Antimicrobial Resistance Laboratory Network Testing

Key points

  • CDC funds 50 states, several cities and two territory public health labs to perform testing on the bacterial and fungal pathogens.
  • All seven regional Antimicrobial Resistance Laboratory Network (AR Lab Network) labs perform a core set of standard tests.
  • To use AR Lab Network services, contact your state healthcare-associated infection (HAI) coordinator or AR regional lab.
AR Lab Network logo. A high-tech map of the United States with gradient colors of teal, blue, purple, dark red, red and orange-red.

Tests offered through the AR Lab Network

The following information is a summary of testing offered through the Antimicrobial Resistance Laboratory Network (AR Lab Network), including:

Core testing performed by seven regional labs:

  • Molecular testing to detect carbapenemase-producing organisms (CPO) or C. auris colonization to prevent spread.
  • Identification and antifungal susceptibility testing (AFST) of Candida species to identify emerging resistance.
  • Whole genome sequence (WGS) testing of healthcare-associated Gram-negative bacteria and C. auris to identify new resistance and understand spread.
  • Detect and characterize emerging and concerning threats.
  • Perform expanded susceptibility testing using new and/or new combination of antimicrobials against metallo-β-lactamase (MBL)-producing Enterobacterales and multi-drug resistant fungi.

Additional testing performed by select regional labs:

  • Special projects for C. diff.
  • Antimicrobial susceptibility testing (AST), WGS and select molecular testing of drug-resistant N. gonorrhoeae.
  • AST and serotyping of multidrug-resistant S. pneumoniae.
  • WGS of all U.S. M. tuberculosis isolates.
  • Screen A. fumigatus isolates for azole resistance, with confirmatory testing performed on isolates that screen positive.

How to request testing services‎

Contact your state/local lab to see what testing is available. If needed testing is not available, please reach out to your AR Lab Network regional lab.
Antimicrobial Resistance Laboratory Network

Descriptions of testing

Colonization screening

  • Some people can carry germs without becoming sick or showing symptoms, known as colonization; people who are colonized can spread the germs to others without knowing it.
  • When unusual resistance is identified in an individual, healthcare workers use lab tests to screen other patients to see if they are colonized with the same antimicrobial-resistant germ, which can prompt additional infection control actions.

Identification of pathogens

  • Labs identify and confirm the genus and species of resistant germs.

Molecular testing

  • A collection of techniques used to detect specific genes within a germ, including those that have and can share resistance.

Carbapenemase activity detection test

  • This is a phenotypic test used to assess whether carbapenemase enzyme's activity is present in an organism. Many bacteria produce this enzyme, not just bacterial pathogens.
  • If a carbapenemase is produced, then a carbapenem antibiotic will not kill the germ.

Antimicrobial susceptibility testing (AST) and antifungal susceptibility testing (AFST)

  • This is a type of lab test that determines how sensitive a germ is to different antibiotics or antifungals.
  • These tests can help select the best drug for treating an antimicrobial-resistant infection and provide data to monitor how a pathogen's resistance to that drug (and others) might change over time.

Whole genome sequencing (WGS)

  • A laboratory procedure that provides a very precise DNA fingerprint to help link cases to one another, helping to identify or confirm transmission.
  • WGS also allows scientists to understand the specific type of resistance mechanisms present and understand how common or uncommon specific DNA fingerprints are.

Testing Carbapenemase-producing Organisms (CPO)

CPOs are types of bacteria that produce a genetically coded an enzyme called carbapenemase. Carbapenemases allow these bacteria to resist the effects of carbapenems and other β-lactam antibiotics. Carbapenems are among the few remaining antibiotics that can treat ESBL-producing bacteria, but resistance is on the rise. Detecting patients who are colonized with CPOs or have an infection caused by a CPO helps prevent spread within and among facilities.

The AR Lab Network screens for the following CPOs:

AR Lab Network CRE Screening
AR Lab Network Testing Carbapenem Resistance
Information on requesting a colonization screening for Carbapenemase-resistant organisms.
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Screening for CPO colonization

Who performs the test

  • Some state/local public health labs.
  • The seven AR Lab Network regional labs.

About this testing

  • Screening test is free, including shipping.
  • High-risk patients include those who have had contact with another patient diagnosed with a CPO, or other patient contacts considered to be high risk (e.g., received health care in a foreign country in the past six months).
  • CPO colonization screening is performed using rectal swabs (FDA-approved Cepheid GeneXpert Carba-R test kit) to detect blaKPC, blaNDM, blaOXA-48, blaVIM and blaIMP-1 genes.
  • Culture-based screening can be used to detect additional genes or variants (i.e., other IMP variants or other OXA genes circulating in the U.S.).

Request testing

  • Public health officials, healthcare facilities, infection preventionists and epidemiologists can request colonization screening of high-risk patients through their HAI coordinator.
  • Screening results are returned to the submitting facility, jurisdictional health department and state public health lab within two business days of specimen receipt for PCR screening.

Testing CRO isolates

Who performs the tests

  • An estimated 56 state/local public health labs.
  • The seven AR Lab Network regional labs.

About this testing

  • Testing is free, including shipping.
  • For Enterobacterales isolates that are resistant to ertapenem, imipenem, doripenem, or meropenem, and Pseudomonas aeruginosa isolates that are resistant to imipenem, doripenem, or meropenem, using standard susceptibility testing methods (i.e., minimum inhibitory concentrations of ≥8 µg/mL), the following is performed:
    • Organism confirmation (e.g., MALDI-TOF mass spectrometry).
    • Carbapenemase production using the mCIM or CarbaNP test.
    • Real time PCR (RT-PCR) to detect targeted carbapenemase genes (KPC, NDM, VIM, OXA-48, and IMP).
    • Antimicrobial susceptibility testing using a broad panel of drugs by broth microdilution, Kirby Bauer testing, and/or gradient diffusion strips.

Request testing

  • Healthcare providers, and clinical and public health labs can contact their state or local public health lab to request testing.
  • Public health labs in the AR Lab Network will:
    • Report the results of isolate tests to the submitting lab or facility.
    • Immediately notify public health officials when concerning novel or emerging resistance is detected (i.e., pan-resistance, rare, or potentially novel carbapenemase genes).

Testing Azole-resistant Aspergillus fumigatus (A. fumigatus)

Aspergillus fumigatus, a fungus found in the environment, can cause serious illness in people with weakened immune systems. This fungus can develop resistance to azoles during long-term treatment of infected patients or when it is exposed to azole fungicides used in the environment. Infections have been identified in the U.S., increasing the need for awareness and action by clinical and public health professionals. The AR Lab Network tests for azole resistance in A. fumigatus to monitor and track the emergence of azole resistance in the U.S.

ar lab network aspergillus
AR Lab Network Aspergillus Fact Sheet
Information for requesting testing of azole-resistance in Aspergillus fumigatus.
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Who performs the tests

About this testing

  • Testing is free, including shipping.
  • Testing A. fumigatus isolates for azole resistance includes:
    • Species confirmation.
    • Screening for azole resistance using an agar plating method.
    • Confirmatory testing via broth microdilution for the following antifungals: posaconazole, voriconazole, itraconazole, and isavuconazole.
  • Healthcare and clinical labs should submit
    • Clinical A. fumigatus isolates from any body site, especially if there was concern for an invasive or azole-resistant infection.
    • If AFST was done previously, all A. fumigatus isolates with AFST results indicating azole resistance from any body site (invasive or non-invasive, sterile or non-sterile).
    • Only submit A. fumigatus or suspected A. fumigatus isolates; do not submit isolates identified as unspecified Aspergillus species or as another Aspergillus species.

Request testing

  • Healthcare, clinical, reference, and public health labs can contact your state public health laboratory, the Maryland Public Health Laboratory, or the Tennessee State Public Health Laboratory to request testing.
    • State requirements vary regarding submitting isolates to the state public health lab or directly to an AR Lab Network Aspergillus Laboratory.
  • Results will be reported back to the submitting institution within two weeks of receipt of the isolate.

Testing Candida, including Candida auris (C. auris)

Candida is one of the most common causes of healthcare-associated bloodstream infections in the U.S., and antifungal resistance in Candida is increasing. New and emerging species, like C. auris, can spread in healthcare settings and cause outbreaks.

AR Lab Network Candida Isolates
AR Lab Network Candida Isolates Fact Sheet
Information for labs on how to send C. auris isolates for testing.
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Testing Candida Isolates

Who performs the test

  • Some state/local public health labs.
  • The seven AR Lab Network regional labs.

About this testing

  • Testing is free, including shipping.
  • Healthcare, clinical and public health laboratories can submit the following isolates:
    • Suspected C. auris from any specimen site.
    • Candida species other than Candida albicans from any specimen site, particularly invasive sites.
    • Yeast isolates that could note be identified by the submitting laboratory.
  • Participating AR Lab Network regional labs:
    • Confirm Candida species using MALDI-TOF mass spectrometry or DNA sequencing.
    • Perform antifungal susceptibility testing using a CDC-developed, custom broth microdilution panel. Some isolates may also be tested against new antifungals, known as expanded AFST, to help understand if a new drug can effectively treat highly-resistant infections.
    • Report confirmed C. auris cases immediately to public health authorities for containment response.
    • Provide whole genome sequencing to track and characterize resistance and strengthen epidemiology investigations to contain an outbreak.
  • Participating state/local public health labs may not perform all tests possible at the regional labs. Therefore, isolates sent to state/local public health labs may receive some testing at that lab before being sent to a regional lab for further testing.

Request Testing

  • To request testing healthcare, clinical and public health lab facilities should contact their state public health lab or AR Lab Network regional lab.

Screening for C. auris colonization

Who performs the test

  • Some state/local public health labs.
  • The seven AR Lab Network regional labs.

About this testing

  • This screening is free of charge, including shipping.
  • Healthcare facilities can request C. auris colonization screening of close contacts of an index patient (first patient identified with an infection) or other patient contacts considered high-risk (e.g., those requiring mechanical ventilation).
  • High-risk patients include those who have had contact with another patient diagnosed with C. auris, or other patient contacts considered to be high risk (e.g., received healthcare in a foreign country in the past six months).
  • C. auris colonization screening is performed using a swab specimen, typically a combined bilateral axillary-groin swab.
  • Additional information about C. auris screenings.

Request testing

  • This work is performed in collaboration with public health officials (e.g., state HAI coordinator), healthcare facilities, infection preventionists and epidemiologists, all of whom can request colonization screening of high-risk patients. Contact your state-based healthcare-associated infection program coordinator to order screening and screening materials.
  • Screening results are returned to submitting institution within two business days of specimen receipt for PCR screening.
  • The AR Lab Network also offers colonization screening for CPOs.

Testing C. difficile

C. difficile causes severe diarrhea and colitis (an inflammation of the colon), which can be life-threatening. Most cases of infection occur in people taking antibiotics or those who have recently finished taking antibiotics.

Who performs the test

About this testing

  • CDC's AR Lab Network's C. difficile labs can provide outbreak investigation support by performing C. difficile isolation, culturing, and whole genome sequencing to assess C. difficile transmission.

Request testing

Expanded AST (ExAST) for Hard-to-Treat Infections: Enterobacterales-producing a metallo-beta-lactamase (MBL)

When antibiotics are newly approved for use, it can take years before susceptibility tests for these antibiotics are made available in clinical labs. CDC's AR Lab Network provides testing for isolates of highly-resistant Enterobacterales that carry MBLs, which can help guide clinical decision making for highly-resistant isolates. MBLs make bacteria resistant to a broad range of antibiotics, including carbapenems, which are often used to treat antimicrobial-resistant infections.

ar lab network expanded antimicrobial susceptibility testing for hard-to-treat infections fact sheet
AR Lab Network Expanded Antimicrobial Susceptibility Testing Fact Sheet
Information for requesting expanded antimicrobial susceptibility testing from the AR Lab Network.
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Who performs the test

  • The seven AR Lab Network regional labs.

About this testing

  • This testing is free.
  • Using the Hewlett-Packard D300e Digital Dispenser, highly resistant Enterobacterales isolates will be tested for susceptibility to the combination of aztreonam and avibactam.
  • Labs can request testing of Enterobacterales isolates that:
    • Are not susceptible to all beta lactams tested, including either ceftazidime/avibactam or meropenem/vaborbactam. These may be MBL-producing isolates that cause infections with few effective treatment options. OR
    • Enterobacterales that test positive for NDM, VIM, or IMP genes (blaNDM, blaVIM, or blaIMP) confirmed by a molecular test.
  • Requests must be accompanied by preliminary lab testing results, including AST results and/or molecular results, to confirm inclusion criteria have been met.
  • Susceptibility results will be reported for ceftazidime/avibactam, aztreonam, and aztreonam/avibactam to help assess utility of combination therapy.
  • Isolates will also be tested for:
    • Susceptibility to more than 20 other antibiotics using a commercially available comprehensive broth microdilution panel.
    • Carbapenemase production using the mCIM.
    • MBL and other carbapenemase genes.

Request testing

  • Healthcare providers, and clinical and public health labs can contact their AR Lab Network regional lab to request ExAST and find potentially effective treatment options. Susceptibility results for confirmed MBL-producing isolates will be returned within 3 business days to help guide treatment decisions. The AR Lab Network regional labs will notify the submitter and public health officials if MBL-producing isolates are confirmed to have an aztreonam/avibactam MIC ≥ 8/4 µg/mL.

Testing N. gonorrhoeae (Gonorrhea)

Gonorrhea has progressively developed antimicrobial resistance to the drugs recommended to treat it. CDC's AR Lab Network offers testing to assist in care of patients with potentially drug-resistant gonorrhea.

AR Lab Network Gonorrhea AST fact sheet
AR Lab Network Rapid AST testing for Gonorrhea Fact Sheet
Information on rapid AST testing for gonorrhea through the AR Lab Network.
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Who performs the test

About this test

  • Testing is free, including shipping.
  • Includes gradient strip AST for four antibiotics: azithromycin, ceftriaxone, cefixime and ciprofloxacin.

Request testing

  • Contact your state/local lab to see if this testing is available. If testing is not available, please reach out to your AR Lab Network regional lab.

Testing Streptococcus pneuomoniae (S. pneuomoniae)

Streptococcus pneumoniae (pneumococcus) is a leading cause of bacterial pneumonia and meningitis in the U.S. It also is a common cause of bloodstream infections, and ear and sinus infections. When labs submit pneumococcus isolates for testing, serotype results can aid clinical practice to evaluate for vaccine failure, immune deficiency and outbreak identification. Clinical isolates are also vitally important to public health programs that monitor changes in circulating serotypes and antimicrobial resistance.

ar lab network strep isolates
AR Lab Network Strep Isolates Fact Sheet
Information to request free serotyping and ID confirmation of S. pneumoniae through the AR Lab Netwo...
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Who performs the tests

About this testing

  • Testing is free, including shipping.
  • Testing includes:
    • Species identification by phenotypic or molecular methods.
    • Serotyping/serogrouping using molecular methods such as conventional and/or real-time PCR or WGS.
    • AST by broth microdilution.
    • AR Labs send identification and serotyping results within ten days of specimen receipt. AST results are for surveillance purposes only and AR Labs will not send these results back.

Request testing

  • Healthcare and clinical labs can contact their state public health lab, the Wisconsin State Laboratory of Hygiene or the Minnesota Department of Health Public Health Laboratory.
  • Healthcare and clinical labs should submit to public health labs:
    • All CSF isolates, regardless of susceptibility test results.
    • Invasive isolates (sterile body site such as blood) that are non-susceptible for any clinically relevant antibiotic according to current CLSI M100 guidance.
    • Possible failure of therapy or vaccine, or possible outbreak-related isolates.

Testing Mycobacterium tuberculosis (M. tuberculosis)

M. tuberculosis, most known as Tuberculosis (TB), is a disease caused by bacteria that are spread from person to person through the air. It is a common infectious disease found worldwide and can cause death if not treated. TB can be resistant to more than one antibiotic used to treat it.

The National Tuberculosis Molecular Surveillance Center provides testing to identify TB strains, free of charge. Any authorized medical or laboratory professionals can submit samples and in consultation/awareness of their state health department or local authorities per institutional policies. Visit the TB laboratory information page for necessary submission forms.

Testing Salmonella

Salmonella bacteria can spread from animals to people through food. Antimicrobial resistance to Salmonella is increasing. Salmonella testing is supported through PulseNet.

Resources for U.S. labs

CDC offers free resources and tools for laboratory scientists to help combat antimicrobial resistance. Email CDC at ARLN@cdc.gov for more information about the AR Lab Network.

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Content Source:
National Center for Emerging and Zoonotic Infectious Diseases (NCEZID)