Evaluation of bacterial pathogen diversity, abundance and health risks in urban recreational water by amplicon next-generation sequencing and quantitative PCR

2017 ◽  
Vol 57 ◽  
pp. 137-149 ◽  
Author(s):  
Qijia Cui ◽  
Tingting Fang ◽  
Yong Huang ◽  
Peiyan Dong ◽  
Hui Wang
Keyword(s):  
Next Generation Sequencing ◽  
Quantitative Pcr ◽  
Health Risks ◽  
Bacterial Pathogen ◽  
Recreational Water ◽  
Next Generation ◽  
Pathogen Diversity ◽  
Generation Sequencing

scholarly journals Toxic Cyanobacterial Bloom Triggers in Missisquoi Bay, Lake Champlain, as Determined by Next-Generation Sequencing and Quantitative PCR

Life ◽  
2015 ◽  
Vol 5 (2) ◽  
pp. 1346-1380 ◽  
Author(s):  
Nathalie Fortin ◽  
Valentina Munoz-Ramos ◽  
David Bird ◽  
Benoît Lévesque ◽  
Lyle Whyte ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Quantitative Pcr ◽  
Cyanobacterial Bloom ◽  
Next Generation ◽  
Lake Champlain ◽  
Generation Sequencing

scholarly journals Detection of Listeria monocytogenes in a patient with meningoencephalitis using next-generation sequencing: a case report

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Zi-Wei Lan ◽  
Min-Jia Xiao ◽  
Yuan-lin Guan ◽  
Ya-Jing Zhan ◽  
Xiang-Qi Tang
Keyword(s):  
Listeria Monocytogenes ◽  
Next Generation Sequencing ◽  
Mammalian Cells ◽  
Clinical Manifestations ◽  
Bacterial Pathogen ◽  
Next Generation ◽  
Accurate Treatment ◽  
The Central Nervous System ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Abstract Background Listeria monocytogenes (L. monocytogenes) is a facultative intracellular bacterial pathogen which can invade different mammalian cells and reach to the central nervous system (CNS), leading to meningoencephalitis and brain abscesses. In the diagnosis of L. monocytogenes meningoencephalitis (LMM), the traditional test often reports negative owing to the antibiotic treatment or a low number of bacteria in the cerebrospinal fluid. To date, timely diagnosis and accurate treatment remains a challenge for patients with listeria infections. Case presentation We present the case of a 66-year-old woman whose clinical manifestations were suspected as tuberculous meningoencephalitis, but the case was finally properly diagnosed as LMM by next-generation sequencing (NGS). The patient was successfully treated using a combined antibacterial therapy, comprising ampicillin and trimethoprim-sulfamethoxazole. Conclusion To improve the sensitivity of LMM diagnosis, we used NGS for the detection of L. monocytogenes. Hence, the clinical utility of this approach can be very helpful since it provides quickly and trust results.

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 Novel PCR-Based Methods Enhance Characterization of Vaginal Microbiota in a Bacterial Vaginosis Patient before and after Treatment

2013 ◽  
Vol 79 (13) ◽  
pp. 4181-4185 ◽  
Author(s):  
Janet A. Lambert ◽  
Apoorv Kalra ◽  
Cristina T. Dodge ◽  
Susan John ◽  
Jack D. Sobel ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Bacterial Vaginosis ◽  
Quantitative Pcr ◽  
Broad Spectrum ◽  
Vaginal Microbiota ◽  
Next Generation ◽  
Healthy Women ◽  
Before And After ◽  
Generation Sequencing

ABSTRACTDeep characterization, even by next-generation sequencing, of the vaginal microbiota in healthy women or posttreatment bacterial vaginosis patients is limited by the dominance of lactobacilli. To improve detection, we offer two approaches: quantitative PCR (qPCR) using phylogenetic branch-inclusive primers and sequencing of broad-spectrum amplicons generated with oligomers that block amplification of lactobacilli.

scholarly journals Minimal Residual Disease Detection by Next-Generation Sequencing in Multiple Myeloma: A Comparison With Real-Time Quantitative PCR

2021 ◽  
Vol 10 ◽  
Author(s):  
Qiumei Yao ◽  
Yinlei Bai ◽  
Shaji Kumar ◽  
Elaine Au ◽  
Alberto Orfao ◽  
...  
Keyword(s):  
Multiple Myeloma ◽  
Next Generation Sequencing ◽  
Real Time ◽  
Quantitative Pcr ◽  
Residual Disease ◽  
Next Generation ◽  
Real Time Quantitative Pcr ◽  
Allele Specific ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Here we compared clonotype identification by allele-specific oligonucleotide real-time quantitative-PCR (ASO RQ-PCR) and next-generation sequencing (NGS) in 80 multiple myeloma patients. ASO RQ-PCR was applicable in 49/55 (89%) and NGS in 62/78 (80%). Clonotypes identified by both methods were identical in 33/35 (94%). Sensitivity of 10−5 was confirmed in 28/29 (96%) by NGS while sensitivity of RQ-PCR was 10−5 in 7 (24%), 5 × 10−5 in 15 (52%), and 10−4 in 7 (24%). Among 14 samples quantifiable by ASO RQ-PCR, NGS yielded comparable results in 12 (86%). Applicability of NGS can be improved if immunoglobulin heavy-chain incomplete DJ primers are included.

scholarly journals Advantages and Limitations of 16S rRNA Next-Generation Sequencing for Pathogen Identification in the Diagnostic Microbiology Laboratory: Perspectives from a Middle-Income Country

Diagnostics ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 816
Author(s):  
Nurnabila Syafiqah Muhamad Rizal ◽  
Hui-min Neoh ◽  
Ramliza Ramli ◽  
Petrick @ Ramesh A/L K Periyasamy ◽  
Alfizah Hanafiah ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
16S Rrna ◽  
Bacterial Pathogen ◽  
Microbiology Laboratory ◽  
Next Generation ◽  
Pathogen Identification ◽  
Middle Income ◽  
Middle Income Countries ◽  
Diagnostic Microbiology ◽  
Generation Sequencing

Bacterial culture and biochemical testing (CBtest) have been the cornerstone of pathogen identification in the diagnostic microbiology laboratory. With the advent of Sanger sequencing and later, next-generation sequencing, 16S rRNA next-generation sequencing (16SNGS) has been proposed to be a plausible platform for this purpose. Nevertheless, usage of the 16SNGS platform has both advantages and limitations. In addition, transition from the traditional methods of CBtest to 16SNGS requires procurement of costly equipment, timely and sustainable maintenance of these platforms, specific facility infrastructure and technical expertise. All these factors pose a challenge for middle-income countries, more so for countries in the lower middle-income range. In this review, we describe the basis for CBtest and 16SNGS, and discuss the limitations, challenges, advantages and future potential of using 16SNGS for bacterial pathogen identification in diagnostic microbiology laboratories of middle-income countries.

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