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Molecular Epidemiology

Overview of the Molecular Diagnostics and Molecular Epidemiology Unit (Molecular Unit)

  • Provides laboratory support for the molecular characterization and surveillance of foodborne disease agents E. coli, Salmonella, Listeria monocytogenes, and norovirus.
  • Provides training to staff in other units who perform molecular-based assays and assists with troubleshooting if problems arise. 
  • Assists other units by performing certain molecular testing including serving as surge capacity for Bordetella pertussis, Mycobacterium tuberculosis and influenza virus molecular testing.
  • Unit partners include the North Carolina Communicable Disease Branch Epidemiologists, local health departments, the North Carolina Department of Agriculture and Consumer Services, and CDC (Antibiotic Resistance Laboratory Network (ARLN), CaliciNet, PulseNet).

Importance of the Molecular Diagnostics and Molecular Epidemiology Unit

The Molecular Unit activities play an important role in foodborne disease prevention, surveillance and response. The analyses performed by the Molecular Unit are critical in assisting with the prevention of further illnesses. Some of the investigations have resulted in:

  • Recalled food products
  • Changes to food production practices
  • Public health guidance about hygiene for visitors and workers at livestock shows and petting zoos

Public Health Emergency Preparedness (PHEP) cooperative agreement supported staff in the Molecular Unit provide molecular testing for high consequence pathogens such as bacterial pathogens including Bacillus anthracis, Brucella spp, and Francisella tularensis.

2016 Analysis

Types of Routine Testing Performed by Unit

Pulsed-Field Gel Electrophoresis (PFGE)

PFGE is performed on all shiga-toxin producing E. coli, Salmonella, and Listeria monocytogenes. This molecular method produces a genetic “fingerprint” for each isolate that can be compared within the state and nationally in order to identify potential outbreaks. Matches or “clusters” are reported to State Epidemiologists and CDC for further investigation. For more information about PFGE, please go to PulseNet at CDC.

Pulsed-Field Gel Electrophoresis

Whole Genome Sequencing (WGS)

CDC PulseNet is in the process of transitioning from PFGE to WGS. As the name indicates, it is the process of sequencing the entire genome of an organism. The information obtained from WGS can tell you everything about the organism, such as genetic relatedness, serotype, resistance and virulence factors. Therefore, this technology will allow for better characterization and improved surveillance.  Currently, WGS is performed on all shiga-toxin producing E. coli, Salmonella, and Listeria monocytogenes. For more information about WGS, please go to PulseNet at CDC.

Whole Genome Sequencing (WGS)

Norovirus Real-time RT-PCR, Conventional PCR, and Sequencing

Norovirus Real-time RT-PCR, Conventional PCR, and SequencingNorovirus testing is performed on outbreaks with 5 or more specimens, which have been approved for testing by State Epidemiologists (Communicable Disease Branch). Real-time RT-PCR is performed on stools from possible outbreak situations. Positive outbreaks are carried through to sequencing for CDC CaliciNet. Specimens for norovirus testing must be accompanied by requisitions filled out appropriately, with the name on sample matching name on requisition and requesting that Norovirus, Norwalk- like virus, or Norwalk testing be done. For more information about norovirus, please go to CaliciNet at CDC.


16S Sequencing

16S sequencing is performed on hard to identify bacteria. All bacterial organisms contain a highly conserved region known as the ribosomal 16S region. The flanking areas in this highly conserved region are extremely varied, especially between bacterial families. The 16S region has been the target of choice when performing the initial sequence of an organism, and has the most references in online genome libraries.

16S Sequencing

Molecular Serotyping of Salmonella

Molecular serotyping of Salmonella is performed on all Salmonella isolates. It is a CDC developed bead based assay based on the science of flow cytometry. It is used to determine the specific serotype of a Salmonella isolate.

Molecular Serotyping of Salmonella

 

Important Links

Molecular Epidemiology Information

Note: All photos on this page taken by SLPH staff.