Fig. 4: Rapid diagnostic of preterm P8 clinically diagnosed with suspected NEC.

a, Time frame diagram showing: sample collection, DNA extraction and quality control (red, 2 h 15 min); library preparation incorporating bead clean-up and DNA repair (yellow, 1 h 45 min); data analysis using local base calling and NanoOK RT (green). Pathogen detection (K. pneumoniae) and K. pneumoniae-specific AMR genes were first detected at 4 h and 38 min (13,000 reads analysed). The left side of the panel indicates the clinical symptoms and general guidelines for antibiotic prescription. b, Taxonomic profiles obtained using MinION at 1 and 6 h since sequencing started. The pie chart legend comprises the eight most abundant taxa classified. Further taxa can be found in Supplementary Table 3. c, Walkout study of P8 reported by the NanoOK RT software showing taxa containing AMR genes. The results shown are for independent bacterial hits (defined as ≥ 50 bp away from the AMR sequence) at 6 h of sequencing. d, Correlation plot of species-level normalized assigned read counts at 1 and 6 h, with log-transformed Pearson’s r = 0.97 (taxa n = 133). The grey region either side of the fit line represents the 95% CIs. e, Heat map displaying the number of CARD hits detected among the most common groups of antibiotic resistance genes found in preterm P8. Further information on all the AMR genes obtained can be found in Supplementary Table 4.