Carbapenem Resistant Enterobacteriaceae

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Continuing Education Activity

Gram-negative bacterial resistance to antibiotics has decreased the physician’s ability to combat infection. Carbapenems are the most potent beta-lactam antibiotics for resistant bacteria, but carbapenem-resistant bacteria inactivate this class of antibiotics. This activity outlines the evaluation and management of carbapenem-resistant infections and reviews the role of the interprofessional healthcare team in evaluating, treating, and managing patients with this condition.


  • Outline the treatment considerations for a patient with carbapenem-resistant Enterobacteriaceae infections.
  • Describe the reasons for a delayed diagnosis of carbapenem-resistant bacterial infections.
  • Review the etiology of carbapenem-resistance and its various mechanisms.
  • Identify the importance of collaboration and communications among the interprofessional team to improve outcomes for patients affected by carbapenem-resistant bacterial infections.


Antibiotic resistance is a growing problem. Resistance genes exist for all known antibiotics in use today, and extremely resistant pathogens are becoming more common. Gram-negative bacteria have developed the broadest spectrum of resistance due to multiple structural adaptations and antibiotic degradation enzymes, including expanded spectrum beta-lactamases (ESBL), AmpC cephalosporinases, and carbapenemases. Carbapenemase-producing Enterobacteriaceae (CRE) are of particular concern.

Carbapenem antibiotics are typically reserved for treating ESBL and AmpC producing bacteria.[1] Structurally, carbapenems are similar to penicillins but have the addition of a carbapenem ring. Both antibiotics degrade the bacterial cell wall at the penicillin-binding protein via a beta-lactam ring. The carbapenem groups of these antibiotics act to protect the beta-lactam ring from some degratory enzymes produced by the bacterium.

Care is necessary when diagnosing, treating, and preventing CRE infections. Bacteria may have multiple resistance mechanisms to carbapenems, but the most common is carbapenemase enzyme production.[2][3][4] These carbapenemase-producing carbapenem-resistant Enterobacteriaceae (cpCRE) use diverse moieties to degrade antibiotics. Other resistance mechanisms include increased efflux pump-action and specific porin blocking at the bacterial cell membrane to limit permeability of the antibiotics, rendering them ineffective.


Carbapenemase enzymes categorize into three groups: Ambler Class A, B, and D.

The most common Class A carbapenemases include KPC (Klebsiella pneumoniae carbapenemase) and IMI (Imipenem-hydrolysing beta-lactamase). KPC is the most prevalent carbapenemase gene amongst all cpCRE.[5]

Class B is defined by a metallo-beta-lactamases (MBL) structures. These enzymes include NDM (New Delhi metallo-lactamase), IMP (Imipenem-resistant Pseudomonas), and VIM (Verona integron-encoded metallo-lactamase). These carbapenemases are usually found on plasmid vectors and other transposable elements, allowing them to spread between bacteria. Due to a high sequence variability of 15% to 70%, these enzymes are difficult to detect with molecular testing, slowing investigations to more fully understand their prevalence.[5]

OXA (Oxacillin-hydrolysing carbapenemase) enzymes make up class D carbapenemases. These genes are genetically similar to ESBL genes, thus making them difficult to differentiate on molecular testing from other ESBL producers.[4] OXA-48 is the most common isolate in this class and is typically found in Klebsiella pneumoniae.


Class A KPC is the most common cpCRE. It is endemic to regions in China, India, Saudi Arabia, Greece, Columbia, and Brazil, but rare in the United States, Australia, and France.[6] Little is known about cpCRE prevalence in Africa. Current epidemiology suggests NDM-1 as the most common cause of carbapenem resistance.[7] Due to international travel, researchers have identified all carbapenemase genes throughout the world.

Molecular testing has been the most effective way of understanding the epidemiology and spread of cpCRE. It can identify specific strains of CRE and map their range within a hospital or across the world. Though uncommon, regional genetic drift in carbapenemase genes may hinder the molecular identification of CRE strains, which could cause phenotypic resistance that is missed by assays that detect specific gene sequences.

Patients usually acquire cpCRE infections in the hospital and long term care facilities.[8] The majority of these patients have a long history of health-care facility exposure due to unrelated diagnoses. If a patient is found to have a CRE infection, healthcare personnel need to utilize proper infection control protocols for the prevention of localized outbreaks.


The prototypical beta-lactam antibiotic, penicillin G, is a simple beta-lactam ring with few R groups. It impairs the function of the bacterial cell wall at the penicillin-binding protein (PBP), leading to the destruction of the organism. The synthesis of beta-lactamases can induce bacterial resistance to this antibiotic. These enzymes hydrolyze penicillin at its beta-lactam ring. Variations of penicillins like cephalosporins or carbapenems have a similar mechanism of action at the PBP but can shield their beta-lactam ring from beta-lactamases with R groups on the adjacent thiazolidine ring without hindering the beta-lactam function. Bacterial beta-lactamases have evolved to circumvent the carbapenem R group shield rendering the antibiotic susceptible to degradation. Carbapenemases are beta-lactamases active against carbapenem antibiotics.

Pathogenic bacteria have gained the ability to circumvent carbapenem hydrolysis through intrinsic and acquired mechanisms. These mechanisms include enzymatic inactivation, porin selectivity, and efflux pumps. The earliest instances of carbapenem resistance appeared in bacteria with intrinsic resistance. These bacteria are typically opportunistic pathogens or environmental organisms that rarely cause infection. Aeromonas hydrophilia, Serratia marcescens, and Enterobacter cloacae were some of the first environmental organisms discovered to cause carbapenem resistance infections[9]. Researchers found extrinsic resistance on plasmids, which spread via bacterial conjugation and which they discovered a few years after first describing intrinsic carbapenem resistance.[10]

Because Gram-negative bacteria have a cell wall and cell membrane, they are better able to control what molecules pass through their outer membrane. This wall/membrane means bulky carbapenem molecules require transport into the bacterial intermembrane space via porin channels to break down the PBP. Thus, porin channels may act as a filter preventing carbapenems from reaching their site of action. Efflux pumps work at this space to remove the irregular or hostile molecules and antibiotics, further regulating the intramembrane environment. The majority of non-cpCRE resistance mechanisms act at this space to prevent degradation of the cell’s defenses without the production of a carbapenem specific beta-lactamase.[4] Researchers well understand that Pseudomonas has intrinsic resistance to ertapenem, and the likely reason is due to the lack of a porin that will let the large ertapenem molecule into the intermembrane space. In some strains, Pseudomonas aeruginosa uses a combination of increased efflux pump expression with down-regulation of OprD porin, leading to increased imipenem resistance. OprD porin resistance to imipenem has also appeared in Enterobacter aerogenes and Klebsiella spp.[11]

History and Physical

Many sites can be the source of CRE, including the urinary tract, lungs, abdomen, surgical site, and bloodstream. Typically patients with CRE infections have a history of long term exposure to health care facilities usually due to unrelated comorbidity. This exposure usually coincides with long term and varied antibiotic use leading to the gradual development of more and more resistant bacterial infections. Other risk factors include travel to an endemic area of CRE, immunocompromised state, mechanical ventilation, and advanced age. All these factors combine to make healthcare-associated CRE the most important factor in the spread of carbapenem resistance and are key points in a patient’s history.

CRE genes do not confer increased pathogenicity, making initial presentation similar to other infections caused by a less resistant strain of the same organism. The key indicator of CRE infections may be the uncontrolled progression of the illness, leading to a more advanced disease state despite empiric antibiotic intervention. Therapeutic failure of empiric therapy may indicate a resistant organism, possibly CRE; a definitive diagnosis of CRE takes place in the lab via phenotypic or molecular techniques.


Phenotypic diagnosis requires bacterial culture and identification. Disk diffusion or automated susceptibility testing is done to identify the carbapenem resistance phenotype. By referencing MIC breakpoints, the final diagnosis of carbapenem resistance is possible. The drawbacks of this process include delayed diagnosis and limited information on specific resistance mechanisms.

Molecular identification is much faster (hours instead of days) and can quickly determine the type of resistance mechanism involved. However, this method simply indicates the presence of a resistance gene and may not determine the efficacy of specific antibiotics. Early detection of CRE infections helps improve treatments and decrease the likelihood of spreading the infection. The most common modality of detection is multiplex PCR and microarray technologies. The development of new molecular assays continues.

Matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) is the newest technology applied to the identification of CRE. This technique uses laser ionization of bacterial proteins to create a proteomic profile. Beta-lactamase and metallo-beta-lactamase specific information are then extrapolated from the profile to determine CRE status.[12] This method is demonstrated to have 98.9% and 97.1% sensitivity and specificity, respectively. Cost, lack of access to MALDI-TOF units, and relative newness of this method are the most significant barriers to further utilization of this diagnostic modality.

Treatment / Management

Treatment of CRE depends on the site of infection, pathogen isolated, resistance profile, and species-specific native resistances (see Table 1). Since CRE have developed resistance to preferred antibiotics, second-line therapies are necessary. Due to the complexity and variability of possible treatments, plans should be driven by in vitro susceptibility testing.[13] An infectious disease specialist and microbiologist should be consulted. Antibiotics that may have activity against CRE include carbapenems, polymyxins, aminoglycosides, tigecycline, fosfomycin, and beta-lactam/beta-lactamase inhibitors (BLBLI).

Combination therapy with multiple unrelated antimicrobial agents has been shown to decrease mortality in the setting of high-risk infections where death is a likely outcome. These data are best described in bloodstream infections (BSI) and septic shock with Class A carbapenemase-producing organisms. Typically treatment is centered on a polymyxin backbone coupled with other targeted antibiotics (see Table 2). This data has its basis from meta-analyses of different CRE therapies, which demonstrated lower mortalities when using polymyxin based treatment, and researchers found synergy between the triple combination of polymyxin, carbapenem, and rifampin or tigecycline.[14][15][16][17] Where available, fosfomycin has also shown increased effectivity in CRE infections and may be considered in triple therapy.[18] In theory, carbapenems (ideally with MIC <16), may have some activity when used in combination with antibiotics of different mechanisms.[15][17] It bears mention these conclusions are extrapolated from a handful of mainly retrospective studies, and further research is needed. Less evidence exists for the role of carbapenem/beta-lactamase inhibitors (CBLI) for treating high-risk infections, but may be considered as a carbapenem alternative in triple therapy.[19]

Relative contraindications for specific dual therapy include polymyxin with an aminoglycoside due to increased kidney injury. Antibiotics from the same class may be contraindicated due to an increase in toxic side effects without added therapeutic benefit. Less data is available for the treatment of infections due to Class B and D carbapenemases. Limited data suggest targeted dual and triple therapy with a similar polymyxin backbone for the treatment of OXA and MBL producing CRE[20].

Polymyxin-resistance CRE (see Table 1) should have treatment with a tigecycline backbone and either an aminoglycoside, fosfomycin, or polymyxin and rifampin depending on susceptibilities.[2][3][21] If facing a pan-resistant infection, a cocktail of meropenem, plus ertapenem (double carbapenem regimen) or ceftazidime-avibactam, plus aztreonam has been a suggestion despite in vitro resistance to individual antibiotics due to presumed synergistic activity, though data in this subgroup is poor.[20] If available, investigational drugs and therapies could merit consideration in the setting of pan-resistance.

Treatment of non-life threatening CRE infections continues to be driven by susceptibility testing. Although no randomized control trials have been done in this population strictly comparing monotherapy to combination therapy, there is little evidence demonstrating decreased mortality with polymyxin based combination therapy to targeted monotherapy.[22][21] Careful monitoring of disease progression and emerging resistance is advisable if using monotherapy in treating such infections.

Complicated urinary tract infections (cUTI) with CRE present in patients with recurrent UTI who have had repeated exposure to multiple antibiotics. Susceptibility and urine drug concentrations should drive effective antibiotic therapy. Aminoglycosides and fosfomycin are preferred therapies for cUTI if susceptible.[18] KPC is typically resistant to aminoglycosides and fosfomycin, making tigecycline and colistin useful in these cases.  Meropenem-vaborbactam monotherapy has been demonstrated effective against KPC-producing bacteria and now has FDA approval for cUTI; however, OXA and MBL CRE can be resistant to this antibiotic.[19]

When treating complicated intra-abdominal infections (cIAI) and soft tissue infections, tissue perfusion, and susceptibility testing help to guide therapy. Tigecycline is often useful as initial therapy for antibiotic-resistant cIAI, but newer BLBLI are becoming increasingly popular.[20][23] Ceftazidime-avibactam and meropenem-vaborbactam reach adequate tissue levels in the abdomen and are effective treatments.[20] The research on this is limited, but ceftazidime-avibactam shows efficacy in vitro during animal studies against KPC and OXA-48 producing CRE.[24] Also, some research suggests the addition of metronidazole improves outcomes of cIAI in CRE infections.[25]

When treating bloodstream infections (BSI), it is important to note that standard dose tigecycline does not usually reach therapeutic blood levels. Doubling the dose to 200 mg for loading and continuing therapy with 100 mg twice daily has been recommended.[26] Fosfomycin should not be used as monotherapy when treating BSI in countries where intravenous formulations are available.

Polymyxin B or inhaled colistin are possible antibiotics for the treatment of localized pneumonia due to CRE, and commonly used in cycstic fibrosis patients.[27] Tigecycline and aminoglycosides are effective treatments for pneumonia when susceptible, but have poor lung penetration. Thus higher doses should be considered when using these antibiotics to treat pulmonary infections.

Differential Diagnosis

Possible causes of carbapenem antibiotic resistance:

  • Carbapenemase production
  • Decreased porin expression
  • Increased efflux pump action


Complicating factors during diagnosis and treatment of CRE is identifying resistance to previously discussed drug regimens. Commonly induced resistance mechanisms in CRE to other active antimicrobials include aminoglycosides, fosfomycin, and BLBLI.

The acquisition of a single point mutation in the 16S rRNA methyltransferase leads to resistance of all aminoglycosides.[28] This mutation can occur de novo or in combination with other resistance mechanisms. It is best studied in NDM cpCRE but can also be present in many other carbapenem producers.[29] Fosfomycin resistance is common in E.coli, but many other Enterobacteriaceae, including ESBL and CRE, do not demonstrate resistance. Resistance to this drug is typically seen by selecting for resistant microbes through monotherapy of fosfomycin.[30] Ceftazidime-avibactam generally is used for OXA-48 and KPC CRE, but when resistance appears among these isolates, mutations in bla and bla induce resistance, respectively.[31]


If a patient demonstrates infection with CRE, an infectious disease consult is necessary. Specialized tests may also need to be run by a microbiologist and thus should be involved in definitive diagnosis and treatment planning.

Deterrence and Patient Education

Any CRE infection is considered complicated, and patients need to understand the risks of their disease. They must understand the risks and benefits of specific therapies for CRE, as well. These risks include but not limited to, nephrotoxicity, ototoxicity, GI effects, QTc prolongation, and paresthesia. In the event of recurrent or colonized CRE, patients should be aware of the increased future risk of pathogenic CRE.

Enhancing Healthcare Team Outcomes

CRE outbreaks are usually uncommon and isolated to institutional or geographic regions. The prevalence of community-acquired CRE has been reported to be 0% to 29.5%, and early screening detection of CRE-colonization in patients can help prevent or limit outbreaks via proper isolation methods.[4] Long term care facilities have been shown to have lower rates of CRE than acute care hospitals, but this may be due to poor detection and surveillance methods.[32] Any healthcare facility should be aware of the risk CRE poses to patients and should take part in regular institutional, local, and national surveillance. An epidemiological assessment should accompany any case of CRE into etiology to limit further spread.

Examples of how an interprofessional team approach applies in the case of CRE infections is bringing in an infectious disease specialist, as well as an infectious disease board-certified pharmacist. They will be more familiar with the latest antibiogram data and resistance patterns and help the team to focus therapy appropriately. Nurses need to be familiar with the proper administration of these drugs, as well as their common adverse events so that they can report any concerns to the team as they develop. These scenarios demonstrate how an interprofessional team can best address the management of therapy for these infections. [Level 5]

(Click Image to Enlarge)
Notable Intrinsic Drug Resistance
Notable Intrinsic Drug Resistance
Hayden Smith, MD

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Possible Treatment Regimens for High-Risk Infections
Possible Treatment Regimens for High-Risk Infections
Hayden Smith, MD
Article Details

Article Author

Hayden Z. Smith

Article Editor:

Brian Kendall


1/16/2023 8:14:56 PM



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