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Genomic Identification and Surveillance



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Over the past few years The Delaware Public Health Laboratory (DPHL) has improved abilities to utilize genomics as a means to identify novel pathogens and their genetics as it relates to outbreak clustering in Delaware. The Microbiology section receives federal funds to perform deoxyribonucleic acid (DNA) analysis in partnership with the CDC’s PulseNet program for identification of foodborne outbreaks. These funds have allowed for the purchase of several next generation sequencing (NGS) instruments, called MiSeq, to perform testing.

The methods incorporate the use of whole genome sequencing (WGS) by identifying the individual letters that make up the code of a pathogen's entire genetic information, otherwise known as a genome, into "raw" data files. These files require the use of computers and software to interpret the "raw" data into usable data to interpret results, otherwise known as bioinformatics. The analyzed data is shared with the Centers for Disease Control and Prevention (CDC) Foodborne Outbreak databases, PulseNet and CaliciNet. This allows DPHL and the Office of Infectious Disease Epidemiology (OIDE) to investigate and identify foodborne outbreaks. Currently the Microbiology section uses WGS and targeted sequencing for surveillance of the following (but not limited to) foodborne pathogens:

  • Salmonella species
  • Shigella species
  • Shiga toxin producing E. coli (STEC)
  • Listeria monocytogenes
  • Campylobacter species
  • Vibrio parahaemolyticus
  • Norovirus-targeted genes for CaliciNet

The Microbiology section will also use our NGS equipment and bioinformatics to support and improve the identification of infectious disease diagnosis through the Advanced Molecular Detection (AMD) program. DPHL plans to utilize this technology to enhance our ability to identify outbreaks or clusters including resistance genes. Currently, the Microbiology section uses targeted sequencing of ribosomal DNA (subunit 16S) for the identification of fastidious and atypical bacteria. This technique provides identification of non-tuberculous Mycobacteria (NTM) or clinically significant organisms ruled out as bioterrorism agents. The Microbiology section utilizes this technology to support identification of novel pathogens, culminating with an October 2018 publication in CDC's Emerging Infectious Disease (EID) Journal.

DPHL continues to expand NGS activities to supplement identification of novel pathogenicity and antibiotic resistant and surveillance activities of multi-drug resistant organisms (MDRO) associated with hospital-acquired infections (HAI). This technology will be supporting advancements in rabies virus surveillance through coordination with regional partners. In the future, there are plans to explore opportunities to use this technology beyond communicable disease testing, including microbiome analysis to aid in child development and associations with suspect autoimmune diseases (i.e. Crohn’s disease), identification of cancer markers to aid in therapy, or supporting work with State organizations for environmental and forensic tracking.

For additional information:


Return to the Microbiology main page

Return to the Delaware Public Health Laboratory home page



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