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 Enterobacterales (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).

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

2020 Tests Performed by Unit

Types of Routine Testing Performed by Unit

Whole Genome Sequencing (WGS)

Whole Genome sequencing (WGS) is a procedure that allows for the sequencing of an organism’s entire genome.  The information obtained from WGS can tell you everything about the organism, such as genetic relatedness, serotype, resistance, and virulence factors. Therefore, this technology allows for better identification, characterization, and improved surveillance.  WGS is performed on all shiga-toxin producing E. coli, Salmonella, and Listeria monocytogenes, for the purposes of reporting Salmonella serotypes to submitters, as well for foodborne disease surveillance.  As a CDC PulseNet participating laboratory, this data is uploaded to a national database to aid the molecular characterization, identification, and surveillance of foodborne disease.  For more information about WGS, please go to PulseNet at CDC.

Real-time PCR for the detection of stx1 and stx2 virulence genes in Shiga toxin producing E. coli (STEC)

Real-time PCR for the detection of stx1 and stx2 virulence gene is performed on suspected Shiga toxin producing E. coli (STEC) colonies. A probe-based real-time PCR assay developed by CDC is performed for the detection of stx1 and stx2 virulence genes in STEC. This information is critical in patient management, as antibiotics are not recommended in patients with STEC infections.

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 testing be done. For more information about norovirus, please go to CaliciNet at CDC.

Sequencing

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.

Carbapenem-resistant Enterobacterales (CRE)

Organisms from the family Enterobacterales 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 and VIM-like gene targets. The Modified Carbapenem Inactivation Method (mCIM) is used to detect carbapenem activity in Enterobacterales 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.

Updated: 05-20-2021