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. 2023 Dec:18:1309-1317.
doi: 10.2217/fmb-2023-0057. Epub 2023 Oct 18.

Ultrafast detection of β-lactamase resistance in Klebsiella pneumoniae from blood culture by nanopore sequencing

Matxalen Vidal-García  1   2 , Mikel Urrutikoetxea-Gutiérrez  1   2 , Juan C Forero Niampira  3 , Miren Basaras  3 , Ramón Cisterna  3 , José L Díaz de Tuesta Del Arco  1   2
Affiliations

Ultrafast detection of β-lactamase resistance in Klebsiella pneumoniae from blood culture by nanopore sequencing

Matxalen Vidal-García et al. Future Microbiol. 2023 Dec.

Abstract

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.

Keywords: blood culture; identification; nanopore; resistance genes; whole-genome sequencing.

Plain language summary

Klebsiella pneumoniae is a bacterium that can cause infections in the blood. These infections can be severe, especially if K. pneumoniae is not susceptible to antibiotics (‘antibiotic resistant’). Tools that can detect this resistance are important. In this study, we tested one such tool called MinION™ with blood samples. In 1 h, we were able to identify the bacteria within the sample and their resistance. This type of testing would help clinicians to give the best treatment to patients. More studies are needed to prove the usefulness of MinION for processing samples from real patients.

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