Whole genome sequencing of extended-spectrum betalactamase-producing Escherichia coli

We aimed to characterize extended-spectrum betalactamase-producing Escherichia coli (ESBL-Ec) genomic diversity within and between human, animal and environmental reservoirs in a suburban, rural area of Madagascar using whole-genome sequencing. We analyzed bacterial population structure through phylogenetic reconstruction of 510 ESBL-Ec and assessed the diversity of their antibiotic resistance genes and accessory genomes in the three reservoirs. At such a scale, characterization of the genetic relatedness of ESBL-Ec allowed us to investigate different risk factors that might contribute to the transmission of ESBL-Ec in humans in Madagascar.