Sequencing of gut microbiome and bloodstream infection isolates identifies gut as the potential source of infection

Tamburini et al. 2018. Precision identification of diverse bloodstream pathogens in the gut microbiome. Nature Medicine.

This is a summary of our DalMUG journal club discussion of this paper written by Jacob Nearing


This paper brings advances in next generation sequencing to the clinic by sequencing bloodstream infection isolates and the corresponding patient’s gut microbiome. They then use this data in their new tool StrainSifter in an attempt to determine whether or not the gut microbiome is the source of infection. We enjoyed reading this paper as it showed a clear clinical use of next generation sequencing in the context of infectious diseases. They presented evidence that challenges the general assumption that non-enteric infections such as Pseudomonas aeruginosa come from the skin or environmental sources.

Points of Interest

  • SNV analysis by StrainSifter shows that in many cases species identified in stool samples are closely related to bloodstream isolates from the same patient.
  • As sequencing turnaround time decreases stool samples and or infection isolates may be useful in determining an infection’s antibiotic resistance profile.
  • In some cases isolates were placed within the same phylogenetic branch of species from stool samples of multiple patients. This could possibly indicate transfer of pathogens between patients. It would have been nice to see how these samples matched up over time.
  • We would be excited to see this tool applied to larger datasets to help identify the source of uncommon clinical infections

Points of Confusion

  • It’s difficult to determine a cut-off value for the number of differing SNVs between isolates and species within the stool to confidently call the gut as the source of the bloodstream infections.
  • Would have been nice to compare isolates to other types of samples such as samples from in and around the skin or intravenous lines to help confirm the gut as a potential source of infection from non-enteric pathogens.
Written on January 30, 2019