PT - JOURNAL ARTICLE AU - Catherine Anscombe AU - Raju.V Misra AU - Saheer Gharbia TI - Rapid whole genome amplification and sequencing of low cell numbers in a bacteraemia model AID - 10.1101/153965 DP - 2017 Jan 01 TA - bioRxiv PG - 153965 4099 - http://biorxiv.org/content/early/2017/06/26/153965.short 4100 - http://biorxiv.org/content/early/2017/06/26/153965.full AB - Whilst next generation sequencing is frequently used to whole genome sequence bacteria from cultures, it is rarely achieved direct from sample, and even more rarely performed in a clinically relevant time frame. To demonstrate the potential of direct from blood sequencing a bacteraemia model was developed, using defibrinated horse blood to model whole human blood infections. Sample processing included removal of erythrocytes and lysis of white blood cells, before rapid and accurate none targeted amplification. The rapid approach to allow direct from sample sequencing, allowed greater than 92% genome coverage of pathogens of interest whilst limiting the sequencing of host genome (less than 7% of all reads). Analysis of de novo assembled reads allowed accurate genotypic antibiotic resistance prediction. The sample processing would be easily applicable to multiple sequencing platforms. Overall this model provides evidence that it is currently possible to rapidly produce whole genome bacterial data from low cell number sterile site infections.