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Bacterial Whole Genome Sequencing

Laboratory Fee Schedule
Procedure Number: NA
 

Synonym(s):   Molecular, Surveillance, WGS, Next Generation Sequencing (NGS), Outbreak, Serotyping, Antibiotic resistance, Carbapenem-resistant organism, (CRO), Foodborne pathogens, Healthcare Acquired Infections (HAI). Salmonella, Escherichia coli, Shigella, Vibrio, Listeria, Neisseria gonorrhoeae, Mycobacterium tuberculosis, TB
Requisition Form G-2B
Exceptions:
G-2E: All Carbapenem-Resistant Organisms 
G-MYCO: All Mycobacterium tuberculosis specimens
 
Test Description Amplification, sequencing, and analysis of extracted bacterial genomic material for the purpose of speciation, serotyping, detection and identification of antimicrobial resistant genes and other characteristics of interest. Cluster analysis and variant calling is carried out as needed.
Pre-Approval Needed
  • Not required but notifying local/regional epidemiologists is helpful. 
  • Refer to the DSHS reporting contacts webpage for a list of public health region epis.  
Supplemental Information Required N/A
Supplemental Form(s) N/A
Performed on Specimens from (sources)
  • Human
  • Food and environmental swabs (from registered food sanitarians only)
Sample/Specimen Type for Testing  Pure isolates and clinical specimens
  • Submission of duplicate specimens, which are specimens obtained from the same source on the same patient within a six-month period is discouraged. 
  • Note: Clinical specimens or isolates obtained from different sources on the same patient (i.e., wound vs. stool) are acceptable since they are not considered duplicate specimens. 
Minimum Volume/Size Required Isolates: At least one viable colony
Clinical Specimens: Please refer to guidance in the test description for the bacterium of interest (such as Salmonella, Shigella or Vibrio).

Storage/Preservation Prior to Shipping

 

 

 

WGS is commonly an internal reflex assay carried out on clinical specimens and isolates submitted for surveillance purposes.Please refer to the LTSM test directory found here for storage and shipping requirements for the organisms of interest ( e.g., Enterobacterales, Escherichia coli, Listeria, Neisseria, Pseudomonas, Salmonella, Shigella, or Vibrio).  
Transport Medium
  • Isolates: Any transport medium that sustains growth (e.g., Stuart’s or Aimes)
  • Clinical Specimens: Please refer to the storage and shipping requirements in the test description for clinical specimens of the bacterium of interest (such as Salmonella, Shigella or Vibrio). 
Specimen Labeling
  • At least two patient identifiers required on specimen (e.g., patient full name, date of birth, medical record number). 
  • Three patient identifiers are preferred.
  • Patient identifiers on specimen label must exactly match identifiers on submission form. (e.g., abbreviated name on label and full name on form is not acceptable.)
  • Additional DSHS Laboratory specimen labeling guidelines available online here.
Shipping and Specimen Handling Requirements
  • Ship according to Dangerous Goods Regulations, IATA, and/or CFR 49.
  • Category B Biological Substance, UN3373 shipping requirements apply.
  • Handle as infectious agent using universal precautions. 
  • Triple-contained in accordance with federal shipping regulations.  
  • Submitters are responsible for packaging and shipping specimens according to regulatory requirements. 
  • Laboratory does not supply collection kits or shipping materials for whole genome sequencing specimens.
  • Additional DSHS Laboratory specimen labeling guidelines online here.
Method 

Whole Genome Sequencing using Illumina sequencing technologies.
Turn-around Time
  • 14 – 21 days from date of specimen receipt at DSHS Laboratory.
  • If isolate is sent to CDC for further study, turnaround time may be longer.
Interferences/Limitations

Specimen results for rare serotypes may be delayed pending CDC review.
Common Causes for Rejection
  • Incorrect specimen collection or submission methods (e.g., not having minimum number of patient identifiers
  • Insufficient specimen growth
  • Non-viable isolates
  • Mixed specimen/contamination
  • Incorrect storage conditions 
  • Expired reagents/media/collection container
  • Discrepancies between submission form and specimen label
  • Missing/incomplete/illegible submission form
Additional Information
  • Duplicate specimens (clinical and isolates) may be received but may not be tested by WGS due to CDC and epidemiological surveillance requirements.
  • Specimens received that are determined to be duplicates will not be sequenced and submitter will not receive a results report. 
  • Duplicate specimens are specimens obtained from the same site on the same patient within a 6-month period.
  • Exceptions include specimens obtained from different sources on the same patient.
  • Please email the Genetic Sequencing Branch at wgs.dshs@dshs.texas.gov, or call (512) 776-6614.