Ultrafast detection of β-lactamase resistance in Klebsiella pneumoniae from blood culture by nanopore sequencing.
Matxalen Vidal-GarcíaMikel Urrutikoetxea-GutiérrezJuan C Forero NiampiraMiren BasarasRamón CisternaJosé Ldt Diaz de Tuesta Del ArcoPublished in: Future microbiology (2023)
Aim: This study aimed to assess the ultra-fast method using MinION™ sequencing for rapid identification of β-lactamase-producing Klebsiella pneumoniae clinical isolates from positive blood cultures. Methods: Spiked-blood positive blood cultures were extracted using the ultra-fast method and automated DNA extraction for MinION sequencing. Raw reads were analyzed for β-lactamase resistance genes. Multilocus sequence typing and β-lactamase variant characterization were performed after assembly. Results: The ultra-fast method identified clinically relevant β-lactamase resistance genes in less than 1 h. Multilocus sequence typing and β-lactamase variant characterization required 3-6 h. Sequencing quality showed no direct correlation with pore number or DNA concentration. Conclusion: Nanopore sequencing, specifically the ultra-fast method, is promising for the rapid diagnosis of bloodstream infections, facilitating timely identification of multidrug-resistant bacteria in clinical samples.
Keyphrases
- klebsiella pneumoniae
- multidrug resistant
- escherichia coli
- single cell
- gram negative
- single molecule
- drug resistant
- high resolution
- acinetobacter baumannii
- bioinformatics analysis
- loop mediated isothermal amplification
- circulating tumor
- genome wide
- cell free
- high throughput
- machine learning
- gene expression
- mass spectrometry
- dna methylation
- transcription factor
- energy transfer
- circulating tumor cells