When a patient is admitted with a possible bacterial bloodstream infection, blood tests are taken to identify which bacteria is causing the infection, but the results can take days to come. Patients are given strong antibiotics that cover most common infections, but it is vital to rapidly identify the bacteria to make sure that their infection is not resistant to the antibiotics given, and also to make sure patients are not given unnecessary antibiotics.
Current laboratory methods are time-consuming. The blood first has to be incubated for 12-24 hours in a blood culture bottle for the bacteria to grow to detectable levels. After this, the bacteria are grown again on petri dishes, to find out which antibiotics will work.
Previously, we have been able to analyse the DNA of bacteria by taking bacteria from the petri dishes. To speed things up, we wished to be able to extract the DNA of bacteria directly from the blood culture bottles. This is more difficult, as blood contains lots of human cells, and human DNA, which has to be removed.
Our scientists developed a laboratory method that allowed us to extract the bacterial DNA and remove human DNA and other substances. When the bacterial DNA was analysed , we could accurately diagnose the bacterial species and predict which antibiotics would kill the bacteria.We also employed the cutting-edge Nanopore MinION WGS platform to identify bacterial species at in around ~4 hours versus current ~24 hour methods.
This work is a significant step forward in demonstrating the potential of DNA analysis to aid routine clinical testing and improve the treatment of patients with bloodstream infections.
Link to original paper: DNA extraction from primary liquid blood cultures for bloodstream infection diagnosis using whole genome sequencing http://jmm.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.000664
Contribution by: Kevin Chau, Research Assistant and laboratory scientist, co-author.
This study was supported by the Health Innovation Challenge Fund [a parallel funding partnership between Wellcome Trust and the Department of Health (grant T5–358)] and the NIHR Health Protection Research Unit (NIHR HPRU). In addition this research was supported by the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre based at Oxford University Hospitals NHS Trust and University of Oxford.