NCM 2022: Long-read sequencing enables in-depth characterization of plasmids encoding KPC-2 in Citrobacter freundii outbreak

Antimicrobial resistance among bacteria such as Citrobacter freundii is a public health concern. Sequencing bacterial isolates to identify genes associated with antimicrobial resistance enhances the capacity to understand and minimize outbreaks. Twelve isolates of C. freundii obtained from patients in Utah exhibited reduced susceptibility to antimicrobials. Nanopore sequencing revealed 11 isolates that harbored a plasmid encoding KPC-2 and one with KPC-3, which are class A carbapenem-hydrolyzing enzymes associated with β-lactam resistance. Phylogenetic analysis was used to compare the core genome of chromosomal sequences (2,822 genes), resulting in two distinct clusters of isolates containing eight and three isolates, respectively. The similarity of the core genomes was suggestive of two concurrent outbreaks. During the process of characterizing the plasmids encoding KPC-2 of the two clusters, a surprising amount of variation was observed in the plasmids of the eight-isolate cluster, with plasmid sizes ranging from 57kb to 208kb (median = 70kb) with large rearrangements observed in three of the eight plasmids.