scholarly journals Pediatric sepsis cases diagnosed with group B streptococcal meningitis using next-generation sequencing: a report of two cases

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Kazuhiro Horiba ◽  
Michio Suzuki ◽  
Nobuyuki Tetsuka ◽  
Yoshihiko Kawano ◽  
Makoto Yamaguchi ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Bacterial Meningitis ◽  
Genetic Material ◽  
Male Infant ◽  
Invasive Infection ◽  
Next Generation ◽  
Group B ◽  
Generation Sequencing ◽  
First Admission ◽  
Csf Findings

Abstract Background Group B Streptococcus (GBS) is an important cause of invasive infection in neonates and infants. Cerebrospinal fluid (CSF) findings and culture may not show evidence of infection early in GBS meningitis. Next-generation sequencing (NGS) has the potential to detect microbial genetic material in patients with infectious diseases. We report two cases of infantile sepsis of GBS meningitis with negative results for CSF culture tests, but positive results for NGS analysis. Case presentation Patient 1 was a 22-day-old male infant diagnosed with sepsis and meningitis. His CSF findings showed pleocytosis, decreased glucose, and increased protein levels. However, CSF and blood culture results at admission were negative. He received a total of 3 weeks of treatment with ampicillin and cefotaxime, and showed clinical improvement. GBS was detected through NGS analysis of CSF collected at admission. Patient 2 was a 51-day-old male infant with sepsis. CSF findings on admission were normal, and blood and CSF cultures were also negative. Intravenous ampicillin and cefotaxime treatment were initiated. Treatment was de-escalated to ampicillin alone because Enterococcus faecalis was cultured from urine. He was discharged after a total of 1 week of antibiotic treatment. Six days after discharge, he was re-hospitalized for sepsis. Blood and CSF cultures were negative, and E. faecalis was again cultured from urine. He received a total of 3 weeks of ampicillin treatment for enterococcal-induced nephritis and did not relapse thereafter. NGS pathogen searches were retrospectively performed on both blood and CSF collected at the first and second admission. GBS was detected in the CSF collected at the first admission, but no significant pathogen was detected in the other samples. Inadequate treatment for GBS meningitis at the first admission may have caused the recurrence of the disease. Conclusion Infantile sepsis may present bacterial meningitis that is not diagnosed by either culture testing or CSF findings. NGS analysis for CSF may be useful for confirming the diagnosis of bacterial meningitis.

scholarly journals Bloody coli: a Gene Cocktail in Escherichia coli O104:H4

mBio ◽  
2013 ◽  
Vol 4 (1) ◽  
Author(s):  
Fernando Baquero ◽  
Raquel Tobes
Keyword(s):  
Escherichia Coli ◽  
Next Generation Sequencing ◽  
Genetic Material ◽  
Next Generation ◽  
Content Type ◽  
Pathogenicity Genes ◽  
Sequencing Technologies ◽  
Population Sizes ◽  
Sequential Acquisition ◽  
Generation Sequencing

ABSTRACT A recent study published in mBio [Y. H. Grad et al., mBio 4(1):e00452-12, 2013] indicates that a rapid introgressive evolution has occurred in Escherichia coli O104:H4 by sequential acquisition of foreign genetic material involving pathogenicity traits. O104 genetic promiscuity cannot be readily explained by high population sizes. However, extensive interactions leading to cumulative assemblies of pathogenicity genes might be assured by small K-strategist populations exploiting particular intestinal niches. Next-generation sequencing technologies will be critical to detect particular “gene cocktails” as potentially pathogenic ensembles and to predict the risk of future outbreaks.

scholarly journals Next-generation sequencing of double stranded RNA is greatly improved by treatment with the inexpensive denaturing reagent DMSO

2019 ◽  
Author(s):  
Alexander H. Wilcox ◽  
Eric Delwart ◽  
Samuel L. Díaz Muñoz
Keyword(s):  
Next Generation Sequencing ◽  
Limit Of Detection ◽  
Genetic Material ◽  
Dsrna Virus ◽  
Next Generation ◽  
Short Read ◽  
Double Stranded Rna ◽  
Ncbi Short Read Archive ◽  
Dmso Treatment ◽  
Generation Sequencing

AbstractDouble stranded RNA (dsRNA) is the genetic material of important viruses and a key component of RNA interference-based immunity in eukaryotes. Previous studies have noted difficulties in determining the sequence of dsRNA molecules that have affected studies of immune function and estimates of viral diversity in nature. Dimethyl sulfoxide (DMSO) has been used to denature dsRNA prior to the reverse transcription stage to improve RT-PCR and Sanger sequencing. We systematically tested the utility of DMSO to improve sequencing yield of a dsRNA virus (Φ6) in a short-read next generation sequencing platform. DMSO treatment improved sequencing read recovery by over two orders of magnitude, even when RNA and cDNA concentrations were below the limit of detection. We also tested the effects of DMSO on a mock eukaryotic viral community and found that dsRNA virus reads increased with DMSO treatment. Furthermore, we provide evidence that DMSO treatment does not adversely affect recovery of reads from a single-stranded RNA viral genome (Influenza A/California/07/2009). We suggest that up to 50% DMSO treatment be used prior to cDNA synthesis when samples of interest are composed of or may contain dsRNA.Data SummarySequence data was deposited in the NCBI Short Read Archive (accession numbers: PRJNA527100, PRJNA527101, PRJNA527098). Data and code for analysis is available on GitHub (https://github.com/awilcox83/dsRNA-sequencing/, doi:10.5281/zenodo.1453423). Protocol for dsRNA sequencing is posted on protocols.io (doi:10.17504/protocols.io.ugnetve).

scholarly journals Next-Generation Sequencing Could be a Promising Diagnostic Approach for Pathogen Detection: Pathogenic Analysis of Pediatric Bacterial Meningitis by Next-Generation Sequencing Technology Directly from Cerebrospinal Fluid Specimens

2018 ◽  
Author(s):  
Ling-yun Guo ◽  
Yong-jun Li ◽  
Lin-lin Liu ◽  
Hong-long Wu ◽  
Jia-li Zhou ◽  
...  
Keyword(s):  
Cerebrospinal Fluid ◽  
Next Generation Sequencing ◽  
Bacterial Meningitis ◽  
Infectious Diseases ◽  
Pediatric Population ◽  
Diagnostic Approach ◽  
Next Generation ◽  
Promising Alternative ◽  
Causative Microorganism ◽  
Generation Sequencing

AbstractBackgroundBacterial meningitis remains one of the major challenges in infectious diseases, leading to sequel in many cases. A prompt diagnosis of the causative microorganism is critical to significantly improve outcome of bacterial meningitis. Although various targeted tests for cerebrospinal fluid (CSF) samples are available, it is a big problem for the identification of etiology of bacterial meningitis.MethodsHere we describe the use of unbiased sequence analyses by next-generation sequencing (NGS) technology for the identification of infectious microorganisms from CSF samples of pediatric bacterial meningitis patients in the Department of Infectious Diseases from Beijing Children’s Hospital.ResultsIn total, we had 99 bacterial meningitis patients in our study, 55 (55.6%) of these were etiologically confirmed by clinical microbiology methods. Combined with NGS, 68 cases (68.7%) were etiologically confirmed. The main pathogens identified in this study were Streptococcus pneumoniae (n=29), group B streptococcus (n=15), Staphylococcus aureus (n=7), Escherichia coli (n=7). In addition, two cases with cytomegalovirus infection and one with Taenia saginata asiatica were confirmed by NGS.ConclusionsNGS could be a promising alternative diagnostic approach for critically ill patients suffering from bacterial meningitis in pediatric population.SummaryWe conducted the study for the identification of microorganisms by next-generation sequencing directly from CSF samples of pediatric bacterial meningitis patients. And the study showed that NGS could be a promising alternative diagnostic approach for bacterial meningitis in pediatric population.

scholarly journals Formalin-Fixed and Paraffin-Embedded Samples for Next Generation Sequencing: Problems and Solutions

Genes ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1472
Author(s):  
Gerardo Cazzato ◽  
Concetta Caporusso ◽  
Francesca Arezzo ◽  
Antonietta Cimmino ◽  
Anna Colagrande ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Genetic Material ◽  
Growth Factor Receptor ◽  
Acid Extraction ◽  
Nucleotide Polymorphisms ◽  
Next Generation ◽  
Tissue Samples ◽  
Dna And Rna ◽  
Sequencing Problems ◽  
Generation Sequencing

Over the years, increasing information has been asked of the pathologist: we have moved from a purely morphological diagnosis to biomolecular and genetic studies, which have made it possible to implement the use of molecular targeted therapies, such as anti-epidermal growth factor receptor (EGFR) molecules in EGFR-mutated lung cancer, for example. Today, next generation sequencing (NGS) has changed the approach to neoplasms, to the extent that, in a short time, it has gained a place of absolute importance and diagnostic, prognostic and therapeutic utility. In this scenario, formaldehyde-fixed and paraffin-embedded (FFPE) biological tissue samples are a source of clinical and molecular information. However, problems can arise in the genetic material (DNA and RNA) for use in NGS due to fixation, and work is being devoted to possible strategies to reduce its effects. In this paper, we discuss the applications of FFPE tissue samples in the execution of NGS, we focus on the problems arising with the use of this type of material for nucleic acid extraction and, finally, we consider the most useful strategies to prevent and reduce single nucleotide polymorphisms (SNV) and other fixation artifacts.

scholarly journals Next-Generation Sequencing in the Diagnosis of Rare Pediatric Sinonasal Tumors

2019 ◽  
pp. 014556131986337
Author(s):  
Atif A. Ahmed ◽  
Divya Vundamati ◽  
Midhat Farooqi ◽  
Elena Repnikova ◽  
Timothy Zinkus ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Spindle Cell ◽  
Male Infant ◽  
Next Generation ◽  
Molecular Tests ◽  
Desmoid Fibromatosis ◽  
Pathologic Features ◽  
Spindle Cell Tumors ◽  
The Right ◽  
Generation Sequencing

The diagnosis of desmoid fibromatosis or other spindle cell tumors in the sinonasal region is very rare in children and needs to be thoroughly confirmed with immunohistochemical and/or molecular tests. We report 2 patients with such rare tumors and describe the use of next-generation sequencing in their evaluation. A 3-year-old female had a 4.4-cm midline nasal cavity mass involving the bony septum and extending into the base of the skull bilaterally. The moderate cellular fibroblastic proliferation revealed areas of thick keloid-like collagen bands and other areas with myxoid edematous stroma. Deep targeted sequencing identified a novel G34V mutation in the CTNNB1 gene consistent with desmoid fibromatosis. An 11-month-old male infant presented with a right nasal mass that extended through the cribriform plate into the anterior cranial fossa and involved the right ethmoid sinus and adjacent right orbit. Histology revealed an infiltrative atypical fibrous proliferation with focal calcifications that was negative for CTNNB1 and GNAS mutations. A novel RET E511K variant was identified in the tumor and later was also found in the germline and hence rendered of unknown significance. Both cases highlight the utility of next-generation sequencing in the evaluation of pediatric sinonasal spindle cell tumors that may have overlapping pathologic features. Reporting of rare or novel variants in tumor-only sequencing should be cautiously evaluated in children and pairing with germline sequencing may be needed to avoid the pitfall of assigning uncommon variants.

scholarly journals DNAscan: a fast, computationally and memory efficient bioinformatics pipeline for the analysis of DNA next-generation-sequencing data

2018 ◽  
Author(s):  
A Iacoangeli ◽  
A Al Khleifat ◽  
W Sproviero ◽  
A Shatunov ◽  
AR Jones ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
High Performance ◽  
Genetic Material ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
Bioinformatics Pipeline ◽  
Bioinformatics Tools ◽  
Ngs Data ◽  
Generation Sequencing

AbstractThe generation of DNA Next Generation Sequencing (NGS) data is a commonly applied approach for studying the genetic basis of biological processes, including diseases, and underpins the aspirations of precision medicine. However, there are significant challenges when dealing with NGS data. A huge number of bioinformatics tools exist and it is therefore challenging to design an analysis pipeline; NGS analysis is computationally intensive, requiring expensive infrastructure which can be problematic given that many medical and research centres do not have adequate high performance computing facilities and the use of cloud computing facilities is not always possible due to privacy and ownership issues. We have therefore developed a fast and efficient bioinformatics pipeline that allows for the analysis of DNA sequencing data, while requiring little computational effort and memory usage. We achieved this by exploiting state-of-the-art bioinformatics tools. DNAscan can analyse raw, 40x whole genome NGS data in 8 hours, using as little as 8 threads and 16 Gbs of RAM, while guaranteeing a high performance. DNAscan can look for SNVs, small indels, SVs, repeat expansions and viral genetic material (or any other organism). Its results are annotated using a customisable variety of databases including ClinVar, Exac and dbSNP, and a local deployment of the gene.iobio platform is available for an on-the-fly result visualisation.

Sign in / Sign up

Export Citation Format

Share Document