Genomic investigation of a suspected Klebsiella pneumoniae outbreak in a neonatal care unit in sub-Saharan Africa

A special-care neonatal unit from a large public hospital in Malawi was noted as having more frequent, difficult-to-treat infections and a suspected outbreak of multi-drug resistant (MDR) Klebsiella pneumoniae was investigated using genomic characterisation. All K. pneumoniae blood stream isolates (BSI) from patients in the neonatal ward (n=62), and a subset of K. pneumoniae BSI isolates (n=38) from other paediatric wards in the hospital, were collected over a 4-year period. After whole genome sequencing, the strain sequence types (ST), plasmid types, virulence and resistance genes were identified. One ST340 clone, part of the clonal complex 258 (CC258) and a ST that drives hospital outbreaks worldwide, harbouring numerous resistance genes and plasmids was implicated as the likely cause of the outbreak. This study contributes necessary molecular information necessary for tracking and characterising this important hospital pathogen in sub-Saharan Africa.