MIcrobial diseases laboratory branch

Expanded Carbapenemase Testing Services Frequently Asked Questions (FAQ) February 1st, 2023 Update

What types of samples should we send?

The following carbapenem-resistant organisms may be submitted to the California Department of Public Health, Microbial Diseases Laboratory (MDL) for further testing.

Carbapenem-resistant Enterobacterales(CRE):
Submit carbapenem-resistant Escherichia coli, Klebsiella oxytoca, Klebsiella pneumoniae, and Enterobacter spp. that are resistant to imipenem, meropenem, doripenem, or ertapenem by standard antimicrobial susceptibility testing (AST) methods (i.e., minimum inhibitory concentrations (MIC) of ≥ 4 µg/mL for doripenem, imipenem or meropenem, or ≥2 µg/mL for ertapenem).
Carbapenem-resistant Pseudomonas aeruginosa(CRPA):
Submit carbapenem-resistant P. aeruginosa isolates that are resistant to imipenem, meropenem, or doripenem by standard AST methods (i.e., MIC of ≥ 8 µg/mL) and nonsusceptible (i.e., intermediate or resistant MIC ≥ 16µg/ml) to cefepime or ceftazidime.
Pan-nonsusceptible Carbapenem-resistant Acinetobacter baumannii(CRAB), CRE,and CRPA:
A pan-nonsusceptible (pan-NS) isolate is defined as an isolate nonsusceptible to all drugs tested to date. Routinely submit all pan nonsusceptible CRE (regardless of species), CRPA, and CRAB to MDL for surveillance purposes. These isolates will be tested at the MDL or an Antibiotic Resistance Laboratory Network (ARLN) Regional Laboratory.
Other CRE not listed in (1.a):
At this time, the CDPH Healthcare-Associated Infections (HAI) Program will provide approval on a case-by-case basis for testing of other CRE, including Providencia, Proteus, Morganella, Citrobacter, and Serratia spp. Please contact the HAI Program at HAIprogram@cdph.ca.gov prior to submission. If approved, these isolates will be tested at the MDL or the Antibiotic Resistance Laboratory Network (AR Lab Network). CRE isolates not listed in (1.a.) that are submitted without prior approval will not be tested.

CRAB isolates (excluding pan-nonsusceptible) may be submitted directly to the ARLN Regional Laboratory for testing as a part of their targeted surveillance program with coordination of the HAI program and MDL.

Submit CRAB isolates that are resistant to imipenem, meropenem, or doripenem by standard susceptibility testing methods (i.e., MIC of >=8 μg/mL). The ARLN Regional Laboratory will perform bacterial identification confirmation, AST, and PCR testing to detect carbapenemase genes for CRAB isolates. Agar slants and shipping materials can be provided to submitting clinical laboratories at no charge. Detailed information for submittal criteria, forms, and shipping instructions can be found at: ARLN Lab Network Test Menu.

Please contact the HAI program at HAIprogram@cdph.ca.gov at and MDL Bacterial Diseases Section (BDS) at MDLBDS@cdph.ca.gov for any assistance.

If your institution uses nonstandard AST method, we will review the provided AST results and perform testing on a case-by-case basis.
Isolates from patients being investigated as part of a cluster or outbreak, or containing novel resistance mechanisms, may be referred for Whole Genome Sequencing (WGS) by the CDPH HAI Program. Approval is required by the HAI Program and the MDL Molecular Characterization Unit (MCU) prior to submission. Contact the HAI Program at HAIprogram@cdph.ca.gov and MDL MCU at MDL.Submissions@CDPH.ca.gov prior to submitting isolates for submittal instructions.
All isolates must be identified to at least the genus level by the submitter.
Mixed cultures received by MDL will not be tested.

How should samples be sent in for the laboratory testing?

Submit isolates to the MDL Bacterial Diseases Section (BDS) for modified Carbapenem Inactivation Method (mCIM) for detection of carbapenemase production, polymerase chain reaction (PCR) for detection of carbapenemase genes, Sensititre^TM AST, and routine submittal of pan-NS isolates for surveillance purposes.

Use the MDL barcode submittal form: MDL General Electronic Submission Form. This barcode submittal form can be found at: MDL Submission Instructions and Forms.
Under the Select Test Requisition field, select the Antimicrobial Susceptibility Testing-AST form.
Please type in the relevant information into the form. Information written in by hand is not coded into the barcode.
Provide identification (ID), AST results, and any available phenotypic and molecular carbapenmase testing results. Attach printouts from ID and AST systems to the submittal form.
Type in the full name of the healthcare facility of origin on the submittal form under “Submitting Facility.”
Type in the test(s) requested:

Phenotypic (mCIM), Molecular (carbapenemase gene detection by PCR), or multiple tests (please specify).
Sensititre ^TM AST testing is currently not available by submitter request. This test is performed on selected isolates for surveillance purposes (please see #7 for details).

Subculture isolates onto a non-selective nutrient agar slant (e.g. Tryptic Soy Agar) with a screw-top cap and ship at ambient temperature or refrigerated (cold pack). Frozen cultures in trypticase soy broth (TSB) with 15% glycerol may also be submitted on dry ice. Ship isolates as soon as possible to ensure viability and to avoid loss of antimicrobial resistance mechanisms. Please see MDL Service and Test Catalog for details.

For WGS, contact MDL MCU for consultation an dthe appopiate submittal form by emailing at MDL.Submissions@CDPH.ca.gov. Consultation and approval is required prior to submission. Submital forms and shipping instructions will be provided after approval.

What is the shipping address?

California Deparment of Public Health
Microbial Diseases Laboratory
ATTN: Bacterial Diseases Section
850 Marina Bay Parkway
Specimen Receiving, Room B-106
Richmond, CA 94804

Who can submit isolates for testing?

Isolates will be accepted from California Local Public Health Laboratories only. Isolates will not be accepted directly from hospitals or other healthcare facilities unless approved by the MDL and CDPH HAI Program, and applicable Local Public Health Laboratories.

If I already have molecular testing results for carbapenemase gene detection, can I still submit my sample?

Yes. CRE and CRPA isolates that have tested negative for known carbapenemase genes by a validated molecular test method can be submitted to MDL for mCIM testing. CRE or CRPA isolates that have tested negative for known carbapenemase genes but are carbapenemase positive by a phenotypic test may indicate a novel or unusual carbapenemase; such isolates may be forwarded to the ARLN Regional Lab for additional characterization. Molecular testing of these isolates will not be repeated at MDL.

Can isolates be submitted for real-time PCR testing for carbapenemase gene detection

Yes. CRE and CRPA isolates determined to be carbapenemase-producers by a phenotypic test may be submitted to MDL for carbapenemase gene testing by real-time PCR, if that has not already been performed.

Do I need to submit isolates for the Sensititre^TM AST?

No. CRE, CRPA and CRAB isolates will be selected for confirmatory Sensititre^TM AST for surveillance purposes based on the priorities detailed below:

Pan-Resistant and pan-NS CRE, CRPA and CRAB
Non-KPC CRE isolates that are positive for bla_NDM, bla_OXA-48-like, bla_VIM, and bla_IMP by real-time PCR
CRPA isolates that are positive for carbapenemase production or/and carbapenemase gene ( bla_KPC, bla_NDM, bla_IMP, bla_VIM and bla_OXA-48-like)
Other isolates that are associated with outbreaks and requested by HAI epidemiologists

Can Enterobacterales be submitted for Expanded AST (ExAST) for hard-to-treat infections?

Yes. With approval from the HAI Program and MDL, ExAST on CRE isolates that are highly resistant (non-susceptible to all beta-lactams) or possess metallo-beta-lactamase genes (NDM, VIM, IMP) for clinical-decision making purposes is available directly through the ARLN Regional Lab. Detailed information for submittal criteria, forms, and shipping instructions can be found here: ARLN Lab Test Menu.

Contact the HAI Program at HAIProgram@cdph.ca.gov and MDL BDS at MDLBDS@cdph.ca.gov prior to submitting isolates. Submitting isolates to MDL may result in delays in testing.

Can duplicate isolates be submitted for testing?

No. Isolates from specimens collected within a 30-day timeframe that are from the same patient, and are the same species, specimen source, and AST profile are considered duplicates. However, if there is a special need to test the duplicate isolates, please contact the HAI Program at HAIProgram@cdph.ca.gov for approval prior to submission.

Can isolates be submitted for WGS only?

Yes. Prior approval is required by the HAI Program and MDL prior to submission. Please contact the HAI Program at HAIProgram@cdph.ca.gov, and MCU/MDL at MDL.Submissions@CDPH.ca.gov to get approval to submit isolates for WGS. Once the submission has been approved, the submittal form and shipping instructions will be provided.

What is the turn-around-time (TAT) for testing?

Turn-around time (TAT) is based on day of receipt and is dependent on the test requested. Additional reflex testing will extend the TAT by the times indicated for the add-on method(s).

Real-time PCR testing: 7 business days
mCIM testing: 14 business days
Sensititre^TM AST (surveillance testing only): 14 business days
Whole Genome Sequencing: 21 calendar days
Results of ExAST for isolates forwarded to the ARLN Regional Lab will be available within 3 business days from time of receipt for CRE, CRPA and CRAB.