The 2019 Centers for Disease Control and Prevention (CDC) report, Antibiotic Resistant Threats in the United States, listed carbapenem-resistant Enterobacterales (CRE) as a top-tier, urgent threat.¹ Approximately 1% to 3% of all Enterobacterales isolates encountered in a clinical setting in the United States are resistant to carbapenems,^2–4 and between 22% and 59% of these isolates carry a carbapenemase, an enzyme that can inactivate many beta-lactam antibiotics including carbapenems.^5–7 The mechanism, frequency, and type of carbapenemase-producing CRE (CP-CRE) can vary by geographic location, bacterial species, and health care facility type.^5,6,8

The potential spread of CP-CRE within health care facilities is a significant threat to patient and public health, primarily due to the mobile nature of carbapenemase genes that are often located on plasmids.¹ The availability of novel therapeutics and their mechanisms of action for specific carbapenemases, however, has added a new dimension to the diagnosis, treatment, and control of CP-CRE.⁹ Against non-CP-CRE, ceftazidime-avibactam, meropenem-vaborbactam, and imipenem-relebactam each have a high likelihood of activity if the isolate tests susceptible to the individual compound.¹⁰ The activity of these compounds in the presence of a carbapenemase, however, may not be accurately reflected in the isolate antimicrobial susceptibility testing (AST),⁹ especially if the beta-lactamase-inhibitor is not effective against the specific carbapenemase present. For example, an oxacillinase (OXA)-48-producing isolate may test susceptible to meropenem-vaborbactam by phenotypic AST but is clinically ineffective due to vaborbactam’s inability to neutralize OXA-48.¹¹ Therefore, from the health care perspective, clinical decision-making is informed by knowing both the specific carbapenemase present and the isolate AST results, which is reflected in the Infectious Diseases Society of America (IDSA)’s mechanism-specific treatment approach for infections caused by CRE (Fig. 1).¹²

Although the identification of carbapenemase mechanisms is important for treatment and infection control, many clinical laboratories continue to rely on reference or public health laboratories (PHLs) to perform this testing.⁴ This review aims to outline why clinical microbiology laboratories should consider implementing carbapenemase mechanism testing for CRE isolates and colonization screening. We will review available diagnostic methods, explore barriers to implementation, and propose actions clinical microbiology laboratories can take in both the near term and long term to implement carbapenemase mechanism testing in their facilities.

Annually, CDC’s National Healthcare Safety Network surveys acute and long-term acute care hospital (LTACH) facilities to understand the landscape of laboratory methods used to detect multidrug-resistant organisms (MDROs). About half of the facilities surveyed in 2015 to 2016 reported performing some type of in-house carbapenemase testing,⁴ but that percentage has not changed over the past decade (CDC, NHSN, 2022, unpublished data).

Alternative approaches, such as surrogate testing (use of expert rules for automated AST systems), cannot fully replace the need for carbapenemase mechanism testing. According to the Clinical and Laboratory Standards Institute, carbapenemase genotype predicts phenotypic carbapenem resistance with an approximate accuracy of 95% to 100%; however, the inverse is not true, which is why mechanism testing is required.¹³ Studies that have attempted to develop predictive antibiograms for carbapenemase production have also been unsuccessful for routine clinical usage.¹⁴ Even the dogma that New Delhi metallo-beta-lactamase (NDM) producers are susceptible to aztreonam, thus suggesting the carbapenemase mechanism present, is no longer as predictive as it once was.¹⁵ NDM does not hydrolyze aztreonam, but many NDM-producing CRE are resistant to aztreonam because of other resistance mechanisms, such as extended-spectrum beta-lactamases.¹⁵ The challenge of mechanism-specific predictive antibiotic susceptibility profiles is compounded by the number and diversity of species in the Enterobacterales, the frequency of different carbapenemases within each species, and the corresponding impact on isolate antimicrobial susceptibility.

Among CP-CRE in the United States, Klebsiella pneumoniae carbapenemase (KPC) is the most common carbapenemase mechanism (73.2%), followed by NDM (16.9%), OXA-48-like (4.1%), and other mechanisms.⁵ The newer β-lactamase inhibitor combinations have been designed to neutralize these specific carbapenemases. In general, ceftazidime-avibactam may have activity against KPC or OXA-48-producing CRE but does not have activity against NDM-producing CRE,^10,16 while meropenem-vaborbactam and imipenem-relebactam may have activity against KPC-producing CRE but not against OXA-48-like or NDM-producing CRE.^17,18 Aztreonam-avibactam (ceftazidime-avibactam in combination with aztreonam) or cefiderocol may have activity against infections caused by NDM-producing CRE.^19,20

To have the greatest impact on patient therapy decisions, carbapenemase mechanism testing must be available quickly.^21,22 Clinical laboratories performing in-house carbapenemase mechanism testing have an average turn-around-time (TAT) of 6 days sooner (range 3–14) than when sending isolates to their PHL,²³ illustrating some of the significant hurdles encountered with interfacility isolate transfer.

In addition to aiding in patient therapy decisions, carbapenemase mechanism testing informs infection prevention and control (IPC) activities intended to prevent the spread of CRE to other patients. Some hospital acquired infection (HAI)-prevention activities, such as initiation of Isolation and Contact Precautions for CP-CRE patients in acute care settings, are aided by knowledge of the presence or absence of carbapenemase activity but do not necessarily require carbapenemase mechanism testing. However, knowing the specific carbapenemase mechanism is needed for the more targeted prevention activities outlined in Public Health Strategies to Prevent the Spread of Novel or Targeted Multidrug-resistant Organisms (MDROs)²⁴ and for activities initiated in response to the detection of specific MDROs.²⁵

Per the Interim Guidance for Public Health to Contain Novel or Targeted Multidrug-Resistant Organisms (MDROs), when infected or colonized patients are identified, IPC response/containment activities should be initiated immediately to prevent future spread of the identified organism/mechanism.²⁵ One of the recommended activities is colonization screening of epidemiologically linked patients to determine whether transmission has occurred and guide how precautions should be applied to prevent future transmission events.²⁴ Cohorting of colonized or infected patients has been demonstrated to decrease additional CRE transmissions (including CP-CRE), and if cohorting multiple patients together, it should be conducted based on the identified resistance mechanism.^26,27

Haverkate and colleagues²⁸ demonstrated that a single patient colonized with KPC led to 0.4 transmission events per LTACH stay; however, 29.3% of patients within the cohort were already colonized, exponentially increasing the potential for a transmission event to occur. In contrast, in a model of CRE colonization screening effectiveness, identifying and placing only 1 out of every 9 colonized persons on contact precautions led to an 8% increase in CRE prevalence over 10 years, but increasing the rate of identifying colonized individuals (to 1 out of every 5) led to a steady decrease in new cases.²⁹

Despite the information colonization screening provides, laboratory capacity for this testing is a major unmet need. One example of this is in colonization assessments within long-term care facilities. The Antimicrobial Resistance Laboratory Network (AR Lab Network) often performs colonization testing in these facilities, which were home to 1.3 million residents in the United States in 2020.³⁰ Even if all AR Lab Network resources were hypothetically dedicated to this population, the current capacity would only allow 2% of residents to be screened annually. This is only one example of this unmet need.

Despite the challenges, there are feasible actions a clinical laboratory can take toward implementing carbapenemase mechanism testing in the short term and long term. First, the clinical laboratory can begin working alongside the facility’s antimicrobial stewardship committee, infection prevention team, clinicians, and the corporate suite to elicit and receive facility-wide support. Clinical laboratories can also begin or increase isolate submissions to their PHL for mechanism testing, working with the PHL to expedite isolate submission, triage, and reporting. Clinical laboratories, or their infection prevention counterparts, can review clinical culture results, follow up on positives with their infection prevention teams, and help coordinate colonization assessments for high-risk contacts.

Next, clinical laboratories can begin investigating available diagnostic platforms for mechanism testing (see Table 1). Once laboratory leadership determines the diagnostic platform and approach they will take, laboratories can procure instrumentation or reagents and begin validation/verification testing. This may be a layered activity but could start with requesting isolates for validation/verification purposes. The CDC and FDA AR Bank (AR Bank; https://wwwn.cdc.gov/arisolatebank/) is a ready resource of well-characterized isolates to support these and other testing activities.

A clinical laboratory could reasonably aim to onboard carbapenemase mechanism testing within the next year. Some ways to expedite this process include sharing workflows or validation/verification materials among peers (eg, plans, templates, and developed tools), reviewing real-world performance data, referencing public health testing guidance, using well-characterized isolates (shared among peers or from the AR Bank), or by working with their manufacturers. Once a laboratory is performing testing on isolates, expansion to colonization screening based on patient or resident risk factors could be the next step.

For the nation to effectively treat patients with CRE infections and generate actionable IPC data in all facilities, additional carbapenemase mechanism testing capacity is needed. Therefore, it is critical that clinical laboratories implement routine carbapenemase mechanism testing to maintain a high standard of patient care. Once implemented, clinical laboratories should routinely perform carbapenemase mechanism testing on relevant CRE isolates to inform patient treatment and expand their testing menus to perform colonization screening assessments to prevent further transmission of CP-CRE.