Whole Genome Sequencing (WGS)

We offer whole genome sequencing (WGS), a powerful testing method that analyzes the complete DNA sequence of an organism. Sequencing AR organisms helps us identify sequence types, gene variants, plasmid types, virulence factors, geographic hotspots of specific clones, and other key aspects related to circulating strains. Our AR Laboratory uses Illumina sequencing technologies.

WGS is commonly an internal reflex assay carried out on clinical specimens and isolates submitted for surveillance purposes. If you have already submitted an isolate or clinical specimen according to the AR isolate submission criteria above, you most likely do not need to send an additional isolate for WGS. Our AR Laboratory team automatically sequences isolates received that meet the sequencing priorities provided by CDC.

Please reach out to TexasARLN@dshs.texas.gov if you are unsure whether you need to submit an additional isolate for WGS or visit the FAQ section regarding duplicate isolate submissions.

Bacterial WGS

Candida WGS

Submitting AR Specimens for WGS

If you have an isolate that the DSHS AR Laboratory has never received before, you need to send an isolate to request WGS.

If an AR isolate has already been submitted within the past 6 months from the same patient, same collection source, and same organism, it does not need to be submitted again.

Please refer to the LTSM directory here for storage and shipping requirements for the organisms of interest (e.g., Candida spp., Enterobacterales, Pseudomonas).

Submit AR WGS specimens using submission form G-2B. Updated submission forms can be requested from LabInfo@dshs.texas.gov.

Section 1. Submitter
- Prefilled for your facility to match our records. To establish or update submitter information, please complete a Submitter ID Request Form and email to LabInfo@dshs.texas.gov or fax to (512) 776-7533.
Section 2. Patient
Name on form must match specimen EXACTLY, or the specimen may be rejected. Three unique identifiers (Name, DOB, Unique ID) are recommended. These identifiers must match exactly on the form and specimen.
- Indicate in the bolded box if this WGS request is related to Outbreak Association or Surveillance.
Section 3. Specimen
- Date and time of collection is required, or the specimen may be rejected.
Section 4. TEST REQUEST
- Section 4.4: Select WGS. Write or print the organism name.
Section 6. Payor Source
- Select box “Other” and write “CDC Special Project (14)” on the blank line.

CDC’s AR Sequencing Priorities for Public Health Laboratories

Carbapenemase-producing/PCR-negative CRE/CRPA isolates. These are isolates that are positive for carbapenemase production by phenotypic methods (e.g., mCIM-positive or CarbaNP-positive) AND negative for the “Big 5” carbapenemase genes by PCR, including blaKPC, blaNDM, blaOXA-48-like, blaVIM, and blaIMP. This profile could suggest the presence of a novel carbapenemase gene.
Please exclude isolates with antimicrobial susceptibility profiles that explain positive phenotypic results for carbapenemase production. For example:
1. mCIM+/PCR- Enterobacter and Klebsiella aerogenes intermediate/resistant to cefotaxime, ceftriaxone, and ceftazidime, but susceptible to cefepime suggests false-positive mCIM results, likely because of high levels of AmpC beta-lactamase(s) (encoded by the blaAmpC gene).
2. mCIM+/PCR- Serratia spp. resistant to carbapenems, but susceptible to third generation cephalosporins suggests the presence of the blaSME gene (encodes a class A carbapenemase), not novel resistance.
CRAB carrying Class A, Class B, or blaOXA-48-like carbapenemase genes. These are CRAB isolates that have targeted Class A and/or Class B carbapenemase genes detected by PCR, including blaKPC, blaNDM, blaVIM, and blaIMP.
Carbapenemase-producing/carbapenemase-gene positive CRPA. These are P. aeruginosa isolates that are positive for carbapenemase production by phenotypic methods (e.g., mCIM-positive or CarbaNP-positive) and positive for carbapenemase genes by PCR, including blaKPC, blaNDM, blaIMP, blaVIM and blaoxa48-like.
Carbapenemase-producing/carbapenemase-gene positive CRE. These are Enterobacterales isolates that are positive for carbapenemase production by phenotypic methods (e.g., mCIM-positive or CarbaNP-positive) and positive for carbapenemase genes by PCR, including blaNDM, blaVIM, blaOXA-48-like, and blaIMP.
Other CRAB with clinically or epidemiologically significant profiles. Generally, the order of precedence are isolates:
1. resistant to all beta-lactams tested;
2. resistant to all carbapenems, but not all beta-lactams tested;
3. positive for other Class D carbapenemase genes (e.g., blaOXA-23-like, blaOXA-24/40-like, blaOXA-58-like) that are NOT common in the submitting jurisdiction.
As resources are available, WGS may be directed to support other epidemiological investigation priorities.

Contacts and Resources

Texas AR Laboratory: TexasARLN@dshs.texas.gov

Contact the laboratory regarding isolate submissions, shipping requirements, FedEx account access, shipping labels, shipping supplies, and other technical questions related to laboratory testing.

HAI Epidemiologists: HAIOutbreak@dshs.texas.gov