How to Participate in CDC’s AR Lab Network: Lab Testing

Healthcare and clinical labs should work with their local or state public health department to submit isolates or specimens for testing. The public health lab should work with their regional lab. Labs will also work with CDC.

AR Lab Network – Antibiotic Resistance Laboratory Network

AST – antimicrobial susceptibility testing

CPO – carbapenemase-producing organism

CRE – carbapenem-resistant Enterobacteriaceae

CRPA – carbapenem-resistant Pseudomonas aeruginosa

DNA – Deoxyribonucleic acid

ESBL – extended-spectrum β-lactamase-producing bacteria

Expanded AST – Expanded Antimicrobial Susceptibility Testing for Hard-to-Treat Infections

FDA – U.S. Food and Drug Administration

HAI – healthcare-associated infection

IMP – Integron-encoded metallo-β-lactamases

KPC – Klebsiella pneumoniae carbapenemase

National TB Center – National Tuberculosis Molecular Surveillance Center

NDM – New Delhi metallo-β-lactamase

MALDI-TOF – Matrix-assisted laser desorption/ionization

mcr – plasmid-mediated colistin resistance

mCIM – modified carbapenemase inactivation method

MRSA – methicillin-resistant Staphylococcus aureus

OXA-48 – oxacillinase-48

PCR – polymerase chain reaction

VIM – Verona integron-encoded metallo-β-lactamase

WGS – whole genome sequencing

Summary of Lab Tests

The following information is a summary of testing offered through the AR Lab Network, including:

  • Examples of pathogens tested
  • Descriptions of testing
  • Tests performed by the AR Lab Network
  • Tests available through the AR Lab Network regional labs

Find Detailed Testing Information for Submission further below on webpage for specifics.

Examples of Pathogens Tested
  • Acinetobacter baumannii
  • Candida, including C. auris
  • CRE
  • CRPA
  • Clostridioides difficile
  • ESBL
  • Neisseria gonorrhoeae
  • Salmonella (via Pulsenet)
  • Streptococcus pneumoniae
  • Mycobacterium tuberculosis
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 a patient, healthcare workers use lab tests to screen, or look at, other patients to see if they are colonized with the same resistant germ, which can prompt additional infection control actions

Identification of Pathogens

  • Labs identify and confirm the genus and species of resistant germs through one of two methods:
    • Biochemical tests: Classifying a particular species by the way it uses different biological chemicals, like proteins or sugars
    • Mass spectrometry: A specialized technique that looks for a pathogen’s protein “fingerprint”

Molecular Testing

  • A collection of techniques used to detect specific genes within a germ, including those that have and can share resistance
  • These tests can be used to diagnose infections and guide treatment for patients

Phenotypic Carbapenemase Test

  • Uses culture to determine if the pathogen produces an enzyme called carbapenemase
  • If carbapenemase is produced, then a carbapenem antibiotic will not kill the pathogen

AST

  • A type of lab test that grows the pathogen to show how sensitive a germ is to different antibiotics
  • These tests can be used to help select the best drug choice for an antibiotic-resistant infection, and also provide data to monitor how a pathogen’s resistance profile might change over time

WGS

  • A laboratory procedure that provides a very precise DNA fingerprint that can help link cases to one another, allowing an outbreak to be detected and solved sooner.
Types of Tests Performed by the AR Lab Network

Isolate Testing for CRE or CRPA

  • Testing performed by: 56 state and local jurisdictions, including seven regional labs
  • Testing includes:
    • Detect carbapenemases in CRE/CRPA isolates
    • Identify the resistance mechanism(s)
    • Perform AST

Core Testing

  • Testing performed by: Seven regional labs
  • Testing includes:
    • Molecular testing to detect colonization of CPO, including CRE
    • Fungal susceptibility of Candida species to identify emerging resistance
    • Identification and colonization screening to detect and help prevent spread of C. auris
    • Detection and characterization of emerging threats and concerning threats, like mcr-1 and carbapenem-resistant Acinetobacter baumannii, and ability to detect changes to known threats, like MRSA

Additional Testing

  • Testing performed by: Select regional labs and the National TB Center to support nationwide needs
  • Testing includes:
    • C. difficile special projects
    • Enhanced detection of drug-resistant N. gonorrhoeae using antimicrobial susceptibility testing and WGS
    • AST and serotyping of multidrug-resistant S. pneumonia
    • Perform WGS for all isolates of M. tuberculosis
    • Perform expanded susceptibility testing to include pan-resistant bacteria to new antibiotics
Regional Lab Testing Availability

All AR Lab Network regional labs perform Core Testing and select labs perform Additional Testing to support nationwide needs.

Central: Minnesota Department of Health Public Health

  • Core Testing + Additional Testing for C. difficile, S. pneumoniae, Expanded Susceptibility Testing

Mid-Atlantic: Maryland Public Health Laboratory

  • Core Testing + Additional Testing for N. gonorrhoeae

Midwest: Wisconsin State Laboratory of Hygiene

  • Core Testing + Additional Testing for S. pneumoniae, Expanded Susceptibility Testing

Mountain: Texas Department of State Health Services Laboratory

  • Core Testing + Additional Testing for N. gonorrhoeae

Northeast: Wadsworth Center Laboratories

  • Core Testing + Additional Testing for Expanded Susceptibility Testing

Southeast: Tennessee State Public Health Laboratory

  • Core Testing + Additional Testing for N. gonorrhoeae, Expanded Susceptibility Testing

West: Washington State Public Health Laboratories

  • Core Testing + Additional Testing for N. gonorrhoeae

National Tuberculosis Molecular Surveillance Center: Michigan Department of Health and Human Services

  • Only Additional Testing for M. tuberculosis
ARLab Network Map May19

Detailed Testing Information for Submission

The following information is for people submitting specimens or isolates, including healthcare providers, laboratories, or healthcare facilities. Contact your local/state health department or regional lab for more information about AR Lab Network testing capabilities (find contact information on the About AR Lab Network webpage).

Colonization Screening for CPOs

CPO colonization screening is performed by the AR Lab Network regional labs 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. Detecting CPO colonization helps prevent transmission within and among facilities.

It is free of charge (including shipment of test kits to the collecting facility and specimen shipment back to the regional lab).

  • High-risk patients include those who have had contact with another patient diagnosed with a CPO, or patients that have received healthcare in a foreign country in the past six months.
  • CPO colonization screening is focused on CRE, CRPA, and carbapenem-resistant Acinetobacter baumannii, and is performed using rectal swabs (FDA-approved Cepheid GeneXpert Carba-R test kit) to detect KPC, NDM, OXA-48, VIM, and IMP-1 genes.
  • Culture-based screening is used to detect additional variants (i.e., other IMPs circulating in CRE and CRPA and other OXA variants circulating in Acinetobacter).

Rectal swab screening results for Cepheid targets are rapidly returned to the submitting facility, jurisdictional health department, and state public health lab within two business days of specimen receipt. Public health officials are notified within one day if any carbapenemase producer is detected.

Isolate Testing for CRE and CRPA

Healthcare and clinical labs should submit to public health labs Enterobacteriaceae isolates that are resistant to ertapenem, imipenem, doripenem, or meropenem, and Pseudomonas aeruginosa isolates that are resistant to imipenem, doripenem, and meropenem. The isolates should be:

  • Species-identified (e.g., MALDI-TOF mass spectrometry)
  • Confirmed as carbapenemase producers using the mCIM or CarbaNP test
  • PCR-tested to detect carbapenemase genes (KPC, NDM, VIM, OXA-48, and IMP)
  • Antimicrobial susceptibility tested using a broad panel of antibiotics by broth microdilution, Kirby Bauer testing, and/or Etest

Public health laboratories in the AR Lab Network report to the submitting lab or facility the results of the isolate test. The public health labs immediately notify public health officials when novel or emerging resistance is detected (i.e., pan-resistance, rare, or potentially novel carbapenemase genes).

Expanded AST

In 2018, CDC’s AR Lab Network piloted a new program called Expanded AST for Hard-to-Treat Infections (Expanded AST), performed by regional labs free of charge. Expanded AST uses adapted inkjet printing technology to “print” AST panels that test new-to-market antibiotics for Enterobacteriaceae isolates resistant to all beta-lactam antibiotics, which can be hard to treat. Expanded AST can help labs and clinicians decide if a new-to-market antibiotic could effectively treat a very resistant infection. Visit the Expanded AST webpage for FAQs and availability information.

Targeted Surveillance Testing of Carbapenem-resistant Acinetobacter baumanii and mcr

Sentinel surveillance sites at healthcare or clinical labs submit isolates to help monitor emerging antibiotic resistance threats like Acinetobacter baumannii that are resistant to carbapenems, or Escherichia coli and Klebsiella species that have the mcr gene.

For Acinetobacter baumannii, submit species that are resistant to imipenem, doripenem, or meropenem using standard susceptibility testing methods (i.e., minimum inhibitory concentrations of ≥8 µg/mL). The isolates should be:

  • Species confirmed using MALDI-TOF mass spectrometry
  • Tested for the presence of carbapenemase genes (KPC, NDM, VIM, OXA-48, OXA-23/24/40/58, and IMP) by multiplex PCR
  • Tested for antibiotic susceptibility to a broad panel of antibiotics by broth microdilution, Kirby Bauer testing, and/or Etest

For mcr genes, submit Escherichia coli and Klebsiella species that are susceptible to all carbapenems and resistant to at least one third-generation cephalosporin by standard susceptibility testing methods (minimum inhibitory concentrations of ≥4 µg/mL for cefotaxime and ceftriaxone or ≥16 µg/mL for ceftazidime). The isolates should be:

  • Species confirmed using MALDI-TOF mass spectrometry
  • Screened for the presence of mcr genes using multiplex PCR assays
  • Tested for antibiotic susceptibility to a broad panel of antibiotics by broth microdilution, Kirby Bauer testing, and/or Etest

The AR Lab Network regional labs share reports with public health officials and notify them within one day if carbapenemase-positive results are found for Acinetobacter baumanii or mcr positive results are found.

Testing Types for Antibiotic-resistant Candida Species

The AR Lab Network’s primary focus for antibiotic-resistant Candida testing is to confirm suspected C. auris from any specimen site, Candida species (other than C. albicans) from any specimen site (particularly invasive sites), and yeast isolates that could not be identified by the submitting laboratory. AR Lab Network regional labs:

  • Confirm Candida species using MALDI-TOF mass spectrometry
  • Perform antifungal susceptibility testing using a CDC-developed, custom broth microdilution panel
  • Report confirmed C. auris cases immediately to public health authorities for containment response
  • Return aggregate antibiogram data (antibiotic susceptibility profiles) to interested facilities upon request

The AR Lab Network regional labs also perform C. auris colonization screening free of charge (including shipment of test kits to collecting facility and specimen shipment back to regional lab). Healthcare facilities and public health departments can request C. auris colonization screening of close contacts of an index patient (first patient identified with an infection) or other patient contacts considered to be high-risk (e.g., those requiring mechanical ventilation). C. auris colonization screening is performed using a swab specimen, typically a combined axillary-groin swab.

Culture-based screening results are returned in less than 9 days to the submitting facility, jurisdictional health department, and state public health laboratory (confirming negative cultures requires 9 days, positive results are returned sooner). PCR-based screening results are available within 3 days.