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.本研究旨在借助全基因组测序（whole-genome sequencing）技术，解析马达加斯加某城郊乡村区域内、人类、动物与环境三类宿主库中产超广谱β-内酰胺酶大肠埃希菌（extended-spectrum betalactamase-producing Escherichia coli, ESBL-Ec）的基因组多样性。研究通过对510株ESBL-Ec进行系统发育重建（phylogenetic reconstruction），分析了该菌的细菌种群结构，并评估了三类宿主库中其抗生素耐药基因（antibiotic resistance genes）与附属基因组（accessory genomes）的多样性。在该研究规模下，对ESBL-Ec遗传相关性的表征使我们得以探究可能推动马达加斯加地区人类间ESBL-Ec传播的各类风险因素。