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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 molecular screening for galactosemia mutations in babies for the NCSLPH Newborn Screening Unit and serves 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 (PulseNet and CaliciNet).

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

2015 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.

Multiple Locus Variable-number Tandem Repeat Analysis (MLVA)

MLVA is performed on all shiga-toxin producing E. coli, and Salmonella Typhimurium and Salmonella Enteritidis on request by CDC or State Epidemiologists. MLVA is a supplemental molecular method that also produces a genetic “fingerprint” by looking for particular repeats in the DNA sequence. MLVA is performed after PFGE to help provide additional information about the outbreak. For more information about MLVA, please go to PulseNet at CDC.


GALT PCR is a reflux test performed on low level Galactosemia Newborn Screening blood spots. Classic Galactosemia is an autosomal recessive inborn error of metabolism disorder caused by deficiency of Galatose-1-phosphate Uridyltransferase (GALT). A conventional PCR method for mutation detection is the Tetra-prime Amplification Refractory Mutation System PCR (ARMS-PCR). With this method, the internal control, wild type and mutant alleles can be amplified simultaneously in a single PCR reaction. Since the amplicons differ in length, the alleles can be discriminated by agarose gel electrophoresis.


Image: Courtesy of Mei Baker, M.D., FACMG, Assistant Professor, Department of Pediatrics University of Wisconsin School of Medicine and Public Health Science Advisor, Newborn Screening Laboratory Wisconsin State Laboratory of Hygiene, “Molecular LDT in Newborn Screening Laboratories” APHL/CDC Newborn Screening Molecular Workshop, Atlanta, GA June 28-30, 2011.

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

Norovirus 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.

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.

Online Resources

Molecular Epidemiology Information