Complete genomic characterization of two Escherichia coli lineages responsible for a cluster of carbapenem-resistant infections in a Chinese hospital

Objectives: The increase in infections as a result of MDR strains of Escherichia coli is a global health crisis. The emergence of globally disseminated lineages of E. coli carrying ESBL genes has been well characterized. An increase in strains producing carbapenemase enzymes and mobile colistin resistance is now being reported, but to date there is little genomic characterization of such strains. Methods: Routine screening of patients within an ICU of West China Hospital identified a number of E. coli carrying the bla_NDM-5 carbapenemase gene, found to be two distinct clones, E. coli ST167 and ST617. Results: Interrogation of publicly available data shows isolation of ESBL and carbapenem-resistant strains of both lineages from clinical cases across the world. Further analysis of a large collection of publicly available genomes shows that ST167 and ST617 have emerged in distinct patterns from the ST10 clonal complex of E. coli, but share evolutionary events involving switches in LPS genetics, intergenic regions and anaerobic metabolism loci. Conclusions: The identification of these lineages of E. coli and their shared genetic traits suggest there may be evolutionary events that underpin the emergence of carbapenem resistance plasmid carriage in E. coli.