Journal: bioRxiv
Article Title: An optimised method for bacterial nucleic acid extraction from positive blood culture broths for whole genome sequencing, resistance phenotype prediction and downstream molecular applications
doi: 10.1101/2022.06.30.497578
Figure Lengend Snippet: Direct metagenomic sequencing from positive blood culture broths compared with culture-based methods and commercial rapid diagnostics. Two DNA extraction methods were compared each using half (n=20) of the samples. AxDx = Accelerate Pheno; BCID = blood culture identification PCR panel (bioMérieux); gDNA = genomic DNA; SPRI = solid-phase reversible immobilization; PCR = polymerase chain reaction; ID = identification; AST = antimicrobial susceptibility testing; WGS = whole genome sequencing; MALDI-TOF = matrix-assisted laser desorption/ionization-time of flight; AMR = antimicrobial resistance; ML = machine learning
Article Snippet: For comparison, positive blood culture broths were also tested using two commercially available platforms that provide rapid species identification and limited AMR gene profiling (Blood Culture Identification Panel [BCID] on the BioFire FilmArray Instrument; bioMérieux) as well as predictive MIC using morphokinetic cellular analysis (Accelerate Pheno; Accelerate Diagnostics).
Techniques: Sequencing, DNA Extraction, Polymerase Chain Reaction