Novel nanopore-based technology helps detect pathogens rapidly and precisely for cancer patients

Recently, a new method was developed for rapidly detecting microbes from cancer patients by a collaborated research team led by Prof. GU Hongcang from Hefei Institutes of Physical Science (HFIPS) at the Chinese Academy of Sciences (CAS).

The method, based on nanopore-based technology, was published in Frontiers in Cellular and Infection Microbiology.

Immunocompromised cancer patients are prone to be infected by various microbes and have an elevated mortality rate compared with other infected patients. Therefore, identifying microbes earlier is crucial for implementing anti-infective therapies in patients.

In this research, researchers collected samples from 56 immunocompromised cancer patients with suspicious infections. The samples included blood and sputum.

They isolated microbes and generated amplicon-based sequencing libraries, then sequenced the libraries utilizing the Oxford Nanopore MinION, a 90 g portable sequencer. Nanopore sequencing showed a significantly higher sensitivity than that of the conventional culture method (83.9% vs. 44.6%, P<0.001). This advantage existed both in blood samples (38.5% vs. 0%, P=0.039) and non-blood samples (97.7% vs. 58.1%, P<0.001).

Compared with traditional method, nanopore amplicon sequencing method showed more samples with bacterial infections (P<0.001), infections from fastidious pathogens (P=0.006), and co-infections (P<0.001). The mean turnaround time (TAT) was approximately 17.5 hours, much shorter than the conventional culture assay.

"We found the method rapid and accurate," said GU Hongcang, first author of the paper, "it can detect pathogens among immunocompromised cancer patients with suspected infections."

This novel and high-sensitive method would improve the prognosis of cancer patients with low immune function by facilitating the prompt diagnosis of infections and the implementation of timely and accurate anti-infective treatments.