Genomic data reveals the emergence of an IncQ1 small plasmid carrying blaKPC-2 in Escherichia coli of the pandemic sequence type 648

Objectives: The global success of carbapenem-resistant pathogens has been attributed to large plasmids carrying bla(KPC) genes circulating among high-risk clones. In this study, we sequenced the genome of a carbapenem-resistant Escherichia coli strain (Ec351) isolated from a human infection. Phylogenomic analysis based on single nucleotide polymorphisms (SNPs) as well as the comparative resistome and plasmidome of globally disseminated bla(KPC-2)-positive E. coli strains with identical sequence type (ST) were further investigated. Methods: Total DNA was sequenced using an Illumina NextSeq 500 platform and was assembled using Unicycler. Genomic data were evaluated through bioinformatics tools available from the Center of Genomic Epidemiology and by in silico analysis. Results: Genomic analysis revealed the convergence of a wide resistome and virulome in E. coli ST648, showing a high-level phylogenetic relationship with a KPC-2-positive ST648 cluster identified in the USA and association with international Glade 2. Additionally, the emergence of an IncQ1 small plasmid (pEc351) carrying blaxec-2 (on an NTEKPC-IId element), aph(3')-VIa, and plasmid regulatory and replication genes in the pandemic clone ST648 is reported. Conclusion: Identification of a bla(KPC-2)-positive IncQ1 plasmid in a high-risk E. coli clone represents rapid adaptation and expansion of these small plasmids encoding carbapenemases to novel bacterial hosts with global distribution, which deserves continued monitoring. (C) 2021 The Authors. Published by Elsevier Ltd on behalf of International Society for Antimicrobial Chemotherapy.

Automated summary

The study sequenced the genome of a carbapenem-resistant Escherichia coli strain, revealing a high-level phylogenetic relationship and a wide resistome with the USA and international Glade 2. Additionally, the emergence of a small plasmid carrying carbapenemase and other genes in the pandemic clone signifies rapid adaptation and global distribution of these small plasmids to new bacterial hosts.