is an evidence gap concerning the prevalence and diversity of ESBL-producing E. coli in poultry. In this study, we screened for ESBL-E. coli at farms (n=50) and markets (n=10) using MacConkey agar supplemented with 4 µg ml−1 ceftriaxone. ESBL-E. coli were detected at every market and at 21 farms, giving a farm-level prevalence of 42%. Seventy isolates were obtained and tested for antimicrobial susceptibility, whilst 69 of these were further analysed by whole-genome sequencing. A total of eight distinct blaCTX-M variants were identified, and 69 out of 70 isolates were multidrug-resistant. Genomic analysis revealed evidence for clonal expansion of an ESBL-producing clone and horizontal gene transfer via plasmids being responsible for the dissemination of ESBL-E. coli. Geographic Information System mapping was used to visualize the distribution of the ESBL-producing clones. For example, ST1141 isolates were clonal, having a highly conserved core genome, and harboured blaCTX-M-15 and 11 additional antimicrobial resistance genes on a ~338 kbp IncHI2 plasmid which was not present in other isolates. This clone was present at nine farms. In contrast, a conserved ~93 kbp IncFII plasmid harbouring blaCTX-M-55 was present in isolates from three different multilocus sequence types obtained from six farms. This study provides insight into the burden and distribution of ESBL-E. coli at poultry farms in Zimbabwe and provides molecular genetic evidence for clonal expansion and plasmid transfer as being important mechanisms for the dissemination of ESBL-E. coli in this setting. This study underscores the importance of adopting measures, such as prudent antimicrobial use and farm biosecurity, that can limit the development and dissemination of ESBL-producing E. coli.

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