Fig. 1

Schematic representation of steps involved in 1mL and 5mL CMg pipelines. Left panel: In triplicates, 50–100 CFU/mL, 5–10 CFU/mL, 1–5 CFU/mL and NTC of E. coli (CTX-M-15), S. aureus, K. pneumoniae or E. faecalis cultures were spiked into 1mL (Standard protocol) or 5mL (Quick-enrichment protocol) of whole blood samples in EDTA or CPD. 5mL samples underwent SepsiPURE extraction and both 5mL and 1mL samples went through saponin-based host DNA depletion and subsequent DNA extraction. DNA extracts were whole genome amplified and debranched/digested. Samples were subjected to either Rapid PCR Barcoding (SQK-RPB004) or Rapid barcoding kit (SQK-RBK004) library preparation and nanopore sequenced (3 h) with Oxford Nanopore MinION. Right panel: Short (≤ 250bp) fastq were removed and then mapped against the human chromosome to eliminate remaining host DNA reads. Remaining bacterial reads were taxonomically classified using minimap2 and filtered according to their taxa_score and AMR determinants identified using KMA. Reports for taxonomic abundance, species coverage mapped metrics and AMR determinants detection data were produced. Samples were deemed positive for infection if bacterial species number of reads was ≥ 5 and relative abundance over the total number of reads ≥ 90%. For AMR gene detection, gene specific coverage had to be ≥ 1 and template identity and coverage ≥ 98%