scholarly journals Bioinformatics in bacterial molecular epidemiology and public health: databases, tools and the next-generation sequencing revolution

2013 ◽  
Vol 18 (4) ◽  
Author(s):  
J A Carriço ◽  
A J Sabat ◽  
A W Friedrich ◽  
M Ramirez ◽  
Collective on behalf of the ESCMID Study Group
Keyword(s):  
Public Health ◽  
Next Generation Sequencing ◽  
Molecular Epidemiology ◽  
Next Generation ◽  
Generation Sequencing ◽  
Epidemiology And Public Health

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

Molecular epidemiology of viral diseases in the era of next generation sequencing

2013 ◽  
Vol 57 (4) ◽  
pp. 378-380 ◽  
Author(s):  
Mayra Cruz-Rivera ◽  
Joseph C. Forbi ◽  
Lilian H.T. Yamasaki ◽  
Carlos A. Vazquez-Chacon ◽  
Armando Martinez-Guarneros ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Molecular Epidemiology ◽  
Viral Diseases ◽  
Next Generation ◽  
Generation Sequencing

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.

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.

scholarly journals Molecular typing of Mycobacterium tuberculosis strains: a fundamental tool for tuberculosis control and elimination

2016 ◽  
Vol 8 (2) ◽  
Author(s):  
Angela Cannas ◽  
Antonio Mazzarelli ◽  
Antonino Di Caro ◽  
Giovanni Delogu ◽  
Enrico Girardi
Keyword(s):  
Next Generation Sequencing ◽  
Molecular Epidemiology ◽  
Disease Control ◽  
Molecular Typing ◽  
Control Strategies ◽  
Next Generation ◽  
Resistance Patterns ◽  
Short Time ◽  
Drug Resistant Strains ◽  
Generation Sequencing

Tuberculosis (TB) is still an important cause of morbidity and mortality worldwide. An improvement of the strategies for disease control is necessary in both low- and high-incidence TB countries. Clinicians, epidemiologists, laboratory specialists, and public health players should work together in order to achieve a significant reduction in TB transmission and spread of drug-resistant strains. Effective TB surveillance relies on early diagnosis of new cases, appropriate therapy, and accurate detection of outbreaks in the community, in order to implement proper TB control strategies. To achieve this goal, information from classical and molecular epidemiology, together with patient clinical data need to be combined. In this review, we summarize the methodologies currently used in molecular epidemiology, namely molecular typing. We will discuss their efficiency to phylogenetically characterize <em>Mycobacterium</em> <em>tuberculosis</em> isolates, and their ability to provide information that can be useful for disease control. We will also introduce next generation sequencing as the methodology that potentially could provide in a short time both, detection of new outbreaks and identification of resistance patterns. This could envision a potential of next generation sequencing as an important tool for accurate patient management and disease control.

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