Bacterial Strain Typing by Whole Genome Sequencing
General Information
Lab Name
Whole Genome Strain Typing
Lab Code
NGSTYP
Description
Whole genome sequencing (WGS) is a relatively new means for tracking disease outbreaks. Using “next-generation” (or “massively parallel”) DNA sequencing technology, it is now possible to sequence and compare the genomes of bacterial isolates, cataloging the polymorphisms that distinguish among strains. This provides information about the genetic relatedness of bacterial isolates that is useful in outbreak investigations when it is coupled with patient biogeographic data and the dates of strain isolation. Although pulsed field gel electrophoresis (PFGE) has long been considered the gold-standard for bacterial strain typing in molecular epidemiological investigations, work by our laboratory and others indicate that WGS substantially outperforms PFGE in terms of discriminatory power and reproducibility (Salipante et al. 2015).
Our lab performs whole genome shotgun sequencing of bacterial isolates using Illumina sequencing chemistries. Our Bacterial Strain Typing by Whole Genome Sequencing [NGSTYP] reports the number of single nucleotide polymorphisms (SNPs) differentiating isolates from one another. Distinguishing SNPs are identified using a reference free method which allows pairwise comparison of genomic sequences shared between isolates (Uricaru et al. 2015). The number of distinguishing SNPs are counted in order to estimate the degree of relatedness among isolates. The number of polymorphisms which distinguish isolate pairs is proportional to their time of divergence from a common ancestor.
Our assay is not intended to (1) identify all genomic differences distinguishing isolates, (2) detect genomic differences resulting from structural variation, gene acquisition or loss, gain or loss of extrachromosomal elements such as plasmids, or large sequence insertions or deletions. Our assay is validated for a broad variety of culturable bacterial species.
Research services are also available.
More information regarding submission of samples can be obtained viewing individual test pages below.
Molecular Microbiology Order Form
Molecular Microbiology Specimen Submission: Additional information regarding specimen submission.
Molecular Microbiology Acceptable Specimens: Full list of acceptable specimens.
Components
| Code | Name |
|---|---|
| NGTPSI | WGS Typing Specimen Info |
| NGTPRS | Whole Genome Typing Results |
Interpretation
Method
DNA extraction, nucleic acid purification, next-generation sequencing
Reference Range
See individual components
Guidelines
Ordering & Collection
Specimen Type
Collection
Isolates should be submitted on whole plate or slant agar media, labeled with a minimum of two identifiers. Provide site/source of isolate, organism identification, and date of primary specimen collection.
Handling Instructions
Ship at room temperature
Quantity
requested: Viable bacterial subculture. Multiple isolates must by submitted for comparison.
minimum: Not applicable
Processing
Outside Laboratory: Organism on slant or plate. Ship at room temperature.
Performance
LIS Dept Code
Micro Molecular Diag (MMD)
Performing Location(s)
| UW-MT |
Microbiology, Molecular Diagnostics
206-520-4600 ---------------------------------------- Shipping Address Attn: Molecular Microbiology Performing Lab Address Clinical Microbiology Lab, NW177 |
Contact Information Please e-mail us with any questions or comments you may have. Your inquiry will be answered as soon as possible. email: molmicdx@uw.edu The Molecular Microbiology lab is open from Monday-Friday, 7am-4pm PDT. Billing inquiries and requests for faxed reports can be made to our Client Services Department at (206) 520-4600 or (800) 713-5198. For results or other inquiries, we can be reached by phone at the following numbers:
For assistance during weekends, holidays and after hours, please contact Lab Medicine Resident at (206) 598-6190 |
|---|
Frequency
Contact lab for details
Available STAT?
No