Klebsiella pneumoniae ST39 neonatal sepsis outbreak in The Gambia
Abstract Background Klebsiella pneumoniae is a critical cause of neonatal sepsis in African countries, and is frequently hospital acquired. We recently reported an outbreak of multidrug-resistant K. pneumoniae sepsis amongst neonates at a rural hospital in The Gambia, West Africa, involving 57 cases and case fatality rate of 60%. Here we undertook a retrospective pathogen genomic epidemiology study of clinical and environmental K. pneumoniae isolated during the outbreak, to identify the outbreak strain and refine the epidemic curve, to confirm the primary environmental sources of contamination, and to characterise the outbreak strain in the context of the local and global pathogen population. Methods and Findings We sequenced all blood culture isolates identified as K. pneumoniae from patients aged 0–59 months (n=46, 85% from neonates), together with all K. pneumoniae cultured from environmental samples during the outbreak investigation (n=24), and 58 stored blood culture surveillance isolates available from the previous decade (27 from neonates). Sequencing was performed using Oxford Nanopore Technologies (ONT) Mk10 flowcells and a PromethION instrument, yielding mostly complete genomes (79%). Genomic analysis revealed 23% of isolates were K. quasipneumoniae, and identified the outbreak strain as K. pneumoniae ST39 with capsular (K) locus KL62. This strain was responsible for 30 cases (16 fatalities) and was identified in three samples of intravenous fluids collected from the neonatal ward during the investigation. It harboured a ~193 kbp IncF plasmid carrying the extended-spectrum beta-lactamase (ESBL) gene blaCTX-M-15  and aac(3)-IId, encoding resistance to third generation cephalosporins and gentamicin, respectively, which are the recommended empirical treatment for neonatal sepsis. The outbreak strain was not identified amongst historical isolates from the hospital, and it was distinct from a KL23-ST39 strain responsible for an earlier outbreak in Sir Edward Francis Small Teaching Hospital in Banjul, 268 km away in The Gambia, seven years prior. Comparing the outbreak strain with publicly available genome data for ST39 and its associated sublineage (SL) 39, we observe SL39 has diversified into three common clonal groups, each associated with multiple K types, that have spread across Africa, Asia and Europe and have been associated with reported outbreaks of neonatal sepsis in Africa (n=3) and elsewhere (n=3). We find SL39 is typically multidrug resistant, however the specific ESBL and carbapenemase genes vary by geographic location. Conclusions Pathogen whole-genome sequencing refined our understanding of the outbreak, allowing for much more precise rule-in/rule-out adjudication to refine case numbers and case fatality rate calculation, and for precise identification of multi-use intravenous fluid bags as the source of the outbreak despite many other samples being culture-positive for unrelated K. pneumoniae. This highlights the crucial importance of infection prevention and control in reducing neonatal fatalities particularly in low-resource settings, and the critical risk associated with multi-use reagents and equipment when caring for vulnerable neonates. The genomic analysis enabled us to identify and characterise the outbreak strain at high resolution, and together with global data highlights SL39 as an emerging high-risk multidrug-resistant globally-distributed clone of K. pneumoniae capable of sustained transmission and high fatality rates.