Ordering Recommendation

Use for epidemiological investigation of infectious outbreaks.

New York DOH Approval Status

This test is not New York state approved. There are no New York state-approved laboratories available. Submit a Non-Permitted Laboratory Request Form (NPL) to the NYDOH prior to collection of specimen. If NPL is approved by NYDOH, and sample is received at ARUP, testing will be performed.

Specimen Required

Patient Preparation

Multiple bacterial isolates that are epidemiologically related.

Specimen Preparation

Transport individual isolates on agar slants or on swabs in bacterial transport media. Package isolates together in a sealed container.

Storage/Transport Temperature

Room temperature.

Unacceptable Conditions

Mixed cultures or non-viable organisms.


Contact the Microbiology Laboratory at (800) 242-2787, extension 2576, prior to submission of the isolates.
One report will be generated for each batch tested; billing is per isolate. Order one test, using "Infection control, ####" (your ARUP client number) as the patient name. Include a list of isolate identifiers (do not use patient names) on the requisition or as an order note for electronic orders. Identifiers on the requisition must match identifiers on the isolate samples. 


Isolate: Ambient: 1 week; Refrigerated: Unacceptable; Frozen: Unacceptable.


Massively Parallel Sequencing




7-21 days

Reference Interval

By report

Interpretive Data

Whole Genome Sequencing (WGS) is performed using Ion Torrent sequencing chemistry. Reference-free pairwise comparisons are performed using short, overlapping sequence matching (kmer) analysis. Relationships are determined by the percent of kmers that match between isolate pairs.

Predicted relatedness is based on the total number of differences between the isolates, applying the thresholds shown in the table. The dendrogram and relationship matrix (see enhanced report) illustrate isolate relatedness. 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 based on any strain typing method should not be used for individual patient management.

WGS Strain Typing provides substantial improvements in resolution and reproducibility when compared to pulsed-field gel electrophoresis (PFGE) and can be performed on a broad range of microorganisms. Test was validated for Staphylococcus, Acinetobacter, Enterococcus, Escherichia, Pseudomonas, Stenotrophomonas, Serratia, and Klebsiella species.

This test was developed and its performance characteristics determined by ARUP Laboratories. It has not been cleared or approved by the US Food and Drug Administration. This test was performed in a CLIA certified laboratory and is intended for clinical purposes.

Category Kmer Identity Epidemiological Interpretation
Indistinguishable ≥99.9 Part of the outbreak
Closely related 99.8-99.2 Probably part of the outbreak
Possibly related 99.1-95.0 Possibly part of the outbreak
Unrelated <95.0 Not part of the outbreak

Compliance Category

Laboratory Developed Test (LDT)


Each Isolate billed separately

Hotline History


CPT Codes



Component Test Code* Component Chart Name LOINC
3002532 Bacterial Strain Typing by NGS 90246-0
3002533 EER Bacterial Strain Typing by NGS 11526-1
* Component test codes cannot be used to order tests. The information provided here is not sufficient for interface builds; for a complete test mix, please click the sidebar link to access the Interface Map.


  • Bacterial Typing
  • Bacterial Whole Genome Sequencing
  • Epidemiology Typing
  • Molecular Typing
  • Next Generation Sequencing
  • NGS
  • PFGE
  • Pulsed-Field Gel Electrophoresis
  • Strain Typing
  • WGS
Bacterial Strain Typing by Next Generation Sequencing