Molecular characterisation of a Klebsiella pneumoniae neonatal sepsis outbreak in a rural Gambian hospital: a retrospective genomic epidemiology investigation

Abstract

Background Klebsiella pneumoniae is a common cause of neonatal sepsis in Africa, 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 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, refine the epidemic curve, confirm the environmental sources of contamination, monitor control of the outbreak, and 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=51 available, 77% from neonates), together with K. pneumoniae cultured from environmental samples during the outbreak investigation (n=16), and 56 stored blood culture surveillance isolates available from the previous decade (34 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 29 cases (16 fatalities) and was identified in three samples of intravenous fluids collected from the neonatal ward during the investigation. It harboured a ~187 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. The outbreak strain was not identified amongst historical surveillance isolates, and it was distinct from a KL23-ST39 strain responsible for an earlier outbreak at the Sir Edward Francis Small Teaching Hospital in Banjul, the capital city of the country 7 years prior. Comparing the outbreak strain with publicly available genome data for ST39 and its associated sublineage (SL) 39, we observed 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 outbreaks of neonatal sepsis in Africa and elsewhere. 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 more precise identification to refine case numbers and case fatality calculations, and for precise identification of multi-use intravenous fluid bags as the source of the outbreak despite other samples being culture-positive for unrelated K. pneumoniae. This highlights the importance of infection prevention and control in reducing neonatal fatalities 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.