Lab Matters Fall Winter 2021 - Page 29


Staying Ahead of Threats : The Role of Next Generation Sequencing Technology

By Chris Mangal , MPH , director , Public Health Preparedness and Response
Laboratories play a vital role in the detection of novel threats . Over the years , technology to detect biological threat agents has evolved to include real-time polymerase chain reaction ( PCR ), matrix-assisted laser desorption / ionization time of flight ( MALDI-TOF ) and now , next generation sequencing ( NGS ), which is widespread in the public health community . Using NGS technology , laboratorians work closely with epidemiologists , bioinformaticians and others to understand the transmission and evolution of pathogen outbreaks such as SARS-CoV-2 .
Laboratories : Sequencing technologies to detect threats
Epidemiology : Using data generated by laboratories and field investigations to identify and stop outbreaks
While NGS technology is typically used to characterize genomes and investigate outbreaks , it is rarely used to sequence samples from clinical patients with unknown etiologies for pathogen identification .
As we look ahead to the next threat , it will be critical for laboratories to have technologies in place to identify unknown pathogens quickly and safely . The US Centers for Disease Control and Prevention ( CDC ) Center for Preparedness and Response ( CPR ) is providing resources to APHL to examine the use of NGS technology for pathogen-agnostic diagnostic assay development . In the coming months , APHL will collaborate with select partners to develop and optimize laboratory workflows for a number of sample types for detection of multiple pathogen types . The objective of this project is to develop robust workflows that provide public health laboratories with the ability to screen samples for a wide variety of pathogens using a single assay . Additionally , this work can be expanded to facilitate metagenomic identification of novel pathogens or known pathogens with mutations using platforms already available in most public health laboratories .
In addition to exploring NGS technologies for pathogen-agnostic diagnostic assay development , APHL plans to collaborate with CDC and other experts in this field to implement a standardized bioinformatics pipeline to support interpreting data , identifying and characterizing pathogens . Bioinformatics pipelines can perform a variety of tasks and typically include quality control and assembly of raw sequencing reads , identification of pathogens within a sample based on database comparison , as well as report generation .
Bioinformatics : Cross-section between computer science , biology and information technology to analyze data
Via the integration of NGS with traditional epidemiology and bioinformatics , public health can see pathogens in ways unimaginable just 10 years ago . These technologies are critical in detecting antimicrobial resistance , identifying known and novel pathogens , rapidly understanding outbreaks and , ultimately , contributing to targeted measures to protect the public ’ s health . Utilizing this technology will be immensely valuable to stay ahead of the next threat . n
DIGITAL EXTRA : Read more about APHL-CDC Bioinformatics Fellowships .
Fall / Winter 2021 LAB MATTERS 27