Pathogen quantitative efficacy of different spike-in internal controls and clinical application in central nervous system infection with metagenomic sequencing.

Metagenomic next-generation sequencing (mNGS) has been used broadly for pathogens detection of infectious diseases. However, there is a lack of method for the absolute quantitation of pathogens by mNGS. We compared the quantitative efficiency of three mNGS internal controls (ICs) , phages, and artificial DNA sequence and developed the most applicable strategies for pathogen quantitation via mNGS in central nervous system infection.

GPMeta: a GPU-accelerated method for ultrarapid pathogen identification from metagenomic sequences.

Metagenomic sequencing (mNGS) is a powerful diagnostic tool to detect causative pathogens in clinical microbiological testing owing to its unbiasedness and substantially reduced costs. Rapid and accurate classification of metagenomic sequences is a critical procedure for pathogen identification in dry-lab step of mNGS test. However, clinical practices of the testing technology are hampered by the challenge of classifying sequences within a clinically relevant timeframe.

Evaluations of Clinical Utilization of Metagenomic Next-Generation Sequencing in Adults With Fever of Unknown Origin.

Introduction: The diagnosis of infection-caused fever of unknown origin (FUO) is still challenging, making it difficult for physicians to provide an early effective therapy. Therefore, a novel pathogen detection platform is needed. Metagenomic next-generation sequencing (mNGS) provides an unbiased, comprehensive technique for the sequence-based identification of pathogenic microbes, but the study of the diagnostic values of mNGS in FUO is still limited.

FRMC: a fast and robust method for the imputation of scRNA-seq data.

The high-resolution feature of single-cell transcriptome sequencing technology allows researchers to observe cellular gene expression profiles at the single-cell level, offering numerous possibilities for subsequent biomedical investigation. However, the unavoidable technical impact of high missing values in the gene-cell expression matrices generated by insufficient RNA input severely hampers the accuracy of downstream analysis. To address this problem, it is essential to develop a more rapid and stable imputation method with greater accuracy, which should not only be able to recover the missing data, but also effectively facilitate the following biological mechanism analysis.

Evaluation of superinfection, antimicrobial usage, and airway microbiome with metagenomic sequencing in COVID-19 patients: A cohort study in Shanghai.

Background: In COVID-19 patients, information regarding superinfection, antimicrobial assessment, and the value of metagenomic sequencing (MS) could help develop antimicrobial stewardship.

Method: This retrospective study analyzed 323 laboratory-confirmed COVID-19 patients for co-infection rate and antimicrobial usage in the Shanghai Public Health Clinical Center (SPHCC) from January 23rd to March 14th 2020. The microbiota composition was also investigated in patients with critically severe COVID-19.

HCMB: A stable and efficient algorithm for processing the normalization of highly sparse Hi-C contact data.

The high-throughput genome-wide chromosome conformation capture (Hi-C) method has recently become an important tool to study chromosomal interactions where one can extract meaningful biological information including P(s) curve, topologically associated domains, A/B compartments, and other biologically relevant signals. Normalization is a critical pre-processing step of downstream analyses for the elimination of systematic and technical biases from chromatin contact matrices due to different mappability, GC content, and restriction fragment lengths. Especially, the problem of high sparsity puts forward a huge challenge on the correction, indicating the urgent need for a stable and efficient method for Hi-C data normalization.

Rapid diagnosis of infection assisted by metagenomic next-generation sequencing in a HIV-negative patient.

is an opportunistic pathogenic fungus commonly reported in southeast Asia. infection predominantly occurs in patients with immunodeficiency and can be fatal if diagnosis and treatment were delayed. Conventional diagnosis of infection relies heavily on tissue culture and histologic analysis, which is time consuming and has limited positive rate.

Improving Pulmonary Infection Diagnosis with Metagenomic Next Generation Sequencing.

Pulmonary infections are among the most common and important infectious diseases due to their high morbidity and mortality, especially in older and immunocompromised individuals. However, due to the limitations in sensitivity and the long turn-around time (TAT) of conventional diagnostic methods, pathogen detection and identification methods for pulmonary infection with greater diagnostic efficiency are urgently needed. In recent years, unbiased metagenomic next generation sequencing (mNGS) has been widely used to detect different types of infectious pathogens, and is especially useful for the detection of rare and newly emergent pathogens, showing better diagnostic performance than traditional methods.

Improved cancer biomarkers identification using network-constrained infinite latent feature selection.

Identifying biomarkers that are associated with different types of cancer is an important goal in the field of bioinformatics. Different researcher groups have analyzed the expression profiles of many genes and found some certain genetic patterns that can promote the improvement of targeted therapies, but the significance of some genes is still ambiguous. More reliable and effective biomarkers identification methods are then needed to detect candidate cancer-related genes.

Diagnostic accuracy of metagenomic next-generation sequencing for active tuberculosis in clinical practice at a tertiary general hospital.

Background: To evaluate the diagnostic accuracy of metagenomic next-generation sequencing (mNGS) for active tuberculosis (TB).

Methods: We retrospectively collected 820 samples at Zhongshan Hospital, Fudan University in Shanghai, China, between 1 April 2017 and 31 March 2018. They were classified into TB cases (125, 15.

The clinical value of metagenomic next-generation sequencing in the microbiological diagnosis of skin and soft tissue infections.

Background: Metagenomic next-generation sequencing (mNGS), with its comprehensiveness, is widely applied in microbiological diagnosis. Etiological diagnosis is of paramount clinical importance in patients with skin and soft tissue infections (SSTIs). However, the clinical application of mNGS in SSTIs is relatively less studied.

Multiple approaches for massively parallel sequencing of SARS-CoV-2 genomes directly from clinical samples.

Background: COVID-19 (coronavirus disease 2019) has caused a major epidemic worldwide; however, much is yet to be known about the epidemiology and evolution of the virus partly due to the scarcity of full-length SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) genomes reported. One reason is that the challenges underneath sequencing SARS-CoV-2 directly from clinical samples have not been completely tackled, i.e.

Pseudorabies virus encephalitis in humans: a case series study.

Pseudorabies virus (PRV) is known to cause severe encephalitis in juvenile pigs and various non-native hosts; recent evidences suggest that PRV might cause encephalitis in humans. In a multicenter cohort study in China, next-generation sequencing of cerebrospinal fluid (CSF) was performed to detect pathogens in all patients with clinically suspected central nervous system infections. This study involved all the patients whose CSF samples were positive for PRV-DNA; their clinical features were evaluated, and species-specific PCR and serological tests were sequentially applied for validation.

Angiostrongyliasis detected by next-generation sequencing in a ELISA-negative eosinophilic meningitis: A case report.

Next-generation sequencing (NGS) is an emerging method with the potential of pan-pathogen screening. This study described a case of eosinophilic meningitis (EoM) with enzyme-linked immunosorbent assay (ELISA)-negative results for Angiostrongylus cantonensis (A. cantonensis), Trichinella spiralis and Paragonimus westermani and a positive identification of A.

Clinical application and evaluation of metagenomic next-generation sequencing in suspected adult central nervous system infection.

Background: Accurate etiology diagnosis is crucial for central nervous system infections (CNS infections). The diagnostic value of metagenomic next-generation sequencing (mNGS), an emerging powerful platform, remains to be studied in CNS infections.

Methods: We conducted a single-center prospective cohort study to compare mNGS with conventional methods including culture, smear and etc.

Diagnostic value and clinical application of next-generation sequencing for infections in immunosuppressed patients with corticosteroid therapy.

Background: Next-generation sequencing (NGS) is a comprehensive approach for sequence-based identification of pathogens. However, reports on the use of NGS in patients with immunosuppression are scarce, especially in subjects with negative microbiological results.

Methods: In this study, NGS was performed on samples obtained from 108 anonymized patients with suspected infection undergoing immunosuppressive corticosteroid therapy.

Transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in COVID-19 patients.

Circulating in China and 158 other countries and areas, the ongoing COVID-19 outbreak has caused devastating mortality and posed a great threat to public health. However, efforts to identify effectively supportive therapeutic drugs and treatments has been hampered by our limited understanding of host immune response for this fatal disease. To characterize the transcriptional signatures of host inflammatory response to SARS-CoV-2 (HCoV-19) infection, we carried out transcriptome sequencing of the RNAs isolated from the bronchoalveolar lavage fluid (BALF) and peripheral blood mononuclear cells (PBMC) specimens of COVID-19 patients.

Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding.

Background: In late December, 2019, patients presenting with viral pneumonia due to an unidentified microbial agent were reported in Wuhan, China. A novel coronavirus was subsequently identified as the causative pathogen, provisionally named 2019 novel coronavirus (2019-nCoV). As of Jan 26, 2020, more than 2000 cases of 2019-nCoV infection have been confirmed, most of which involved people living in or visiting Wuhan, and human-to-human transmission has been confirmed.

Coronavirus disease 2019 (COVID-19): diagnosis and prognosis.

Coronavirus disease 2019 (COVID-19) has become a global pandemic with a high rate of transmission. Currently, there is a lack of vaccines and specific drugs for this newly-emerged virus. Timely diagnosis and treatment, as well as isolation of patients and virus carriers, contribute to the effective prevention and control of this epidemic.

Clinical Evaluation of Diagnosis Efficacy of Active Complex Infection via Metagenomic Next-Generation Sequencing of Direct Clinical Samples.

Tuberculosis (TB) is now the leading cause of death from infectious disease. Rapid screening and diagnostic methods for TB are urgently required. Rapid development of metagenomics next-generation sequencing (mNGS) in recent years showed promising and satisfying application of mNGS in several kinds of infectious diseases.

Diminishing microbiome richness and distinction in the lower respiratory tract of lung cancer patients: A multiple comparative study design with independent validation.

Objectives: Current evidence suggests that microorganisms are associated with neoplastic diseases; however, the role of the airway microbiome in lung cancer remains unknown. To investigate the taxonomic profiles of the lower respiratory tract (LRT) microbiome in patients with lung cancer.

Materials And Methods: BALF samples were collected in a discovery set comprising 150 individuals, including 91 patients with lung cancer, 29 patients with nonmalignant pulmonary diseases and 30 healthy subjects, and an independent validation set including 85 participants.

Incremental value of metagenomic next generation sequencing for the diagnosis of suspected focal infection in adults.

Objectives: Microbiological diagnosis is essential during clinical management of focal infections. Metagenomic next generation sequencing (mNGS) has been reported as a promising diagnostic tool in infectious diseases. However, little is known about the clinical utility of mNGS in focal infections.