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NC Department of Health and Human Services
State Laboratory of Public Health
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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, norovirus, and carbapenemase-producing (CP) carbapenem resistant Enterobacteriaceae (CRE) and CP-Pseudomonas aeruginosa.
  • 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.
  • Assists other units with validation and implementation of new molecular-based assays
  • 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, National Antimicrobial Resistance Monitoring System for Enteric Bacteria [NARMS], and PulseNet).
  • Provides molecular testing for high consequence pathogens such as bacterial pathogens including Bacillus anthracis, Brucella spp, Francisella tularensis, Ebola virus, and Middle Eastern Respiratory Syndrome – Coronovirus (MERS-CoV).

Importance of the Molecular Diagnostics and Molecular Epidemiology Unit

The Molecular Unit activities play an important role in foodborne disease prevention, surveillance and response as well as surveillance and response to CRE.  The analyses performed by the Molecular Unit are critical in assisting with the prevention of further illnesses.

Outbreak investigations associated with foodborne illnesses have resulted in:

  • Recalled food products identified as possible sources of bacteria
  • Changes to food production practices
  • Public health guidance about hygiene for visitors and workers at livestock shows and petting zoos

Outbreak investigations associated with identification of CP-CRE have resulted in:

  • Development of CRE screening and confirmatory testing recommendations and guidelines
  • Public health intervention at long-term care facilities and hospitals
  • Changes in infection control practices

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., Francisella tularensis, Ebola virus, and Middle Eastern Respiratory Syndrome - Coronovirus (MERS-CoV).


Types of Routine Testing Performed by Unit

Pulsed-Field Gel Electrophoresis (PFGE)

Pulsed-Field Gel Electrophoresis (PFGE) - PFGE is performed on all shiga-toxin producing E. coli and Salmonella isolates. 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. 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 testing be done. For more information about norovirus, please go to CaliciNet at CDC.


Sequencing is performed on hard to identify bacteria, as well as strain typing of viruses for epidemiologic investigations and surveillance. Sequence data is analyzed and compared to reference sequences found in CDC databases and online genome libraries.

16S Sequencing

Carbapenem-resistant Enterobacteriaceae (CRE)

Organisms from the family Enterobacteriaceae that are resistant to carbapenems have been detected throughout the United States and are the cause of increasingly hard to eradicate healthcare-associated infections. Testing is performed on all isolates received from healthcare facilities and reference laboratories for confirmation of carbapenem resistance. Molecular and phenotypic methods are used for the accurate determination and detection of organisms resistant to carbapenems. Currently, a CDC-developed real-time PCR method is used to detect KPC, NDM, and OXA-48-like gene targets. The Modified Carbapenem Inactivation Method (mCIM) is used to detect carbapenem activity in Enterobacteriaceae and Pseudomonas aeruginosa in organisms producing the KPC, NDM, VIM, IMP, OXA-48-like, SPM, SME, or IMI/NMC group enzymes. The NCSLPH reports results to the submitting facility and to the NC Epidemiology Communicable Disease branch for surveillance purposes. More information about CRE in North Carolina.

Real-time PCR graph

Real-time PCR

Modified Carbapenem Inactivation Method (mCIM)


Important Links

Molecular Epidemiology Information

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