scholarly journals Use of Metagenomic Next-Generation Sequencing in the Clinical Microbiology Laboratory

2021 ◽  
Vol 23 (11) ◽  
pp. 1415-1421
Author(s):  
Charles W. Stratton ◽  
Ted E. Schutzbank ◽  
Yi-Wei Tang
Keyword(s):  
Next Generation Sequencing ◽  
Clinical Microbiology ◽  
Clinical Microbiology Laboratory ◽  
Microbiology Laboratory ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Implementation of Next-Generation Sequencing for Hepatitis B Virus Resistance Testing and Genotyping in a Clinical Microbiology Laboratory

2015 ◽  
Vol 54 (1) ◽  
pp. 127-133 ◽  
Author(s):  
Christopher F. Lowe ◽  
Linda Merrick ◽  
P. Richard Harrigan ◽  
Tony Mazzulli ◽  
Christopher H. Sherlock ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Hepatitis B ◽  
Sanger Sequencing ◽  
Clinical Microbiology ◽  
Resistance Testing ◽  
Clinical Microbiology Laboratory ◽  
Next Generation ◽  
Low Sensitivity ◽  
Pcr Targeting ◽  
Generation Sequencing

Sanger sequencing or DNA hybridization have been the primary modalities for hepatitis B (HBV) resistance testing and genotyping; however, there are limitations, such as low sensitivity and the inability to detect novel mutations. Next-generation sequencing (NGS) for HBV can overcome these limitations, but there is limited guidance for clinical microbiology laboratories to validate this novel technology. In this study, we describe an approach to implementing deep pyrosequencing for HBV resistance testing and genotyping in a clinical virology laboratory. A nested PCR targeting thepolregion of HBV (codons 143 to 281) was developed, and the PCR product was sequenced by the 454 Junior (Roche). Interpretation was performed by ABL TherapyEdge based on European Association for the Study of the Liver (EASL) guidelines. Previously characterized HBV samples by INNO-LiPA (LiPA) were compared to NGS with discordant results arbitrated by Sanger sequencing. Genotyping of 105 distinct samples revealed a concordance of 95.2% (100/105), with Sanger sequencing confirming the NGS result. Resistance testing by NGS was concordant with LiPA in 85% (68/80) of previously characterized samples. Additional mutations were found in 8 samples, which related to the identification of low-level mutant subpopulations present at <10% (6/8). To balance the costs of testing for the validation study, reproducibility of the NGS was investigated through an analysis of sequence variants at loci not associated with resistance in a single patient sample. Our validation approach attempts to balance costs with efficient data acquisition.

scholarly journals Application of next generation sequencing in clinical microbiology and infection prevention

2017 ◽  
Vol 243 ◽  
pp. 16-24 ◽  
Author(s):  
Ruud H. Deurenberg ◽  
Erik Bathoorn ◽  
Monika A. Chlebowicz ◽  
Natacha Couto ◽  
Mithila Ferdous ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Clinical Microbiology ◽  
Infection Prevention ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Digital PCR—An Emerging Technology with Broad Applications in Microbiology

2019 ◽  
Vol 66 (1) ◽  
pp. 117-123 ◽  
Author(s):  
Stephen J Salipante ◽  
Keith R Jerome
Keyword(s):  
Next Generation Sequencing ◽  
Quantitative Pcr ◽  
Clinical Microbiology ◽  
Clinical Laboratory ◽  
Digital Pcr ◽  
Emerging Technology ◽  
Next Generation ◽  
Powerful Technique ◽  
Advantages And Disadvantages ◽  
Generation Sequencing

Abstract BACKGROUND The PCR and its variant, quantitative PCR (qPCR), have revolutionized the practice of clinical microbiology. Continued advancements in PCR have led to a new derivative, digital PCR (dPCR), which promises to address certain limitations inherent to qPCR. CONTENT Here we highlight the important technical differences between qPCR and dPCR, and the potential advantages and disadvantages of each. We then review specific situations in which dPCR has been implemented in clinical microbiology and the results of such applications. Finally, we attempt to place dPCR in the context of other emerging technologies relevant to the clinical laboratory, including next-generation sequencing. SUMMARY dPCR offers certain clear advantages over traditional qPCR, but these are to some degree offset by limitations of the technology, at least as currently practiced. Laboratories considering implementation of dPCR should carefully weigh the potential advantages and disadvantages of this powerful technique for each specific application planned.

scholarly journals Metagenomic Next-Generation Sequencing in Clinical Microbiology

2019 ◽  
Vol 37 (2) ◽  
pp. 133-140 ◽  
Author(s):  
Jobin John Jacob ◽  
Balaji Veeraraghavan ◽  
Karthick Vasudevan
Keyword(s):  
Next Generation Sequencing ◽  
Clinical Microbiology ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Reprint of “Application of next generation sequencing in clinical microbiology and infection prevention”

2017 ◽  
Vol 250 ◽  
pp. 2-10 ◽  
Author(s):  
Ruud H. Deurenberg ◽  
Erik Bathoorn ◽  
Monika A. Chlebowicz ◽  
Natacha Couto ◽  
Mithila Ferdous ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Clinical Microbiology ◽  
Infection Prevention ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Next-Generation Sequencing: A Critical Review of Its Applications in Clinical Microbiology

2020 ◽  
Vol 1 (1) ◽  
pp. 1-5
Author(s):  
Shuaibu Abdullahi Hudu ◽  
Saadatu Haruna Shinkafi ◽  
Shuaibu Umar ◽  
Babazhitsu Makun ◽  
Khadijah Muhammad Dada
Keyword(s):  
Public Health ◽  
Next Generation Sequencing ◽  
Clinical Microbiology ◽  
Diagnostic Procedures ◽  
Distinct Advantage ◽  
Next Generation ◽  
Genomic Changes ◽  
Diagnostic Microbiology ◽  
Personalized Cancer ◽  
Generation Sequencing

Next-generation sequencing (NGS) technology is fast supplementing and improving the current conventional sequencing. This is as a result of its ability to sequence pathogen genomes and interpret the information in near real-time. The aim of this paper is to review the applications of next-generation sequencing in clinical microbiology. With the speedy advances in NGS innovations, clinical and public health microbiology labs are progressively accepting NGS innovation in their workflows into their diagnostic procedures. In this review, it has been found that the applications of NGS in the clinical and public health microbiology settings are not disposable, and have the potential to guide clinicians in tailoring treatment to dynamic genomic changes of microbes. Next-generation sequencing has opened a broad new area of research with the potential to revolutionize personalized cancer medicine. Advances in NGS have demonstrated a distinct advantage in diagnostic microbiology, fundamentally lessening the time from diagnosis to clinical treatment.

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