Submitting AR Specimens to DSHS Lab

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How to Use This Submission Guide

The steps to submitting specimens to the Texas AR Laboratory are outlined in the graphic below. Clinical specimens or isolates that meet the criteria identified in the Submission Criteria table below should be submitted.

Select a step from the list below to go to more detailed guidance for each type of clinical specimen or isolate. 

1. (New Users Only) Request a Submitter ID
2. Obtain a Specimen Submission Form
3. Collect and Label Specimen
4. Ship Specimen to Texas AR Lab

If you have questions about this submission guide, email TexasARLN@dshs.texas.gov.

AR Specimen Submission Criteria

Clinical specimens and isolates that meet the criteria identified in the table below should be submitted to DSHS for further testing.

Recommendation	CRPA	CRE	CRAB	Neisseria gonorrhoeae (GC)	Candida spp
Recommended Clinical Specimen Types	Rectal swab	Rectal swab	Rectal swab	Vaginal swab  Endocervical swab  Urethral swab  Oral swab  Rectal swab Nasopharyngeal swab  Penile Meatal swab  Conjunctival swab (neonates)	Rectal swab Axillary swab* Groin swab* Nares swab Oropharynx swab External ear swab Vaginal swab  (*Axilla and groin should be swabbed together using one swab)
Recommended Isolates	P. aeruginosa resistant to at least one imipenem, meropenem, or doripenem AND Nonsusceptible (intermediate or resistant) to cefepime or ceftazidime	Escherichia coli, Klebsiella oxytoca, K. pneumoniae and Enterobacter spp. resistant to any imipenem, meropenem, doripenem, or ertapenem. Providenicia, Proteus, Morganella, Citrobacter and Serratia resistant to any meropenem, doripenem, or ertapenem.	Acinetobacter baumanii resistant to imipenem, meropenem, or doripenem	At least one viable colony of N. gonorrhoeae isolate	At least one viable colony of C. auris.
CLSI breakpoints: (Minimum Inhibitory Concentrations in µg/mL	Imipenem ≥8 Meropenem ≥8 Doripenem ≥8 Cefepime ≥16 Ceftazdime ≥16	Imipenem ≥4 Meropenem ≥4 Doripenem ≥4 Ertapenam ≥2	Imipenem ≥8 Meropenem ≥8 Doripenem ≥8	Azithromycin >1 NS Cefixime >0.25 NS Ceftriaxone >0.25 NS Ciprofloxacin ≥1 R NS= Nonsusceptible R=Resistant OR In the absence of AST, any GC in which treatment failure rather than reinfection is suspected.	N/A
Transport Media for Isolates	Any non-inhibitory, non-selective agar plate or slant (e.g. Sheep Blood Agar, Tryptic Soy Agar, etc.), or broth			Chocolate agar slants	Sabouraud’s Dextrose Agar slant or other appropriate media. CHROMagarTM Candida plates, if available, are best for isolation.
Lab Test Offered	MALDI-TOF mass spectrometry ID Confirmation Antibiotic susceptibility testing (AST) Modified Carbapenem Inactivation Method (mCIM) Note: For CRE and CRPA only.  Real-time polymerase chain reaction (PCR)			Ceftriaxone susceptibility (ETest); Ciprofloxacin susceptibility; MALDI-TOF mass spectrometry; Beta lactamase detection. Azithromycin and Cefixime susceptibility (for research use only)	MALDI-TOF mass spectrometry

Specimen Submission Steps

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

NEW USERS and users updating any information previously submitted, please complete every applicable field of a Submitter ID Request Form and email the completed form to labinfo@dshs.texas.gov, or fax it to (512) 776-7533.

2. Obtain a Specimen Submission Form

Once you have a Submitter ID, request a master copy of the required specimen submission form from Laboratory Reporting by emailing LabInfo@dshs.state.tx.us or calling (512) 776-7578.
A submission form is required for each specimen.
Please refer to the table below to identify the correct submission form for each organism type.

Organism: Clinical Specimen or Isolate	Required Submission Form	Special Instructions
		For Clinical Specimen	For Isolate
CRE (Escherichia coli, Klebsiella oxytoca, K. pneumoniae and/or Enterobacter spp.)	G-2E	Check off “Colonization Testing Only” in Box 2 and write “CRE” in space provided.	Check off “CRE: Carbapenem Resistant Enterobacterales” in Box 1 of Section 4
CRAB	G-2E	Check off “Colonization Testing Only” in Box 2 and write “CRAB” in space provided.	Check off “CRAB: Carbapenem Resistant Acinetobacter” in Box 1 of Section 4
CRPA	G-2E	Check off “Colonization Testing Only” in Box 2 and write “CRPA” in space provided.	Check off “CRPA: Carbapenem Resistant Pseudomonas Aeruginosa” in Box 1 of Section 4
Candida spp.	G-2E	Check off “Colonization Testing Only” in Box 2 and write “Candida auris” in space provided.	Check off “Candida identification by MALDI (Candida susceptibility may be performed) in Box 1 of Section 4
Suspected treatment resistant Neisseria gonorrhoeaea	G-2B	In Section 5, under “Definitive Identification” column, mark “Neisseria” and under “Clinical specimen” column, write “GC AST Test”. Leave Section 9 empty.	In Section 5, under “Definitive Identification” column, mark “Neisseria” and write “GC AST Test” next to it. Leave Section 9 empty.

3. Collect and Label Specimen

It is vital that specimens are collected, labeled, and submitted correctly. Failure to submit a specimen as required will result in DSHS’ refusal to perform the requested services. (Tex. Admin. Code §73.31). Collection guidance Refer to the Laboratory Testing Services Manual for test-specific submission requirements.

Specimen Labeling Requirements

The following specimen labeling/submission requirements must be met otherwise the specimen will not be tested.

• Every specimen must have at least two unique patient identifiers affixed to it.
• Every specimen must have an accompanying submission form.
• Patient-specific identifiers on the specimen and the submission form must match exactly.

Acceptable specimen identifiers include but are not limited to

1. Patient’s Name
2. Patient’s Date of Birth
3. Patient’s Medical Record Number
4. Specimen ID Number
5. CDC Number
6. Unique Random Number
7. Medicaid Number
8. Date of Collection

Note: Location-based identifiers such as hospital room number or street address are NOT acceptable.

 

Three patient identifiers are provided on this label
1.    patient’s name, 
2.    date of birth, and 
3.    specimen ID number. 
A minimum of two is required. 

 

Providing a completed submission form with each specimen is critical to successful testing. The unique patient identifiers on the specimen must exactly match the identifiers on the submission form. Missing information and/or mismatches between patient identifiers on specimens and submission forms will result in specimens not being tested, causing delays in patient treatment and potentially unnecessary morbidity and mortality.

 

 

 

 

 

 

 

 

 

 

 

 

 

All three patient identifiers on specimen label match submission form exactly.

 

Patient’s name on specimen label is shortened and ID number provided does not match submission form. Only one patient identifier on label and form match, so the specimen is unsatisfactory for testing. 

 

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AR Laboratory Specimen Submission Guidance by Organism

Use the table of contents below for quick links to AR organism-specific submission guidance. 

•    CRO Specimen Submission Criteria 
•    CRO Specimen Submission Steps 
•    CRO Specimen Collection Instructions 
•    CRO Specimen Labeling Requirements 
•    CRO Specimen Submission Form (G-2E) Instructions  

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•    Candida Specimen Submission Criteria 
•    Candida Specimen Submission Steps 
•    Candida Specimen Collection Instructions 
•    Candida Specimen Labeling Requirements 
•    Candida Submission Form (G-2E) Instructions  

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•    AR GC Submission Criteria 
•    AR GC Specimen Submission Steps 
•    AR GC Specimen Collection Instructions 
•    AR GC Specimen Labeling Requirements 
•    AR GC Specimen Submission Form (G-2B) Instructions  

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CRO Clinical Specimen Swab Collection 

Before collecting CRO specimens, permission must be obtained from a DSHS healthcare-associated infections (HAI) epidemiologist. Please email the HAI epidemiology team at ICAR@dshs.texas.gov. The Laboratory will provide swabs, mailing boxes, and UN3373 labels to CRO submitters upon request from an HAI epidemiologist.
The HAI epidemiologist can help coordinate with shipping specimens to the Laboratory.

Only CRO rectal swab specimens collected using rayon-tipped, plastic applicator Copan Cepheid dual swab collection devices can be accepted for testing. Specimens collected with other swab kits will not be tested.

• Use Copan Cepheid Sterile Transport Dual Swab collection and transport kits (Cepheid Catalog # 900-0370) for specimen collection.
• Make sure the collection kit being used is not expired!
• Swabs may be stored at ambient temperatures before shipping.
• Ship CRO swabs within one day of collection as testing must begin within five days of collection.

Detailed guidance on specimen collection protocol for CRE, CRAB, CRPA (CROs) may be found

Appropriate Transport Media for CRO Isolates 

• Submit CRO isolates on a non-inhibitory, non-selective agar plate or slant (e.g., sheep blood agar, tryptic soy agar).
• A pure, low-passage CRPA isolate is preferred as some carbapenem resistance mechanisms are plasmid-based and can be lost following multiple subcultures.

Candida spp. Clinical Specimen Swab Collection

Use nylon flocked Copan ESwab^TM collection and transportation kit to collect specimen for C. auris colonization testing. Swabbing the skin of the groin and axilla (armpits) reportedly yields the highest concentration of C. auris. The preferred collection method is for the groin and axilla to be swabbed with the same swab. Other areas that may be swabbed include nares, oropharynx, external ear canal, vagina, and rectum.
Please DO NOT USE Copan Transystem swabs, which are designed for CRO Colonization testing.
Check to make sure the lid of each ESwab is firmly closed and appropriately labeled.

Make sure the collection kit is not expired!

PLEASE NOTE:

• Permission must be obtained from a DSHS healthcare-associated infections (HAI) epidemiologist before collecting and submitting Candida surveillance specimens to the Laboratory.
• Please email the HAI epidemiology team at ICAR@dshs.texas.gov to obtain permission.
• The HAI epidemiologist can help provide swab collection kits and coordinate with shipping specimens to the Laboratory.

_{ESwab^TM Collection Kit for Candida specimens. Copan Regular Size Nylon flocked swab with liquid Amies may also be used for specimen collection. Photo Source: DSHS (2022)}

*If an ESwab specimen container is accidentally spilled, please recollect the sample with a new ESwab. Do not add liquid into the ESwab tube or attempt to retrieve spilled liquid.

• Ship Candida swabs within 1 day of collection.

Detailed CDC instructions for collection of patient swabs for C auris testing can be found here.

Appropriate Transport Media for Candida Isolates

• Submit isolates on Sabouraud’s Dextrose Agar (SDA) slants or other appropriate media.
• CHROMagar^TM Candida Chromogenic agar (if available) is the most appropriate medium for isolating colonies. Isolates may be submitted on CHROMagar^TM Candida Chromogenic agar.
• Multiple commercial companies sell CHROMagar^TM Candida media and at least one company sells powder for making the media in-house.

The AR Laboratory will provide SDA slants to submitters upon request. Call the AR lab at (512) 776 – 7342 to request slants.
Permission from an HAI epidemiologist is not needed prior to submission of isolates. The Laboratory does not supply CHROMagar^TM Candida Chromogenic agar slants to submitters.

• Multiple commercial companies sell CHROMagar^TM Candida media and at least one company sells powder for making the media in-house.

The AR Laboratory will provide SDA slants to submitters upon request. Call the AR lab at (512) 776 – 7342 to request slants.
Permission from an HAI epidemiologist is not needed prior to submission of isolates. The Laboratory does not supply CHROMagar^TM Candida Chromogenic agar slants to submitters.

 

Neisseria gonorrhoeae (GC) Clinical Specimen Swab Collection  

Neisseria gonorrhoeae is fastidious and requires special collection and handling for enhanced survival. Clinical specimens from patients with suspected gonorrhea treatment failure may be submitted using the Copan Liquid Amies Elution Swab (ESwab™) collection and transport system. Pure cultures may be submitted on Chocolate II Agar slants or other appropriate media. Specimen collection kits and mailing containers can be provided by DSHS. Specimens from the following swab sites may be submitted for GC susceptibility testing: 

• Vaginal 
• Endocervical 
• Urethral 
• Oral 
• Rectal 
• Nasopharyngeal 
• Penile Meatal
• Conjunctival (neonates)

Copan Liquid Amies Elution Swab (ESwab™) collection kits are required for GC collection. Please note the swab size required will depend on the collection site. Refer to Obtaining AR Specimen Collection Kits and Mailing Containers from DSHS Laboratory for shipping details.

For penile, urethral, or conjunctival specimens: Use Copan ESwab™ Minitip Nylon flocked swab with liquid Amies (Copan Catalog # 481C).