scholarly journals Metagenomic Next-Generation Sequencing In Febrile Neutropaenia of Children Hematological And Malignant Diseases

2021 ◽  
Author(s):  
Linglong Hu ◽  
Juxiang Wang ◽  
Zhen Huang ◽  
Zhou Yang ◽  
Tingting Huang ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Malignant Tumor ◽  
Pathogen Detection ◽  
Treatment Strategies ◽  
Diagnostic Value ◽  
Clinical Treatment ◽  
Next Generation ◽  
High Positive Rate ◽  
Positive Rate ◽  
Generation Sequencing

Abstract Objective: To evaluate the diagnostic value of metagenomic next-generation sequencing in febrile neutropaenia of Hematological and malignant tumor children. Methods: We retrospectively studied the diagnostic value of metagenomic next-generation sequencing in febrile neutropaenia of Hematological and malignant tumor children in the Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University from July 2018 to December 2019. Children with neutropenia and fever for more than 72 hours were sent for mNGS analysis together with traditional pathogen detection tests. The positive rate of pathogen detection and the following change of clinical treatment strategy was analyzed. Furthermore the duration of fever was compared between patients receiving both mNGS and traditional tests and those only had pathogen detected by traditionally methods. Results: The positive rate of mNGS was 75.6% (28/37cases), and that of the two methods combined was 86.4% (32/37cases). In these patients with long duration of fever, the detection positivity for bacteria, fungi, and viruse detection was high, and mycoplasma and rickettsias were also found. Among all the cases reported, clinical treatment strategies were changed in 9 cases due to the pathogen detection. The duration of fever of patients receiving mNGS together with traditional tests was shorter than those only had traditional ones (7.84d±0.17 vs. 8.39d±0.25, respectively, P<0.001) .Conclusion: Due to high positive rate of mNGS in pathogen detection, active treatment can be taken in time, infections can be controlled earlier. It has a positive effect on the outcome of febrile neutropaenia patients.

Diagnostic value of a combination of next-generation sequencing, chorioretinal imaging and metabolic analysis: lessons from a consanguineous Chinese family with gyrate atrophy of the choroid and retina stemming from a novel OAT variant

2018 ◽  
Vol 103 (3) ◽  
pp. 428-435 ◽  
Author(s):  
Junting Huang ◽  
Jiewen Fu ◽  
Shangyi Fu ◽  
Lisha Yang ◽  
Kailai Nie ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Low Income ◽  
Autosomal Recessive ◽  
Diagnostic Value ◽  
Consanguineous Marriage ◽  
Chinese Family ◽  
Next Generation ◽  
Gyrate Atrophy ◽  
Metabolic Analysis ◽  
Generation Sequencing

Background/AimGyrate atrophy of the choroid and retina (GACR) is an extremely rare autosomal recessive inherited disorder characterised by progressive vision loss. To identify the disease-causing gene in a consanguineous Chinese pedigree with GACR, we aimed to accurately diagnose patients with GACR through a combination of next-generation sequencing (NGS) genetic diagnosis, clinical imaging and amino acid metabolic analysis.MethodsA consanguineous Chinese pedigree with GACR, including two patients, was recruited and a comprehensive ophthalmological evaluation was performed. DNA was extracted from a proband and her family members, and the sample from the proband was analysed using targeted NGS. Variants ‎detected by NGS were confirmed by Sanger sequencing and subjected to segregation analysis. Tandem mass spectrometry (MS/MS) was subsequently performed for metabolic assessment.ResultsWe identified a ‎novel, deleterious, homologous ornithine aminotransferase (OAT) variant, c.G248A: p.S83N, which contributes to ‎the progression of GACR in patients. Our results showed that the p.S83N autosomal recessive ‎variant of OAT is most likely ‎pathogenic, with changes in protein stability drastically decreasing functionality. MS/MS verified that ornithine levels in patients were significantly elevated.ConclusionsRecruitment of a third-degree first cousin consanguineous marriage family with GACR allowed us to identify a novel pathogenicOATvariant in the Chinese population, broadening the mutation spectrum. Our findings reported the diagnostic value of a combination of NGS, retinal imaging and metabolic analysis of consanguineous marriage pedigrees in low-income/middle-income and low-incidence countries, including China, and may help to guide accurate diagnosis and ‎treatment of this disease.

scholarly journals A Comparison of Blood Pathogen Detection Among Droplet Digital PCR, Metagenomic Next-Generation Sequencing, and Blood Culture in Critically Ill Patients With Suspected Bloodstream Infections

2021 ◽  
Vol 12 ◽  
Author(s):  
Bangchuan Hu ◽  
Yue Tao ◽  
Ziqiang Shao ◽  
Yang Zheng ◽  
Run Zhang ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Blood Culture ◽  
Critically Ill ◽  
Critically Ill Patients ◽  
Pathogen Detection ◽  
Bloodstream Infections ◽  
Digital Pcr ◽  
Droplet Digital Pcr ◽  
Next Generation ◽  
Generation Sequencing

Metagenomic next-generation sequencing (mNGS) and droplet digital PCR (ddPCR) have recently demonstrated a great potential for pathogen detection. However, few studies have been undertaken to compare these two nucleic acid detection methods for identifying pathogens in patients with bloodstream infections (BSIs). This prospective study was thus conducted to compare these two methods for diagnostic applications in a clinical setting for critically ill patients with suspected BSIs. Upon suspicion of BSIs, whole blood samples were simultaneously drawn for ddPCR covering 20 common isolated pathogens and four antimicrobial resistance (AMR) genes, mNGS, and blood culture. Then, a head-to-head comparison was performed between ddPCR and mNGS. A total of 60 episodes of suspected BSIs were investigated in 45 critically ill patients, and ddPCR was positive in 50 (83.3%), mNGS in 41 (68.3%, not including viruses), and blood culture in 10 (16.7%) episodes. Of the 10 positive blood cultures, nine were concordantly identified by both mNGS and ddPCR methods. The head-to-head comparison showed that ddPCR was more rapid (~4 h vs. ~2 days) and sensitive (88 vs. 53 detectable pathogens) than mNGS within the detection range of ddPCR, while mNGS detected a broader range of pathogens (126 vs. 88 detectable pathogens, including viruses) than ddPCR. In addition, a total of 17 AMR genes, including 14 blaKPC and 3 mecA genes, were exclusively identified by ddPCR. Based on their respective limitations and strengths, the ddPCR method is more useful for rapid detection of common isolated pathogens as well as AMR genes in critically ill patients with suspected BSI, whereas mNGS testing is more appropriate for the diagnosis of BSI where classic microbiological or molecular diagnostic approaches fail to identify causative pathogens.

scholarly journals Depletion of Human DNA in Spiked Clinical Specimens for Improvement of Sensitivity of Pathogen Detection by Next-Generation Sequencing

2016 ◽  
Vol 54 (4) ◽  
pp. 919-927 ◽  
Author(s):  
Mohammad R. Hasan ◽  
Arun Rawat ◽  
Patrick Tang ◽  
Puthen V. Jithesh ◽  
Eva Thomas ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Pathogen Detection ◽  
Clinical Samples ◽  
Metagenomic Sequencing ◽  
Next Generation ◽  
Simple Method ◽  
Clinical Specimens ◽  
Human Dna ◽  
Pathogen Dna ◽  
Generation Sequencing

Next-generation sequencing (NGS) technology has shown promise for the detection of human pathogens from clinical samples. However, one of the major obstacles to the use of NGS in diagnostic microbiology is the low ratio of pathogen DNA to human DNA in most clinical specimens. In this study, we aimed to develop a specimen-processing protocol to remove human DNA and enrich specimens for bacterial and viral DNA for shotgun metagenomic sequencing. Cerebrospinal fluid (CSF) and nasopharyngeal aspirate (NPA) specimens, spiked with control bacterial and viral pathogens, were processed using either a commercially available kit (MolYsis) or various detergents followed by DNase prior to the extraction of DNA. Relative quantities of human DNA and pathogen DNA were determined by real-time PCR. The MolYsis kit did not improve the pathogen-to-human DNA ratio, but significant reductions (>95%;P< 0.001) in human DNA with minimal effect on pathogen DNA were achieved in samples that were treated with 0.025% saponin, a nonionic surfactant. Specimen preprocessing significantly decreased NGS reads mapped to the human genome (P< 0.05) and improved the sensitivity of pathogen detection (P< 0.01), with a 20- to 650-fold increase in the ratio of microbial reads to human reads. Preprocessing also permitted the detection of pathogens that were undetectable in the unprocessed samples. Our results demonstrate a simple method for the reduction of background human DNA for metagenomic detection for a broad range of pathogens in clinical samples.

Diagnostic value of ultra-deep targeted next-generation sequencing in patients with suspect pancreatic and periampullary lesions

Pancreatology ◽  
2017 ◽  
Vol 17 (3) ◽  
pp. S68
Author(s):  
Babs Sibinga Mulder ◽  
Sven Mieog ◽  
Akin Farina Sarasqueta ◽  
Henricus Handgraaf ◽  
Hans Vasen ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Diagnostic Value ◽  
Next Generation ◽  
Targeted Next Generation Sequencing ◽  
Generation Sequencing

The diagnostic value of next generation sequencing in familial nonsyndromic congenital heart defects

2015 ◽  
Vol 167 (8) ◽  
pp. 1822-1829 ◽  
Author(s):  
Yaojuan Jia ◽  
Jacoba J. Louw ◽  
Jeroen Breckpot ◽  
Bert Callewaert ◽  
Catherine Barrea ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Congenital Heart Defects ◽  
Congenital Heart ◽  
Heart Defects ◽  
Diagnostic Value ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Detection of Respiratory Pathogens in Parapneumonic Effusions by Hypothesis-free, Next-Generation Sequencing (NGS)

2017 ◽  
Vol 4 (suppl_1) ◽  
pp. S17-S17
Author(s):  
Krow Ampofo ◽  
Andrew Pavia ◽  
Anne J Blaschke ◽  
Robert Schlaberg
Keyword(s):  
Next Generation Sequencing ◽  
Pathogen Detection ◽  
Respiratory Pathogens ◽  
Bacterial Identification ◽  
Next Generation ◽  
University Of Utah ◽  
Species Specific ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Generation Sequencing

Abstract Background Species-specific polymerase chain reaction (PCR) testing of pleural fluid (PF) from children with parapneumonic effusion (PPE) has increased pathogen identification in pediatric PPE. However, a pathogen is not detected in 25–35% of cases. Hypothesis-free, next-generation sequencing (NGS) provides a more comprehensive alternative and has led to pathogen detection in PCR-negative samples. However, the utility of NGS in the evaluation of PF from children with PPE is unknown. Methods Archived PF (n = 20) from children younger than 18 years with PPE and hospitalized at Primary Children’s Hospital, Utah, in 2015 and previously tested by PCR were evaluated. Ten PCR-negative and 10 PCR-positive PF specimens were tested using RNA-seq at an average depth of 7.7×106 sequencing reads per sample. NGS data were analyzed with Taxonomer. We compared pathogens detected by blood and PF culture, PCR, and NGS. Results Overall, compared with blood/PF culture, PF PCR and PF NGS testing of PF increased bacterial identification from 15% to 50% (P &lt; 0.05) and 65% (P = 0.003), respectively. Pathogen detection in PF by PCR and NGS were comparable (50 vs. 65%, p = NS) (Table). However, compared with PF PCR, NGS significantly increased detection of S. pyogenes (20% vs. 55%; P &lt; 0.05), with 100% concordance when detected by PCR and culture. Detection of Fusobacterium spp. (10 vs. 10%) by PF NGS and PF PCR were comparable. In contrast, there was no detection of S. pneumoniae (15 vs. 0%) by PF NGS compared with PF PCR. Conclusion PF NGS testing significantly improves bacterial identification and comparable to PF PCR testing, which can help inform antimicrobial selection. However there were differences in detection of S. pneumoniae and S. pyogenes. Further studies of NGS testing of PF of children with PPE are needed to assess its potential in the evaluation of PPE in children. Disclosures A. J. Blaschke, BioFire Diagnostics LLC: Collaborator, Have intellectual property in BioFire Diagnostics through the University of Utah and Investigator, Licensing agreement or royalty and Research support; R. Schlaberg, IDbyDNA: Co-founder, Consultant and Shareholder, Stock

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