Bacterial Strain Typing by Next Generation Sequencing
Also known as: STRAIN NGS
Use
Bacterial Strain Typing by Next Generation Sequencing (NGS) is used for the epidemiological investigation of infectious outbreaks. Whole Genome Sequencing (WGS) is performed using Ion Torrent sequencing chemistry. Relationships are determined by the percent of kmers that match between isolate pairs, providing substantial improvements in resolution and reproducibility compared to pulsed-field gel electrophoresis (PFGE). The test is validated for analysis of Staphylococcus, Acinetobacter, Enterococcus, Escherichia, Pseudomonas, Stenotrophomonas, Serratia, and Klebsiella species.
Special Instructions
Contact the Microbiology Laboratory at (800) 242-2787, extension 2576, prior to submission of the isolates. One report will be generated per batch tested, and billing is per isolate. Order one test using 'Infection control, ####' (ARUP client number) as the patient name. Include a list of isolate identifiers on the requisition.
Limitations
Interpretation of strain relatedness should be performed by an investigator knowledgeable about whole genome strain typing procedures and based on all available epidemiological evidence. Inferred relationships using strain typing methods should not be used for individual patient management. Mixed cultures or non-viable organisms are unacceptable conditions.
New York Approved
Methodology
NGS (Whole Genome Sequencing)
Biomarkers
LOINC Codes
- 90246-0
- 11526-1
Result Turnaround Time
7-21 days
Related Documents
For more information, please review the documents below
Specimen
Other
Volume
Not provided
Minimum Volume
Not provided
Collection Instructions
Transport individual isolates on agar slants or on swabs in bacterial transport media. Package isolates together in a sealed container.
Causes for Rejection
Mixed cultures or non-viable organisms.
Stability Requirements
| Temperature | Period |
|---|---|
| Room Temperature | 1 week |
| Refrigerated | Unacceptable |
| Frozen | Unacceptable |