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

• Published in: Journal of global antimicrobial resistance. 2021-06, Vol.25, p.8-13
• Main Authors: Fuga, Bruna, Cerdeira, Louise, Moura, Quézia, Fontana, Herrison, Fuentes-Castillo, Danny, Carvalho, Albalúcia C., Lincopan, Nilton
• Format: Article
• Language: English
• Subjects: Carbapenemase; Enterobacterales; KPC-2; Phylogenomics; Plasmidome; Resistome
• ISSN: 2213-7165; 2213-7173
• DOI: 10.1016/j.jgar.2021.02.014

•Epidemiological success of KPC has been linked to plasmids carrying blaKPC genes.•An IncQ1 small plasmid carrying blaKPC-2 was found in pandemic Escherichia coli ST648.•Plasmid analysis revealed blaKPC-2 on an NTEKPC-IId element with the aph(3')-VIa gene.•Plasmid phylogeny confirmed >99% identity with IncQ/blaKPC-2 from Klebsiella pneumoniae.•The emergence and rapid expansion of IncQ1/blaKPC-2 to novel hosts is discussed. The global success of carbapenem-resistant pathogens has been attributed to large plasmids carrying blaKPC 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 blaKPC-2-positive E. coli strains with identical sequence type (ST) were further investigated. 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. 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 clade 2. Additionally, the emergence of an IncQ1 small plasmid (pEc351) carrying blaKPC-2 (on an NTEKPC-IId element), aph(3')-VIa, and plasmid regulatory and replication genes in the pandemic clone ST648 is reported. Identification of a blaKPC-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.