A dual-process of targeted and unbiased Nanopore sequencing enables accurate and rapid diagnosis of lower respiratory infections

BACKGROUND

Nanopore metagenomics has been used for infectious disease diagnosis for bacterial pathogens. However, this technology currently lacks comprehensive performance studies in clinical settings for simultaneous detection of bacteria, fungi, and viruses.

METHODS

We developed a dual-process of Nanopore sequencing for one sample, with unbiased metagenomics in Meta process and target enrichment in Panel process (Nanopore Meta-Panel process, NanoMP) and prospectively enrolled 450 respiratory specimens from multiple centers. The filter system of pathogen detection was established with machine learning and receiver operator characteristic (ROC) curve to optimize the detection accuracy based on orthogonal test of 21 species. Antimicrobial resistance (AMR) genes were identified based on the Comprehensive Antibiotic Resistance Database (CARD) and single-nucleotide polymorphism matrix.

FINDINGS

Our approach showed high sensitivity in Meta process, with 82.9%, 88.7%, and 75.0% for bacteria, fungi (except Aspergillus), and Mycobacterium tuberculosis groups, respectively. Moreover, target amplification improved the sensitivity of virus (>80.0% vs. 39.4%) and Aspergillus (81.8% vs. 42.3%) groups in Panel process compared with Meta process. Overall, NanoMP achieved 80.2% sensitivity and 98.8% specificity compared with the composite reference standard, and we were able to accurately detect AMR genes including blaKPC-2, blaOXA-23 and mecA and distinguish their parent organisms in patients with mixed infections.

INTERPRETATION

We combined metagenomic and enriched Nanopore sequencing for one sample in parallel. Our NanoMP approach simultaneously covered bacteria, viruses and fungi in respiratory specimens and demonstrated good diagnostic performance in real clinical settings.

FUNDING

National Key Research and Development Program of China and National Natural Science Foundation of China.

Applications of promiscuity of FDA-approved kinase inhibitors in drug repositioning and toxicity

Promiscuity of therapeutics has important implications in treatment and toxicity. So far, a comprehensive understanding of promiscuity related to kinase inhibitors is lacking and such an analysis may offer potential opportunities for drug repurposing. In the present study, profiling of inhibitor-specific kinases based on the available biochemical IC50s was performed, fold-change of IC50 values for additional targets were calculated by taking the primary target as the reference kinase, and finally the promiscuity degree (PD) for FDA-approved kinase inhibitors was calculated. Surprisingly, class II inhibitors showed more PD than that of the class I inhibitors. We further identified cancer types and sub-types in which additional kinase targets or off-targets of inhibitors were overexpressed for potential drug repurposing. In addition, the expression of these kinases in normal human tissues were also profiled to predict toxicity following drug repositioning. Taken together, the study offers opportunities for cancer treatment in a kinase-specific manner.

Target Amplification and Distractor Inhibition: Theta Oscillatory Dynamics of Selective Attention in a Flanker Task

Selective attention is a key mechanism to monitor conflict-related processing and behaviour, by amplifying task-relevant processing and inhibiting task-irrelevant information. Conflict monitoring and resolution is typically associated with brain oscillatory power increase in the theta frequency range (3-8 Hz), as indexed by increased midfrontal theta power. We expand previous findings of theta power increase related to conflict processing and distractor inhibition by considering attentional target amplification to be represented in theta frequency as well. The present study (N = 41) examined EEG oscillatory activities associated with stimulus and response conflict in a lateralized flanker task. Depending on the perceptual (in)congruency and response (in)compatibility of distractor-target associations, resulting stimulus and response conflicts were examined in behavioural and electrophysiological data analyses. Both response and stimulus conflict emerged in RT analysis. Regarding EEG data, response-locked cluster analysis showed an increase of midfrontal theta power related to response conflict. In addition, stimulus-locked cluster analysis revealed early clusters with increased parietal theta power for nonconflicting compared to conflicting trials, followed by increased midfrontal theta power for both stimulus and response conflict. Our results suggest that conflict resolution in the flanker task relies on a combination of target amplification, depicted by parietal theta power increase, and distractor inhibition, indexed by midfrontal theta power increase, for both stimulus and response conflicts. Attentional amplification of sensory target features is discussed with regard to a domain-general conflict monitoring account.

[Molecular detection and genotyping of human papillomavirus]

The development of cervical cancer is associated with persistent infection of high-risk human papillomavirus. The detection and genotyping of HPV could be used to evaluate the epidemiology of HPV infections, monitor HPV vaccine efficacy, and screen cervical cancer. There are a lot of commercially available molecular tests for HPV, based on different methodologies and detection systems. In principle, it mainly includes two categories, namely signal amplification and target amplification. Most of them are based on PCR amplification, such as fluorescent PCR, PCR-reverse hybridization, etc. The performances of detection reagents are different. In addition, HPV genotyping assays based on next-generation sequencing and quantitative HPV detection kits are developed. However, only a small number of commercial assays have been clinically verified. A large number of assays which may bring greater values in the screening of cervical cancer are needed to be clinically validated.

A multiplex primer design algorithm for target amplification of continuous genomic regions

Background

Targeted Next Generation Sequencing (NGS) assays are cost-efficient and reliable alternatives to Sanger sequencing. For sequencing of very large set of genes, the target enrichment approach is suitable. However, for smaller genomic regions, the target amplification method is more efficient than both the target enrichment method and Sanger sequencing. The major difficulty of the target amplification method is the preparation of amplicons, regarding required time, equipment, and labor. Multiplex PCR (MPCR) is a good solution for the mentioned problems.

Results

We propose a novel method to design MPCR primers for a continuous genomic region, following the best practices of clinically reliable PCR design processes. On an experimental setup with 48 different combinations of factors, we have shown that multiple parameters might effect finding the first feasible solution. Increasing the length of the initial primer candidate selection sequence gives better results whereas waiting for a longer time to find the first feasible solution does not have a significant impact.

Conclusions

We generated MPCR primer designs for the HBB whole gene, MEFV coding regions, and human exons between 2000 bp to 2100 bp-long. Our benchmarking experiments show that the proposed MPCR approach is able produce reliable NGS assay primers for a given sequence in a reasonable amount of time.