Submitting Clinical Bacteriology Specimens to the DSHS Laboratory

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Specimen Submissions

The steps to submitting clinical bacteriology specimens are similar to those of many other specimens sent to the Laboratory. The submission process is outlined in the four-step graphic

Please refer to the DSHS’ LTSM test menu for test-specific guidance on specimen types, required volumes, and shipping temperatures. Refer to the DSHS’ online Specimen Collection and Submission Guidance and Specimen Shipping and Mailing Guidance content for additional guidance on submitting clinical specimens to the Laboratory.

"A graphic representation of the specimen submission steps. Steps are numbered 1 to 4. "

1. Request a DSHS Laboratory Submitter ID Number (Facilities with a current Submitter ID, skip this step)

New users and users updating previously submitted information must fill out all applicable fields of a Submitter ID Request Form and email the completed form to or fax to (512) 776-7533.

2. Obtain a Specimen Submission Form

Once you have a Submitter ID number, request a master copy of the required specimen submission form from Laboratory Reporting by emailing or calling (512) 776-7578.

A G-2B submission form is required for each submission to "A glass tube with a black twist off lid"the Clinical Bacteriology Laboratory. Master copies of submission forms may be obtained by email. Visit the DSHS Forms and Fee Schedule information page here for more information on obtaining DSHS submission forms.


Please use the most current version of the submission forms. Old forms may be missing required information and cause a specimen to be rejected.
Email to order updated forms.

3. Collect and Label Specimen 

High-quality specimens are vital for accurate testing. All submitted specimens must be labeled with at least two unique identifiers, preferably three. Patient identifiers on the specimen label and in the submission form must be identical.

  • Additional specimen collection guidance for clinical bacteriology testing is available here.
  • Please refer to the requested test’s LTSM description page for additional collection details, in the DSHS test directory, found here.

Sputum and Bronchial Washing Specimens

The Laboratory accepts sputum and bronchial washings for Legionella testing.

  • Sputum should be collected in a leak proof container under the direction of a trained healthcare professional.
  • Minimum volume required for testing is 3 mL up to a maximum of 15 mL in each container. Do not overfill.
  • Specimens must be submitted to the DSHS Laboratory as soon as possible to be tested within 24 hours of collection. If shipping is delayed by more than 2 hours, refrigerate specimen at 2°C to 4°C.

Stool Specimens

Stool specimens are accepted for aerobic bacteria identification and enterohemorrhagic E. coli (EHEC) Shiga-like toxin assays. All fecal specimens must be submitted in appropriate transport media.

  • Stool specimens must be submitted in transport medium such as Cary Blair, Gram Negative (GN) Broth, etc.
  • Specimens must be kept cold or frozen immediately at - 70°C after collection (unless for Vibrio testing, which should be kept at ambient temperature).
  • Minimum volume required for testing is 5 mL in each container. Do not overfill.
  • Please ensure the collection kits are not out of date. Specimens collected with expired kits cannot be tested.
  • Raw stool specimens and rectal swabs are not acceptable for diagnostic testing but are acceptable for surveillance purposes only.

Printable guidance on submitting stool specimens to the Laboratory is available here.

Miscellaneous Body Fluid Specimens

A variety of body fluid specimens are accepted for aerobic bacteria identification tests. Body fluids are specimens other than plasma, serum, or urine. They include cerebrospinal fluid (CSF), dialysate, postsurgical drain fluid, wound fluid, and other fluids often obtained using ultrasound-guided aspiration (such as pancreatic, pericardial, and pleural fluid).

Pure Isolate Specimens

Pure isolates may be submitted on growth-supporting solid or liquid media for definitive identification or serotyping. Specimens must be pure and actively growing. The Laboratory does not supply isolation media to submitters.

  • Solid media must contain visible growth of more than one colony.
  • Minimum volume of 2 mL liquid media is required.
  • Specimen should not be older than 4 to 5 weeks. The sooner the specimen is submitted, the more likely recovery is. Please transfer old specimens onto new media for submission.
  • Overnight colony growth is preferred.
  • Neisseria meningitidis isolates should be submitted on chocolate agar slants at ambient temperature.
  • Neisseria gonorrhoeae isolates should be grown on a non-selective medium such as chocolate II or GC base with 1% growth supplements.
  • Legionella spp. isolates should be submitted on buffered charcoal yeast extract (BCYE) agar slants and submitted at refrigeration temperatures.
  • Overnight isolate growth may be collected with a sterile swab and resuspended in an appropriate freezer medium.
  • Unidentified isolates may be shipped as Category B Infectious Substance, UN3373.

Pure Isolates or Clinical Specimens for CDC Referral

Isolates for CDC referral testing must first be submitted to the DSHS Austin Laboratory. Providers may not submit isolates directly to CDC. 

Questions about CDC referrals? Call the Clinical Bacteriology Group at (512) 776-512-776-7582, or 1- 888-963-7111 ext. 7582 (toll free).


Swab specimens in appropriate transport media are accepted for a variety of tests.

  • Autopsy swab specimens must be collected and stored on Amies or Stuart’s transport medium.
  • Neisseria gonorrhoeae swab specimens for antimicrobial susceptibility testing must be submitted in Copan ESwab transport medium.

Blood and Blood Culture Specimens

Whole blood specimens are accepted for bacterial isolation testing.

  • Use red-top, tiger top, or blood culture bottles to collect specimen.
  • 1 mL minimum volume required for testing.
  • Specimens must be submitted as soon as possible after collection.

Specimens for Reportable Conditions

Isolates are preferred over clinical specimens. Specimens must be submitted to the Laboratory as soon as they become available. If the original specimen no longer exists, the provider should collect a new sample and submit it to the DSHS Laboratory with a G-2B specimen submission form.

Specimens for Surveillance Programs

The DSHS Laboratory collaborates in several surveillance programs such as PulseNet and GenomeTrakr for the collection and molecular characterization of pathogenic bacteria, parasites, and viruses. Clinical laboratories are encouraged to submit surveillance specimens to the DSHS for molecular analysis and/or forwarding to the CDC to identify and sequence the organisms in the specimens, which may help connect cases in outbreak investigations.

Specimen Type and Volume Guidelines

Specimen Type

Required Vol. and Specimen Preparation

Storage and Shipping 

Replica Limits


>20 mL/set (higher volume most productive)

Transport time and temp:<2 h, room temperature

Storage time:<2 h, room temperature, or per instructions

3 set in 24 h

Blood, blood culture bottles, CSF, tissues, lymph nodes,


2 to 3 mL of tissue in sterile saline. Minimum of 1 g of tissue.

Aspirates are preferred over swab specimens.

Collect in sterile leak-proof container such as a 50 mL conical tube.

Ship overnight on cold packs, ASAP after collection.

If shipping is delayed, refrigerate specimen; do not freeze or preserve.

Swabs submitted in transport medium or culturette tubes are unacceptable.


Cervical swab 


<2 h, room temperature

<24 h, room temperature


Cerebrospinal Fluid (CSF)

Bacterial testing, >1 mL; Acid Fast Bacilli testing, >5 mL

  • If only one tube of CSF is collected, submit it for microbiology testing first, otherwise submit two tubes.

  • Aspirates of brain abscess or a biopsy specimen may be necessary to detect anaerobic bacteria or parasites.

Transport time and temp: Do not refrigerate or freeze. Keep at room temperature.

Storage time: <2 hours, room temperature

Ship to Laboratory as soon as possible after collection.


Eye, conjunctiva


  • Medium may be inoculated at time of collection (Blood Agar (BAP) and/or Chocolate Agar (CHOC).

  • Smear may be prepared at time of collection; roll swab over 1-2-cm area of slide.

  • Alternate collection: place swab in approved transport container such as a Copan ESwab.

Culture media: Incubate for 16 – 18 hrs. at 35 – 37 °C in a 4 – 6% CO2-enriched atmosphere. Ship for overnight delivery to Laboratory.

Transport system: Store and submit according to manufacturer’s guidance.


Fluids: abdominal, amniotic, ascites, bile, joint, paracentesis, pericardial, peritoneal, pleural, synovial, thoracentesis

>1 mL

  • Collect specimen in anaerobic transport system, sterile screw-cap tube, or blood culture bottle for bacteria.

  • Always submit as much fluid as possible.

  • Never submit a swab dipped in fluid.

Transport immediately to laboratory.

Transport time and temp: <15 min, room temperature

Storage time:<24 h, room temperature; store pericardial fluid and fluids for fungal cultures, <24 h, 4°C


Rectal swab

Feces should be visible on the swab for detection of diarrheal pathogens.

Swab transport system:  <24 h room temperatures



>2 g

>5 mL

Pass liquid, soft, or bloody stool directly into a sterile, dry, wide mouthed container or Cary-Blair holding medium. (Soft stool is defined as stool assuming the shape of its container.)

Sterile, leak-proof, wide-mouth container

Unpreserved stool: <1 hour after collection, keep at room temperature;
1–24 h. after collection keep at 4°C; 
>24 h after collection keep at -20°C, or colder



for Shiga toxin assay

>2 g

Collect in sterile, leak-proof, wide-mouth container or in Cary-Blair holding medium.

Bloody or liquid stools collected within 6 days of onset among patients with abdominal cramps have the highest yield.  Shiga toxin assay for all EHEC serotypes is better than sorbitol MacConkey culture for O157:H7 only.

Unpreserved: <1 h, room temperature. Swab transport system:  <24 h, room temperature or 4°C


Sputum (Natural or Expectorated)

>1 mL

Collect in a sterile container.

<2 h, room temperature

<24 h, 4°C


Throat or pharyngeal swab


Collect from the posterior pharynx, tonsils, and inflamed areas with a sterile swab.

<24 h, 4°C




<2 h, room temperature

<24 h, room temperature


Vaginal swab


Use a second swab if a smear is also needed.

<2 h, room temperature

<24 h, room temperature



Specimen Labeling Requirements

The following specimen labeling/submission requirements must be met for all specimens submitted to the Laboratory, otherwise they will not be tested.

  • Every specimen must have at least two unique patient identifiers affixed to it. Three identifiers are preferred.
  • Every specimen must be submitted with a submission form.
  • Patient-specific identifiers on the specimen and the submission form must match exactly.
  • All required fields in the forms must be completed.

Refer to the DSHS’ LTSM specimen labeling guidance for additional specimen labeling requirements.

Required Fields on Specimen Submission Forms for Bacteriology Specimens

A G-2B submission form is required for every specimen submitted for bacteriological testing. Submitters must ensure they are using the correct submission form.

If filling out the form by hand, please use BLOCK lettering. Avoid using cursive script to maximize legibility and minimize transcription errors.

Please refer to DSHS LTSM specimen collection guidance pages found here for more details on the required information on submission forms.
Providing a completed specimen submission form with each specimen is critical to successful testing.

4. Shipping Clinical Bacteriology Specimens to the DSHS Laboratory

To minimize exposing mail handlers and carriers to infectious substances, specimens must be tripled contained for shipping to the Laboratory as Category B Biological Substances.

As a submitter, you are legally responsible for the proper training of personnel in handling, labeling, and shipping infectious substances to the DSHS Laboratory.

Additional information on shipping infectious substances to the DSHS Austin Laboratory may be found in the Laboratory’s general specimen shipping and mailing guidance pages.

Before shipping specimens to the Laboratory, make sure you have

  • labeled the specimen with the required patient identifiers (two minimum, three are preferred),
  • secured the lid of the specimen container to prevent leaks,
  • completed the correct specimen submission form for the specimen and requested test,
  • provided the date of collection on the submission form,
  • selected the test being requested on the submission form,
  • attached a copy of previous lab results, if available,
  • packed the specimen correctly according to Category B, UN3373 shipping requirements,
  • affixed all required shipping labels to the outer mailer, and
  • packed cold packs, not dry ice with specimens that need refrigeration.

Questions about Clinical Bacteriology Submissions?

For questions about submitting bacteriology specimens to the DSHS Laboratory or CDC, call the Clinical Bacteriology team at (512) 458-7582 or 1-888-963-7111 ext. 7582 (toll-free).