The spread of carbapenem-resistant Enterobacteriaceae (CRE) has become not only a clinical challenge but also a global public health problem. It is critical for laboratorians and physicians to collaborate closely, as rapid identification of colonized or infected patients can help prevent CRE transmission.

Enterobacteriaceae are part of the normal human gastrointestinal flora but are also commonly isolated from patients with urinary tract infections, as well as from hospitalized patients with blood stream infections and nosocomial pneumonia. CRE-related infections are associated with a high mortality rate, as much as 50% in some reports.

In addition to resistance to almost all β-lactams including carbapenems, CRE tend to show high levels of resistance to other classes of antibiotic agents due to the frequent occurrence of other resistance genes on the same mobile genetic elements (1). Furthermore, a multitude of genes conferring resistance have been identified in countries around the world, making this truly a global concern. Resistance mechanisms spread quickly to resident or colonizing enterobacteria in the healthcare setting, creating a potential reservoir for outbreaks in hospital wards and long-term care facilities. Table 1 shows the classification of carbapenemases, the enzymes CRE produce that mediate resistance to antimicrobials. The most common carbapenemase in the United States is Klebsiella pneumoniae carbapenemase (KPC), which was first reported in a clinical specimen from a patient in North Carolina in 2001.

Implications for Clinical Microbiology Laboratories

Laboratories should establish clear definitions and cutoff parameters to detect CRE (2). The typical susceptibility profile for carbapenemase-producing enterobacteria is resistance to carbapenems, penicillins, cephalosporins, and aztreonam, as well as resistance or intermediate susceptibility to ertapenem, imipenem, and meropenem using original interpretative criteria.

CLSI issued lowered interpretative criteria in June 2010 (M100-S20) that may not require confirmation testing (Table 2). However, some laboratories still use Food and Drug Administration (FDA) cutoffs for susceptibility testing they perform on automated instruments. Reporting policies and algorithms should be designed and followed carefully to avoid under- or over-reporting—and most importantly—to recognize possible outbreaks.

Laboratories may need to perform additional testing if results are uncertain. These include the modified Hodge test (MHT), carba-NP test, and PCR tests for carbapenemases. The MHT detects in vivo production of carbapenemases, but the technique is time-consuming and often lacks specificity. In addition, it not uncommonly produces false-positive results for high-level AmpC producers and CTX-M-type ESBL producing Enterobacter spp., and has poor sensitivity associated with NDM producers. It does work well, however, for detecting KPC and OXA-48 producers (3).

Microbiology laboratories must also offer susceptibility testing for some drugs that have no breakpoints recommended by CLSI or FDA, such as colistin and tigecycline, as well as newer drugs with susceptibility dilution gradient strips or disks that are not yet FDA-cleared, such as ceftazime-avibactam. Each laboratory should establish a policy on how to test and report these agents.

Another issue associated with CRE is screening patients for gastrointestinal carriage of these strains. In exploring the best way to process and report these samples, laboratories need to collaborate with all parties involved, including infectious disease, infection control, pharmacy, and clinical and nursing staff.

Implications for Infection Control

Due to the potential risk of CRE spreading among hospitalized patients—especially in those with invasive monitoring and treatment devices—any CRE isolated from inpatient samples of any source should be reported to and investigated by a hospital’s infection control personnel (4). Monitoring positive cases not only provides useful statistics but also enables the hospital to implement containment and preventive measures, including strict hand hygiene, contact precautions, healthcare personnel education, minimal use of devices, positive case isolation, antimicrobial stewardship, and screening for CRE carriage (Table 3) (5).

Clinical Implications

The biggest challenge for clinicians is determining an appropriate antibiotic regimen to treat infections with CRE. As previously noted, carbapenemase-producing organisms tend to be resistant to most other antibiotic classes, leaving very few antimicrobial options available. These options include polymyxins, newer aminoglycosides, tigecycline, and ceftazidime-avibactam.

Several combination therapy strategies have been explored, such as high-dose prolonged-infusion carbapenem therapy plus one of the previously listed agents (6). Other authors have explored the use of double-carbapenem therapy, finding that, for example, the combination of doripenem and ertapenem demonstrated enhanced efficacy over either agent alone (7). Published data indicate that combined regimens are independently associated with survival (8).

A review comparing monotherapy versus combination found mortality with colistin monotherapy was as high as 57%, compared with 67% for carbapenem-colistin and up to 64% for tigecycline-colistin. Mortality in cases of monotherapy with tigecycline was up to 80% versus 50% with tigecycline-gentamicin combination (9).

Unfortunately, there have been reports of isolates resistant to colistin, including an outbreak in Michigan (10). However, new drugs have entered the battle against CRE. FDA recently approved ceftazidime-avibactam (Avicaz, Actavis Labora­tories) to treat complicated intra-abdominal infections and complicated urinary tract infections. This combination agent—which includes a cephalosporin and a new-lactamase inhibitor with activity against KPC—should be used only in patients with no other available therapy (11).

Screening for Gastrointestinal CRE Carriage

CRE screening can be done either universally on all new admissions to the hospital using rectal swabs or whenever positive cases are identified. The former is still not a widely used or recommended practice as few studies have explored its benefits (12). On the other hand, the majority of healthcare institutions practice the latter for point prevalence studies or to screen epidemiologically linked patients. Point prevalence studies are effective to assess the prevalence of CRE quickly in certain services or units where CRE cases have been detected recently (4). Screening epidemiologically linked contact extends the scope of investigations and might be useful for cases in which patients have been transferred between several hospital services.

Rectal swabs are the most frequent screening method, but sample processing and result analysis have not been well standardized. The Centers for Disease Control and Prevention (CDC) recommends culturing these specimens using traditional culture media (Table 4). However, this process is lengthy and time consuming as it requires a selection/enrichment phase before plating and work-up (13). Commercial chromogenic agars and rapid screening methods do not have FDA clearance for in vitro diagnostic use in the U.S., but are available for research purposes.

Data published evaluating the use and performance of these products is still limited. Moreover, the phenotypical patterns of resistance to carbapenems vary significantly among the different resistance mechanisms. Some of these methods only detect high levels of carbapenem resistance and therefore are not suitable to screen for all types of CRE (14) (15).

Medical Equipment as Source of Outbreaks

In February 2015, the chief medical and quality officer and the medical director of clinical epidemiology and infection prevention at UCLA Health System gave a press conference in Los Angeles after an outbreak in CRE infections associated with the use of contaminated duodenoscopes. Shortly thereafter, FDA published its first warning about the use of duodenoscopes without recommending discontinuing their use. In May 2015, FDA gathered a panel of experts that supported the decision not to discontinue the use of duodenoscopes, despite finding that their design makes them extremely difficult to sterilize. Problems with duodenoscope sterilization had been noted as early as April 2009. Additional cases had been reported in multiple other cities in the intervening years, prompting some investigations and reports (16) that were not widely disseminated in the medical community until the UCLA outbreak. FDA asked duodenoscope manufacturers to review and update their cleaning and disinfecting procedures; however, it appears that adequate sterilization may not be possible without changing the design of the devices, prompting manufacturers to start exploring new safer duodenoscope designs.

CRE Species and Resistance

The Centers for Disease Control and Prevention’s proposed definition of CRE includes all those that are non-susceptible to carba­penems—ertapenem, doripenem, meropenem, or imipenem—and resistant to all of the following third-­generation cephalosporins: ceftriaxone; cefotaxime; and ceftazidime. For surveillance purposes, only the most common carbapenemase producers that are frequently isolated in each individual institution should be monitored using minimum inhibitory concentration (MIC) or zone size interpretations recommended by the Food and Drug Administration (FDA) or the Clinical and Laboratory Standards Institute (CLSI).

The enterobacterial species most commonly found to be CRE are Klebsiella spp., Escherichia coli, and Enterobacter spp. However, other Enterobacteriaceae and non-Enterobacteriaceae such as Pseudomonas aeruginosa and Acinetobacter spp. can also acquire these resistance mechanisms. The most commonly used epidemiological surveillance definition employs the susceptibility breakpoints established by CLSI in 2012 (M100-S22, 2012). Ertapenem is the usual “indicator drug” since most carbapenemases confer resistance to it.

Broad-spectrum β-lactamase enzymes called carbapenemases mediate resistance to carbapenems in CRE by hydrolyzing the antimicrobials. However, resistance can also occur when an isolate produces an extended-spectrum cephalosporinase, such as an AmpC-type β-lactamase, in combination with porin loss. The Ambler molecular classification system based on amino acid homology is the most commonly used system to classify β-lactamases. Ambler designates four enzyme classes. Carbapenemases are usually class A or class B enzymes but can also belong to class D (17). Class A enzymes typically are called serine proteases due to the presence of an active serine in position 70.

Carbapanemases in this group can have chromosomally encoded carbapenem resistance genes or plasmid mediated resistance genes. Class B enzymes are also known as metallo-β-lactamases because they contain zinc. These resistance genes can also be either chromosomally encoded or plasmid mediated. Class D enzymes hydrolyze oxacillin instead of penicillin and are mainly transmitted in plasmids; the carbapenemases that belong to this group (OXA 23, 24 / 40, or 58) are mainly found in Acinetobacter spp. and Pseudomonas spp.


The carbapenemases are broad-spectrum β-lactamases, including metallo-β-lactamases, serine proteases, or OXA-β-lactamases. CRE carbapenemases result in resistance to penicillins, cephalosporins, carbapenems, and monobactams. The most common carbapenemases in North America are plasmid-borne KPCs. CRE can be transmitted through contaminated equipment and material which constitutes a public health risk. New antibiotic options are being developed, with one agent, ceftazidime-avibactam, now available for clinical use.


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