APHL is coordinating pilot projects that apply Advanced Molecular Detection (AMD) technologies to detect and monitor infectious diseases. These projects, which support technological innovation at public health laboratories (PHLs), advance the Centers for Disease Control and Prevention's (CDC)
Advanced Molecular Detection initiative.
Earlier AMD activities strengthened detection and response to foodborne disease outbreaks, for example, a
multi-state outbreak of
Listeria monocytogenes associated with caramel apples. The current pilot projects aim to optimize AMD technologies for multiple infectious diseases.
APHL is assisting the AMD project leads with PHL selection, contracts, scheduling, project management and advising on the potential effects of new technologies on the PHL community. APHL contributions to five of these projects include:
Hepatitis C Virus, 2016
APHL, in collaboration with CDC's Division of Viral Hepatitis, has selected four state PHLs to test and troubleshoot the Global Hepatitis Outbreak Surveillance and Technology (GHOST). The laboratories will perform amplicon sequencing of Hepatitis C virus (HCV) and submit data through a web portal that hosts an automated analytic pipeline to identify transmission networks. This approach will speed detection of outbreaks to mitigate the transmission of HCV.
APHL oversees the three PHLs that serve as National Influenza Reference Centers (NIRCs). Two are poised to begin national influenza surveillance testing using next generation sequencing (NGS) in real time. The third will begin testing in January 2017. Influenza NGS data is transmitted from the NIRCs to APHL's AIMS cloud environment where it is automatically analyzed within two to three hours of a run completion. As a result, CDC's turnaround time on genetic data has been cut by two weeks or more. This has expedited influenza surveillance and vaccine strain selection.
Legionnaires' Disease, 2016
APHL, working with CDC and two PHLs, is piloting NGS methods and bioinformatics tools for
Legionella pneumophila. The PHLs and CDC are testing the accuracy and reproducibility of a developmental wgMLST database as they perform parallel sequencing and analysis of archived
L. pneumophila isolates. This technology will facilitate linking of outbreak-related clinical and/or environmental isolates.
APHL is working with the Division of Tuberculosis Elimination and five PHLs to perform whole genome sequencing of TB isolates. These isolates were either collected in their jurisdiction or submitted to CDC for outbreak investigations. Within the project's first six months, 954 isolates were sequenced at the five PHLs, and an additional 2700 are to be sequenced within the subsequent year. The data will be used to improve databases and help determine the future role of NGS in TB control.
Unexplained Respiratory Disease Outbreaks, 2015-2016
APHL, working with CDC's Respiratory Diseases Branch and two PHLs, is developing a multiplex assay that can detect and characterize a wide array of possible outbreak pathogens using NGS technologies. The laboratories are working to optimize targets and evaluate reproducibility of the assays with the goal of multiplexing up to hundreds of targets on a single chip.