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Same-Day Simultaneous Diagnosis of Bacterial and Fungal Infections in Clinical Practice by Nanopore Targeted Sequencing

By Ming Wang, Aisi Fu, Ben Hu, Gaigai Shen, Ran Liu, Wanxu Zhao, Shupeng Jiang, Xuan Cai, Congrong Li, Juan Li, Qing Wu, Kai Feng, Jiashuang Gu, Jia Chen, Mingyue Shu, Binghong Zhang, Zixin Deng, Lilei Yu, Yan Li, Tiangang Liu

Posted 11 Apr 2020
medRxiv DOI: 10.1101/2020.04.08.20057604

BACKGROUND: As approximately 19% of global deaths are attributable to infectious diseases, early diagnosis of infection is very important to reduce mortality. Traditional infection detection strategies have limited sensitivity, detection range, and turnaround times; a detection technology that can simultaneously detect bacterial and fungal infections within 24 h is urgently need in clinical settings. METHODS: We developed nanopore targeted sequencing (NTS) for same-day simultaneous diagnosis of fungal and bacterial infections. NTS was developed by amplification of 16s rRNA gene (for bacteria), IST1/2 gene (for fungal), and rpoB (for Mycobacterium spp.) using multiple primers, and sequenced by a real-time nanopore sequencing platform. An in-house bioinformatic analyze pipeline was used to diagnose the infectious pathogens by mapping the sequencing results with the constructed databases. RESULTS: Comparison of 1312 specimens from 1257 patients using NTS and culture method; NTS detected pathogens in 58.71% of specimens from patients, compared to 22.09% detected using the culture method. NTS showed significantly higher sensitivity than culture methods for many pathogens. Importantly, a turnaround time of <24 h for all specimens, and a pre-report within 6 h in emergency cases was possible in clinical practice. Modification of antibiotic therapy and maintenance of original anti-infection regimens in 51.52% (17/33) and 36.36% (12/33) of patients was in accordance with NTS results, and quantitative monitoring of clinical treatment effects was evaluated in four patients by continuous NTS tests. CONCLUSIONS: Application of NTS in clinically detected pathogens can improve targeted antibiotic treatment and therapeutic monitoring.

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