Genomic Sequencing
The Rhode Island Department of Health (RIDOH) State Health Laboratories includes a Sequencing Core Laboratory, which uses cutting-edge technology to understand the genetic makeup of various pathogens. Pathogens are microorganisms that can cause diseases, including viruses, bacteria, fungi, and parasites. Learn more about genomic sequencing.
What we do
Sequence the genomes of:
- Respiratory viruses, including SARS CoV-2 (the virus that causes COVID-19), Influenza, and RSV (Respiratory Syncytial Virus)
- Human Mpox (Monkeypox Virus)
- Arboviruses, including West Nile virus, and EEE virus
- Bacteria causing foodborne illnesses, including Salmonella, Shigella, Shiga-toxin producing E. coli (STEC), Listeria, Vibrio, Campylobacter, Yersinia, and Cronobacter
- Bacteria with antimicrobial resistant strains and healthcare-associated infections (HAI), such as invasive Group A Streptococcus, Carbapenem-resistant Enterobacterales (CRE), and Neisseria gonorrhoeae
Analyze samples from multiple sources, including clinical, wastewater, animal, food, and environmental samples.
Participate in a variety of national laboratory surveillance networks.
Benefits
Understanding the information encoded in the genes of disease-causing bacteria, viruses, and fungi can help public health officials better understand how microorganisms cause disease, move through communities, and change over time. These data allow scientists to identify new pathogens, find clusters of related species, identify vehicles of infection, track how viruses evolve in real time, and identify appropriate treatments and vaccines. This technology has the potential to revolutionize how the State monitors and treats infectious diseases.
Research and Surveillance Partnerships
The Sequencing Core Lab submits anonymous genomic sequencing surveillance data to a variety of national biomedical research efforts. These projects allow labs across the country to share data in real time to help detect outbreaks, emerging threats to patient safety, and more.
Current Efforts
The lab submits data to the National Center for Biotechnology Information (NCBI). Sequencing data is submitted to multiple BioProjects supported and managed by the Centers for Disease Control and Prevention, as well as the following BioProjects supported by RIDOH and other collaborators:
- Campylobacter
- Candida auris
- Escherichia coli and Shigella
- Influenza A virus (H1)
- Influenza A virus (H3)
- Influenza B virus
- Klebsiella pneumoniae
- Listeria
- Mpox virus
- Neisseria meningitidis
- Pseudomonas aeruginosa
- Salmonella enterica
- SARS-CoV-2 virus (COVID-19)
- SARS-CoV-2 virus (COVID-19) in wastewater
- Streptococcus pyogenes
- Vibrio
- West Nile virus
New Collaborations
The Sequencing Core Lab continues to seek opportunities to collaborate with academic groups, industry partners, or other State agencies on mutually beneficial sequencing projects. Current areas of interest include increasing the availability of environmental samples for sequencing, such as enteric bacteria recovered from surface water or shellfish sampling, diseases of interest transmitted by mosquitos, and bacterial samples from agriculture. Please contact us to discuss specific opportunities for collaboration.
Partners
- Centers for Disease Control and Prevention PulseNet Network
- US Food and Drug Administration GenomeTrakr Network
- Centers for Disease Control and Prevention Office of Advanced Molecular Detection
- Centers for Disease Control and Prevention Antimicrobial Resistance Laboratory Networks
Resources
Research
- Notes from the field: Multistate Outbreak of Escherichia coli O26 Infections Linked to Raw Flour — United States, 2019
- Campylobacter jejuni Outbreak Linked to Raw Oysters in Rhode Island, 2021 - PubMed
- Limited Short-Term Evolution of SARS-CoV-2 RNA-Dependent RNA Polymerase under Remdesivir Exposure in Upper Respiratory Compartments
- Development of an amplicon-based sequencing approach in response to the global emergence of mpox
- 1896. Statewide Genomic Surveillance of SARS-CoV-2 Variants in Rhode Island
- Genomic deletions and rearrangements in monkeypox virus from the 2022 outbreak, USA
- A pyrosequencing protocol for rapid identification of SARS‐CoV‐2 variants
- Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA
- SARS-CoV-2 Variants in Rhode Island
- SARS-CoV-2 Variants in Rhode Island; May 2022 Update
- SARS-CoV-2 Omicron Variant Infection in 10 Persons within 90 Days of Previous SARS-CoV-2 Delta Variant Infection - Four States, October 2021-January 2022
- Antimicrobial Resistance of N. gonorrhoeae at a Community-Based Sexual Health Clinic, 2023-2024