Tracking clonal and plasmid transmission in colistin- and carbapenem-resistant Klebsiella pneumoniae

The surveillance of mobile genetic elements facilitating the spread of antimicrobial resistance genes has been challenging. Here, we tracked both clonal and plasmid transmission in colistin- and carbapenem-resistant Klebsiella pneumoniae using short- and long-read sequencing technologies. We observed three clonal transmissions, all containing Incompatibility group (Inc) L plasmids and New Delhi metallo-beta-lactamase bla_NDM-1, although not co-located on the same plasmid. One IncL-bla_NDM-1 plasmid had been transferred between sequence type (ST) 392 and ST15, and the promiscuous IncL-bla_OXA-48 plasmid was likely shared between a singleton and a clonal transmission of ST392. Plasmids within clonal outbreaks and between clusters and STs had 0–2 single nucleotide polymorphism (SNP) differences, showing high stability upon transfer to same or different STs. The simplest explanation, without a comprehensive analysis with long-read sequencing, would be the spread of a single common IncL-bla_NDM-1 plasmid. However, here, we report bla_NDM-1 in five different plasmids, emphasizing the need to investigate plasmid-mediated transmission for effective containment of outbreaks.