Progress Report: Next-Generation Sequencing (NGS), Multiplex Polymerase Chain Reaction (PCR), and Broad-Range Molecular Assays as Diagnostic Tools for Fever of Unknown Origin (FUO) Investigations in Adults

2021 ◽  
Author(s):  
William F Wright ◽  
Patricia J Simner ◽  
Karen C Carroll ◽  
Paul G Auwaerter
Keyword(s):  
Next Generation Sequencing ◽  
Fever Of Unknown Origin ◽  
Unknown Origin ◽  
Diagnostic Tools ◽  
Rrna Gene ◽  
Next Generation ◽  
Potential Cost ◽  
Microbial Identification ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Abstract Even well into the 21st century, infectious diseases still account for most causes of fever of unknown origin (FUO). Advances in molecular technologies, including broad-range PCR of the 16S rRNA gene followed by Sanger sequencing, multiplex PCR assays, and more recently, next-generation sequencing (NGS) applications, have transitioned from research methods to more commonplace in some clinical microbiology laboratories. They have the potential to supplant traditional microbial identification methods and antimicrobial susceptibility testing. Despite the remaining challenges with these technologies, publications in the past decade justify excitement about the potential to transform FUO investigations. We discuss available evidence using these molecular methods for FUO evaluations, including potential cost-benefits and future directions.

scholarly journals 665. Clinical and Financial Impact of Next Generation Sequencing (NGS) in addition to Conventional Microbiology Testing in our Urban Referral Health Center

2021 ◽  
Vol 8 (Supplement_1) ◽  
pp. S434-S435
Author(s):  
Vikram Saini ◽  
Tariq Jaber ◽  
James D Como ◽  
Rasha Abdulmassih ◽  
Zaw Min ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Financial Burden ◽  
Tissue Fluid ◽  
Next Generation ◽  
Financial Cost ◽  
Clinical Specimens ◽  
Microbial Identification ◽  
Soc Testing ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Abstract Background Clinical microbiology traditionally relies on culture methodology and serological testing, that have inherent limitations. Newer diagnostic techniques such as Next Generation Sequencing (NGS) have shown promise to improve microbial identification. In select scenarios, we send clinical specimens to reference laboratories for NGS testing in addition to current standard of care (SOC) diagnostics. We wanted to determine how this diagnostic approach has impacted patient care. We also wanted to review the financial burden through cost-benefit analysis for these ‘send-out’ tests. Methods We performed a retrospective chart review of all cases over a 3-year period in which NGS was submitted. Data, including demographics, comorbidities, antimicrobial use, and diagnosis (by SOC and NGS) were gathered. We delineated how often there was concordance or discordance between SOC and NGS. We also obtained information on financial cost (direct and indirect) and turnaround time (TAT) for NGS results. Results A total of 33 clinical specimens from 25 patients were sent for NGS. The majority of specimens comprised joint tissue/fluid, organ tissue and CSF. Concordance occurred between SOC and NGS testing in 75.8% (25/33) of samples; of those, 88% excluded infection. NGS identified a pathogen in 20% (5/25) patients in which concomitant SOC testing was negative. A subsequent change in antimicrobial management occurred in 16% (4/25) of patients. The mean TAT was 14 days and average cost per specimen was &821.52 (range: &573-&1590). Table 1. Pathogens identified by NGS with negative traditional microbiological test results Figure 1. Distribution of specimen site (in %) sent for NGS Conclusion NGS can provide additional diagnostic sensitivity in infectious diseases, which at our institution identified a new pathogen in 20% and a resultant treatment change in 16% of our patients. This testing may also allow physicians to reaffirm the absence of an infection diagnosis. A larger NGS testing population may reveal more significant benefits. While the attributable cost of NGS was substantial, it should be measured against the costs of administration of unnecessary antibiotics, inaccurate diagnosis, and adverse patient outcomes that may result from SOC testing alone. Considering its financial cost and extended TAT, in-house NGS testing may be warranted to facilitate a higher volume of testing. Disclosures All Authors: No reported disclosures

scholarly journals Genomic constitution of diploid species of the genus Avena L. with A-genome according to the data of the next-generation sequencing (NGS)

2021 ◽  
Vol 20 (1) ◽  
pp. 333-335
Author(s):  
N. N. Nosov ◽  
A. A. Gnutikov ◽  
I. G. Loskutov ◽  
E. V. Blinova ◽  
A. V. Rodionov
Keyword(s):  
Next Generation Sequencing ◽  
Diploid Species ◽  
Rrna Gene ◽  
Next Generation ◽  
Illumina Platform ◽  
5.8S Rrna Gene ◽  
A Genome ◽  
5.8S Rrna ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

For diploid (2x) species with the A-genome, as well as for hexaploid (6x) from the genus Avena, a locus-specific next-generation sequencing (NGS) of the sequence of the region of the internal transcribed spacer ITS1 and the beginning of the 5.8S rRNA gene was carried out on the Illumina platform. The high diversity and heterogeneity of the genomes of diploid species are shown. It was revealed that the genomes of modern diploid oat species are relatively far removed from the hexaploid species. It was found that A. canariensis occupies an isolated position among other diploid species, and also takes only an insignificant role in the formation of hexaploid genomes.

The origin of Alopecurus × brachystylus Peterm. according to the results of next-generation sequencing (NGS)

2020 ◽  
Vol 19 (1) ◽  
pp. 5-7
Author(s):  
A. A. Gnutikov ◽  
N. N. Nosov ◽  
E. O. Punina ◽  
A. V. Rodionov
Keyword(s):  
Next Generation Sequencing ◽  
Phylogenetic Study ◽  
Rrna Gene ◽  
Next Generation ◽  
Illumina Platform ◽  
Its1 Sequence ◽  
Molecular Phylogenetic Study ◽  
Molecular Phylogenetic ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

A molecular phylogenetic study of the hybrid species Alopecurus × brachystylus Peterm. and somesupposed ancestral taxa was carried out. Next-generation sequencing (NGS) of the ITS1 sequence and the start of the5.8S rRNA gene was used on the Illumina platform. According to NGS sequencing, genome of the A. × brachystylusforms common subgenomes with representatives of the section Alopecurium: A. geniculatus and A. aequalis, as well asrepresentatives of the type section: A. pratensis, A. arundinaceus, and alpine A. vlassowii. In addition, it was found thatA. vlassowii (section Alopecurus) contains sequences identical to the species of another section, Alopecurium.

scholarly journals Exotic airborne bacteria identified in urban resuspended dust by next generation sequencing

2019 ◽  
Vol 99 ◽  
pp. 04009
Author(s):  
Nora Kováts ◽  
Eszter Horváth ◽  
Katalin Hubai ◽  
András Hoffer ◽  
Beatrix Jancsek-Turóczi ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Large Scale ◽  
Rrna Gene ◽  
Pathogenic Microorganisms ◽  
Next Generation ◽  
Culture Independent ◽  
Next Generation Sequencing Ngs ◽  
Siberian Permafrost ◽  
Generation Sequencing ◽  
Airborne Transport

The airborne transport of bacteria is a well-known phenomenon, making it possible to exchange species between ecosystems, but it also provides a tool for spreading of pathogenic microorganisms. As part of a large-scale study, microbial community of inhalable and respirable fractions (PM1-10) of resuspended dust collected in Budapest (Hungary) has been characterised by culture-independent next generation sequencing (NGS) of variable 16S rRNA gene regions. Apart from common, mostly ubiqituos soil and organic material-dwelling bacteria, exotic airborne species have been identified, such as Variovorax ginsengisoli, previously isolated from Korean ginseng fields or Exiguobacterium sibiricum, isolated from the Siberian permafrost.

Initial Next-Generation Sequencing (NGS) Results of Alport Syndrome

2019 ◽  
Author(s):  
Altuğ Koç ◽  
Elçin Bora ◽  
Tayfun Cinleti ◽  
Gizem Yıldız ◽  
Meral Torun Bayram ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Alport Syndrome ◽  
Next Generation ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing
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