Ten years of population-level genomic Escherichia coli and Klebsiella pneumoniae serotype surveillance informs vaccine development for invasive infections

Abstract

<jats:p>The incidence of bloodstream infections (BSIs) caused by Enterobacteriaceae (e.g. Escherichia coli, Klebsiella pneumoniae) continues to increase globally and the threat of untreatable disease is significant1. Prophylactic vaccines potentially represent an alternative approach to combating antimicrobial resistance (AMR) by reducing antibiotic usage and infections caused by AMR-associated strains. To investigate the utility of such an approach, we performed in silico serotyping on 4029 E. coli/K. pneumoniae BSI in Oxfordshire (2008-2018) in addition to 3536 isolates from previous studies. Most infections, including those associated with AMR, are caused by isolates with a small subset of O-antigens, with no evidence that the proportion of BSIs caused by these changed significantly over time. O-antigen targeted vaccines might therefore be useful in reducing the significant morbidity and mortality2 associated with BSIs. Vaccines may also have a role in preventing the spread of carbapenem resistance genes into common serotypes associated with community-onset disease.</jats:p>

The mobilome associated with Gram-negative bloodstream infections: A large-scale observational hybrid sequencing based study

“…We have previously reported analyses of short read sequencing data from E. coli and Klebsiella spp. bloodstream infection isolates in Oxfordshire between 2009 and 2018 as described previously(18, 19). In this study, we additionally sequenced all E. coli and Klebsiella spp.…”

“…Sequencing was performed on GridIons with R9.4 flowells, which were reused multiple times utilising the ONT Flow Cell Wash kit and our previously validated protocol (20). Illumina (short-read) data was created as previously described (19).…”