Genomic characterization of extended-spectrum beta-lactamase-producing and carbapenem-resistant Escherichia coli from urban wastewater in Australia

Abstract

This study investigates extended-spectrum beta-lactamase-producing and carbapenem-resistant Escherichia coli isolates from Sydney's wastewater. These isolates exhibit resistance to critical antibiotics and harbor novel resistance mechanisms. The findings highlight the importance of wastewater-based surveillance in monitoring resistance beyond the clinical setting.

Keywords: Escherichia coli; emerging strain; novel resistance mechanism; wastewater-based surveillance; whole-genome sequencing.

Figure 1

Maximum likelihood phylogenetic trees of Escherichia coli isolates from wastewater. (a) The tree was inferred from the alignment of concatenated MLST gene alleles (adk–fumC–gyrB–icd–mdh–purA–recA) extracted from the genome assembly applying the general time reversible (GTR)‐Gamma model with 1000 bootstraps in RAxML and is midpoint rooted. (b) The phylogeny was inferred from an alignment of concatenated core CDS (n = 3289) determined by Roary and RAxML with the GTR‐Gamma model and 1000 bootstrap iterations and is midpoint rooted. The tree nodes are labeled with the origin, year of isolation, and ID of the isolates. The colored strips indicate different phenotypes, sequence types (ST), and the respective ST complexes of the isolates.