Temporal genome dynamics of ST39 Klebsiella pneumoniae in a neonatal unit in Blantyre, Malawi

In this study, we investigated the genomic changes that occurred during long-term circulation of a Klebsiella pneumoniae ST39 clone, causing a disproportionate number of infections on the neonatal ward at a tertiary healthcare facility in Malawi in 2017. We analysed whole genome sequences of Klebsiella pneumoniae ST39 collected from Queen Elizabeth Central Hospital over a 20-year period, including generation of several high-quality hybrid genomes. We compared virulence markers, antibiotic resistance determinants, and mobile genetic elements, focusing on variable regions between strains from the outbreak clone in 2017 to genomes from other co-occurring ST39 lineages.