Lab Matters Fall Winter 2021 - Page 28


Advancing Capabilities to Detect Genetic Engineering and Antimicrobial Resistance in Biological Threat Agents

By Tyler Wolford , MS , manager , Emergency Preparedness and Response
Center , completed a pilot study of a method for rapid WGS of Bacillus anthracis . LRN laboratory scientists at the Wadsworth Center analyzed 11 different strains of B . anthracis in a Biosafety Level 3 ( BSL-3 ) lab using the portable Oxford Nanopore MinION sequencer and BDRDdeveloped protocols . The laboratory completed WGS and onsite analysis using a custom-built bioinformatics software system . Laboratory scientists profiled plasmids , mutations and genetic signatures associated with AR in less than five hours . This pilot study demonstrated that trained LRN laboratory staff could rapidly sequence and analyze B . anthracis , strengthening public health emergency preparedness and response .
Research Scientist Dominick Centurioni processing samples during the Bacillus anthracis whole genome sequencing pilot study . Photo : New York State Department of Health – Wadsworth Center
Prior to 2014 , whole genome sequencing ( WGS ) was primarily used as a research tool . Today , WGS is being used to characterize microbial pathogens , guide therapeutic intervention in clinical settings and enhance epidemiological investigations .
Lengthy time-to-results and the burdensome cost of equipment and reagents previously delayed widespread implementation of WGS technology in the biological threat arena . However , today ’ s WGS instruments and approaches are faster and more affordable and could provide vital information about biological threat agents to public health laboratories in the Laboratory Response Network ( LRN ), leading scientists to quickly uncover sources , potential genetic engineering and detect evidence of antimicrobial resistance ( AR ).
The LRN is the nation ’ s laboratory emergency response system for biological , chemical and radiological threats . Since its inception in 1999 , the LRN is continuously exploring advanced technology and has evolved to address all hazard threats . Although the LRN for Biological Threats Preparedness ( LRN-B ) is primarily concerned with how quickly threat agents are identified , technology such as WGS can provide vastly more information than standard technologies like polymerase chain reaction ( PCR ). As the LRN-B evolves , WGS could prove a valuable tool for member laboratories .
WGS has the ability to detect evidence of AR in biological threat agents . In 2021 , APHL , in collaboration with the US Centers for Disease Control and Prevention ( CDC ) Biodefense Research and Development ( BDRD ) laboratory and the New York State Department of Health - Wadsworth
Rapid detection of AR in B . anthracis provides valuable insight into which antibiotics will be effective during patient intervention . In Fiscal Year 2022 , APHL and CDC will expand the study to a multicenter evaluation with three additional LRN Advanced Reference laboratories . This expanded multicenter evaluation will further define the usefulness of rapid WGS for B . anthracis and assist in determining an implementation strategy to enhance the LRN ’ s capabilities for biological threat detection . n
Equipment setup and supplies used for whole genome sequencing using the Oxford Nanopore MinION
26 LAB MATTERS Fall / Winter 2021
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