Comparative genomics of blood and faecal E. coli and K. pneumoniae isolates from neonates with bloodstream infections in Tanzania.

Bloodstream infections (BSIs) are a major cause of hospitalisation and death for children under the age of five in sub-Saharan Africa, with Gram-negative bacteria such as Klebsiella pneumoniae and Escherichia coli among the most common causative agents. These bacteria usually colonise the human gastrointestinal (GI) tract, which has been identified as a reservoir for invasive infections into extra-intestinal environments such as the urinary tract and bloodstream. In this study we used comparative genomics to compare hybrid genome assemblies of blood and faecal bacterial isolates taken from the same patients (all neonates under 19 days old) to determine if the BSI associated isolates and the GI tract associated isolates were related. Multiple pairs of highly related E. coli and K. pneumoniae were found, suggesting that translocation between the GI tract and the bloodstream occurred in multiple cases of BSI. We also highlight key virulence genes and acquired mutations that are indicative of pathogenic strains capable of BSI. These findings expand our understanding of the Gram-negative bacteria involved in BSI pathogenicity and could help guide targeted interventions to prevent future BSI infections in neonates.