scholarly journals Towards Translational Epidemiology: Next-Generation Sequencing and Phylogeography as Epidemiological Mainstays

mSystems ◽  
2019 ◽  
Vol 4 (3) ◽  
Author(s):  
Crystal M. Hepp
Keyword(s):  
Public Health ◽  
Next Generation Sequencing ◽  
Phylogenetic Analyses ◽  
Federal State ◽  
Next Generation ◽  
Public Health Agencies ◽  
Health Agencies ◽  
Collaborative Activities ◽  
User Friendly ◽  
Generation Sequencing

ABSTRACT Next-generation sequencing, coupled with the development of user-friendly software, has achieved a level of accessibility that is revolutionizing the way we approach epidemiological investigations. We can sequence pathogen genomes and conduct phylogenetic analyses to assess transmission, identify from which country or city a pathogen originated, or which contaminated potluck item resulted in widespread foodborne illness. However, until recently, these types of studies have been rarities, limited to specific investigations usually conducted over the short term. Given the feasibility and realized public health benefits of ascertaining pathogen relationships, federal, state, and county agencies are building their sequencing capacities, either through acquisition of equipment or collaborative activities. In this perspective, I detail research projects that our group collaborates on with county and state public health agencies, where the objective is to identify pathogen source locations with the longer-term goal of implementing proactive interventions.

scholarly journals Practical Guidance to Implementing Quality Management Systems in Public Health Laboratories Performing Next-Generation Sequencing: Personnel, Equipment, and Process Management (Phase 1)

2019 ◽  
Vol 57 (8) ◽  
Author(s):  
Rebecca J. Hutchins ◽  
Kristy L. Phan ◽  
Adeeba Saboor ◽  
Joseph D. Miller ◽  
Atis Muehlenbachs
Keyword(s):  
Public Health ◽  
Next Generation Sequencing ◽  
Quality Management ◽  
Process Management ◽  
Quality Management System ◽  
Phase 1 ◽  
Quality System ◽  
Clinical Diagnostics ◽  
Next Generation ◽  
Generation Sequencing

ABSTRACT Quality standards as part of an effective quality management system (QMS) are the cornerstone for generating high-quality test results. Next-generation sequencing (NGS) has the potential to improve both clinical diagnostics and public health surveillance efforts in multiple areas, including infectious diseases. However, the laboratories adopting NGS methods face significant challenges due to the complex and modular process design. This document summarizes the first phase of quality system guidance developed by the Centers for Disease Control and Prevention (CDC) NGS Quality Workgroup. The quality system essentials of personnel, equipment, and process management (quality control and validation) were prioritized based on a risk assessment using information gathered from participating CDC laboratories. Here, we present a prioritized QMS framework, including procedures and documentation tools, to assist laboratory implementation and maintenance of quality practices for NGS workflows.

scholarly journals A platform for leveraging next generation sequencing for routine microbiology and public health use

2015 ◽  
Vol 3 (S1) ◽  
Author(s):  
Laura I Rusu ◽  
Kelly L Wyres ◽  
Matthias Reumann ◽  
Carlos Queiroz ◽  
Alexe Bojovschi ◽  
...  
Keyword(s):  
Public Health ◽  
Next Generation Sequencing ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Comparison of two next-generation sequencing kits for diagnosis of epileptic disorders with a user-friendly tool for displaying gene coverage, DeCovA

2015 ◽  
Vol 7 ◽  
pp. 19-25 ◽  
Author(s):  
Sarra Dimassi ◽  
Thomas Simonet ◽  
Audrey Labalme ◽  
Nadia Boutry-Kryza ◽  
Amandine Campan-Fournier ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation ◽  
Gene Coverage ◽  
User Friendly ◽  
Generation Sequencing

scholarly journals Pediatric Brainstem Encephalitis Outbreak Investigation with Metagenomic Next-Generation Sequencing

2018 ◽  
Author(s):  
Kristoffer E. Leon ◽  
Didac Casas-Alba ◽  
Akshaya Ramesh ◽  
Lillian M. Khan ◽  
Cristian Launes ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Phylogenetic Analyses ◽  
P Value ◽  
Brainstem Encephalitis ◽  
Next Generation ◽  
Single Nucleotide Variants ◽  
Qrt Pcr ◽  
Mcnemar’S Test ◽  
Generation Sequencing ◽  
Mcnemar's Test

AbstractIn 2016, Catalonia experienced a pediatric brainstem encephalitis outbreak caused by enterovirus A71 (EV-A71). Conventional testing identified EV in peripheral body sites, but EV was rarely identified in cerebrospinal fluid (CSF). RNA was extracted from CSF (n=20), plasma (n=9), stool (n=15) and nasopharyngeal samples (n=16) from 10 children with brainstem encephalitis or encephalomyelitis and 10 contemporaneous pediatric controls with presumed viral meningitis or encephalitis. Unbiased complementary DNA libraries were sequenced, and microbial pathogens were identified using a custom bioinformatics pipeline. Full-length virus genomes were assembled for phylogenetic analyses. Metagenomic next-generation sequencing (mNGS) was concordant with qRT-PCR for all samples positive by PCR (n=25). In virus-negative samples (n=35), mNGS detected virus in 28.6% (n=10), including 5 CSF samples. mNGS co-detected EV-A71 and another EV in 5 patients. Overall, mNGS increased the proportion of EV-positive samples from 42% (25/60) to 57% (34/60) (McNemar’s test; p-value = 0.0077). For CSF, mNGS doubled the number of pathogen-positive samples (McNemar’s test; p-value = 0.074). Using phylogenetic analysis, the outbreak EV-A71 clustered with a neuroinvasive German EV-A71 isolate. Brainstem encephalitis specific, non-synonymous EV-A71 single nucleotide variants were not identified. mNGS demonstrated 100% concordance with clinical qRT-PCR of EV-related brainstem encephalitis and significantly increased the detection of enteroviruses. Our findings increase the probability that neurologic complications observed were virus-induced rather than para-infectious. A comprehensive genomic analysis confirmed that the EV-A71 outbreak strain was closely related to a neuroinvasive German EV-A71 isolate. There were no clear-cut viral genomic differences that discriminated between patients with differing neurologic phenotypes.

BPHL SARS-CoV-2 Tiled Amplicon Illumina Sequencing v2

2021 ◽  
Author(s):  
Jason Blanton
Keyword(s):  
Public Health ◽  
Next Generation Sequencing ◽  
Illumina Sequencing ◽  
Library Preparation ◽  
Next Generation ◽  
Florida Department ◽  
Wet Lab ◽  
Generation Sequencing

This protocol details the Florida Department of Health's Bureau of Public Health Laboratories' (BPHL) wet lab portion of our SARS-CoV-2 next generation sequencing workflow. The method is a tiled amplicon approach using ARTIC V3 primers. The amplicon generation was adapted from the Matteson protocol1. The library preparation is Illumina NexteraXT. Library pooling and normalization were adapted from the Gohl protocol3. This protocol is for loading a MiSeq, but we have had equal success running on iSeqs and NextSeqs as well. Up to 96 libraries can be run on a MiSeq and up to 384 on a NextSeq.

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