Integrated chromosomal and plasmid sequence analyses reveal diverse modes of carbapenemase gene spread among <i>Klebsiella pneumoniae</i>

Abstract

Significance In many clinically important bacteria, antibiotic resistance genes are primarily carried on plasmids. These can spread horizontally between different strains and species. However, current surveillance systems track chromosomal lineages of bacteria only, leading to an incomplete understanding of how resistance spreads, from within an individual hospital to across country borders. We present an integrated, high-resolution analysis of both chromosome and plasmid sequences using Klebsiella pneumoniae isolates sampled during a European survey. We show that carbapenemase genes, which confer resistance to last-line antibiotics, have spread in diverse ways including via one plasmid/multiple lineages ( bla OXA-48-like ), multiple plasmids/multiple lineages ( bla VIM , bla NDM ), and multiple plasmids/one lineage ( bla KPC ). These different trajectories must be considered in genomic surveillance systems and the design of new interventions.