RT Journal Article SR Electronic(1) A1 Anson, Luke W. A1 Chau, Kevin A1 Sanderson, Nicholas A1 Hoosdally, Sarah A1 Bradley, Phelim A1 Iqbal, Zamin A1 Phan, Hang A1 Foster, Dona A1 Oakley, Sarah A1 Morgan, Marcus A1 Peto, Tim E. A. A1 Modernizing Medical Microbiology Informatics Group (MMMIG) A1 Crook, Derrick W. A1 Pankhurst, Louise J.YR 2018 T1 DNA extraction from primary liquid blood cultures for bloodstream infection diagnosis using whole genome sequencing JF Journal of Medical Microbiology, VO 67 IS 3 SP 347 OP 357 DO https://doi.org/10.1099/jmm.0.000664 PB Microbiology Society, SN 1473-5644, AB Purpose. Speed of bloodstream infection diagnosis is vital to reduce morbidity and mortality. Whole genome sequencing (WGS) performed directly from liquid blood culture could provide single-assay species and antibiotic susceptibility prediction; however, high inhibitor and human cell/DNA concentrations limit pathogen recovery. We develop a method for the preparation of bacterial DNA for WGS-based diagnostics direct from liquid blood culture. Methodology. We evaluate three commercial DNA extraction kits: BiOstic Bacteraemia, Amplex Hyplex and MolYsis Plus. Differential centrifugation, filtration, selective lysis and solid-phase reversible immobilization bead clean-up are tested to improve human cells/DNA and inhibitor removal. Using WGS (Illumina/MinION), we assess human DNA removal, pathogen recovery, and predict species and antibiotic susceptibility inpositive blood cultures of 44 Gram-negative and 54 Staphylococcus species. Results/Key findings. BiOstic kit extractions yield the greatest mean DNA concentration, 94–301 ng µl−1, versus 0–2.5 ng µl−1 using Amplex and MolYsis kits. However, we note higher levels of inhibition (260/280 ratio 0.9–2.1) and human DNA (0.0–4.4×106 copies) in BiOstic extracts. Differential centrifugation (2000  g , 1 min) prior to BiOstic extraction reduces human DNA by 63–89 % with selective lysis minimizing by a further 62 %. Post-extraction bead clean-up lowers inhibition. Overall, 67 % of sequenced samples (Illumina MiSeq) contain <10 % human DNA, with >93 % concordance between WGS-based species and susceptibility predictions and clinical diagnosis. If >60 % of sequencing reads are human (7/98 samples) susceptibility prediction becomes compromised. Novel MinION-based WGS (n=9) currently gives rapid species identification but not susceptibility prediction. Conclusion. Our method for DNA preparation allows WGS-based diagnosis direct from blood culture bottles, providing species and antibiotic susceptibility prediction in a single assay., UL https://www.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.000664