Clinical and Health Affairs
A Review of Multidrug-Resistant Enterobacteriaceae
By Edwin C. Pereira, M.D., Kristin M. Shaw, M.P.H., Paula M. Snippes Vagnone, M.T. (ASCP), Jane Harper, B.S.N., M.S., CIC, and Ruth Lynfield, M.D.
In early 2009, a 50-year-old man with gastric cancer was admitted to a Minneapolis-St. Paul area intensive care unit (ICU) with severe dehydration and presumed Clostridium difficile infection. He spent a month in the hospital and was treated with several broad-spectrum antibiotics before being discharged to a local long-term acute care hospital. Midway through his hospitalization, a tracheal aspirate culture grew Klebsiella pneumoniae that was resistant to all cephalosporins and carbapenems. Polymerase chain reaction (PCR) testing by the Centers for Disease Control and Prevention (CDC) confirmed that the isolate carried the resistance gene for K. pneumoniae carbapenemase (KPC), blaKPC. This was the first time this highly resistant bacterium was detected in Minnesota.
Choosing the right antibiotic for the right microbe is becoming increasingly difficult. Gram-negative organisms carrying multiple resistance genes that make them extremely drug-resistant have emerged; some are even pan-drug-resistant. The emergence of these highly resistant bacteria is rapidly changing the way health care providers and public health officials approach the treatment and control of bacterial infections, requiring us to invest heavily in the development of new antibiotics and to practice careful antimicrobial stewardship and infection control and prevention.
Brief History of ß-Lactamases
Among the many resistance mechanisms available to bacteria for circumventing antibiotics are the ß-lactamases, enzymes that target the ß-lactam ring found in penicillins, cephalosporins, monobactams, and carbapenems. They are naturally found in most Gram-negative bacteria (GNB).
Gram-negative resistance became a clinical concern soon after the introduction of ampicillin, the first semisynthetic penicillin shown to be active against GNB. In 1963, a strain of Escherichia coli discovered in Athens carried the first plasmid-encoded ß-lactamase, named TEM-1, which conferred resistance against ampicillin.1 As different resistance mechanisms have evolved, plasmids and other mobile genetic elements have been instrumental in the horizontal transmission of resistance genes, with multiple genes conferring resistance to multiple antibiotics.
Plasmid-mediated ß-lactamases have spread worldwide. TEM-1 and another ß-lactamase, SHV-1, once were the most frequently occurring enzymes among the Enterobacteriaceae.2 By the 1970s, resistant GNB had become the prominent nosocomial pathogen. Many of these organisms carried plasmids encoding multiple antibiotic-resistant genes in addition to ß-lactamases. Interestingly, TEM-1 and SHV-1 remained relatively unchanged for 20 years. However, in the early 1980s, several new antibiotics were introduced, including third-generation cephalosporins. By 1983, the first extended-spectrum ß-lactamase (ESBL) was found in strains of Klebsiella isolated in Germany. These mutants of SHV-1, designated SHV-2, inactivated the extended-spectrum cephalosporins.3 As these enzymes mutated to make different classes of antibiotics inactive, the number of identified ß-lactamases has multiplied, and there are now hundreds.
The latest iteration of ß-lactamases is the carbapenemase. This enzyme inactivates carbapenem, a class of antibiotics indicated for the treatment of ESBL-producing bacteria. The most common carbapenemase is the KPC, which was first isolated in North Carolina in 1996.4 K. pneumoniae carbapenemase has spread worldwide and has been responsible for a number of reported outbreaks of carbapenem-resistant Enterobacteriaceae (CRE). Hospitals in New York and New Jersey have been particularly affected. The most recent data collected by the CDC show that CRE caused by the KPC enzyme have been reported in 36 states.5
Another emerging carbapenemase is NDM-1, a metallo- ß-lactamase first isolated from a Swedish patient of Indian decent who had frequent hospitalizations in India.6 Metallo-ß-lactamases differ from other ß-lactamases in that they require zinc for the active site instead of the amino acid serine. NDM-1 has been associated with receiving medical care in India and Pakistan, and is now the most common carbapenemase in the United Kingdom.7 Metallo-ß-lactamases are not inactivated by monobactam antibiotics such as aztreonam, but isolates recovered in the United States carrying NDM-1 have expressed additional resistance to monobactams, presumably through a secondary resistance mechanism.8
Local to Global Transmission
The evolution of the ß-lactamases demonstrates that resistance mechanisms are in constant flux. Most concerning is how readily plasmid-mediated ß-lactamases are transferred between species of Enterobacteriaceae. Bacteria with mutations that confer resistance are expected to thrive when selective pressure caused by antibiotics occurs. Horizontal transmission of KPC between Enterobacteriaceae species within a single patient has been documented.6,9,10 Surveillance cultures from documented cases have revealed that a different species of Enterobacteriaceae isolated from a different site harbored the same resistance gene as the original organism that infected the patient.
Beyond the transmissibility of genes via plasmids, the multidrug-resistant Enterobacteriaceae are readily spread within hospitals, between health care facilities, and across national borders. A surveillance study of multidrug-resistant GNB (defined as resistance to three or more different antibiotic classes) by D’Agata showed an increase from 0.5% to 17% of multidrug-resistant K. pneumoniae isolates in a U.S. tertiary care hospital between 1994 and 2001.11 The Meropenem Yearly Susceptibility Test Information Collection (MYSTIC) Program reported 10.9% of Klebsiella spp. and 3.1% of E. coli isolates with ESBL from 15 U.S. medical centers in 2005.12 MYSTIC data from 41 medical centers in 11 European countries in 2004 revealed 13.6% of Klebsiella spp. and 10.8% of E. coli isolates with ESBL.13
Klebsiella pneumoniae carbapenemase and other carbapenemases have not been disseminated to the extent that ESBLs have, but outbreaks have been documented worldwide. Particularly well-documented was a KPC outbreak in New York City hospitals, where 38% of K. pneumoniae isolates were KPC-positive. Isolates from 10 area hospitals were examined. Seventy-eight of 95 KPC-positive isolates belonged to the same ribotype, demonstrating likely transmission between facilities.14,15 Reports of KPC outbreaks have come from several other countries as well. In 2009, a tertiary care hospital in Greece reported an outbreak of KPC-producing K. pneumoniae that began in May 2007. The majority of patients identified with KPC were housed in the ICU. During this outbreak, a total of 61 KPC-producing K. pneumoniae isolates were recovered from 23 patients. The hospital instituted outbreak control measures including adherence to strict hand hygiene practices and contact precautions. The outbreak culminated with closure of the ICU for decontamination in January 2008, after which only three additional patients with KPC-producing K. pneumoniae isolates were identified.16
Multidrug-resistant GNB also have been detected in Minnesota, and ESBL-producing organisms are already frequently seen in both inpatient and outpatient isolates. In February 2009, the first blaKPC gene in a KPC isolate was confirmed by PCR by the Department of Health’s Public Health Laboratory. The number of identified KPC isolates is not as high as that reported from the Northeast,14 but isolates continue to be identified. It is not uncommon for these highly resistant isolates to be recovered from patients with a history of travel to or prior hospitalization in areas where KPCs are endemic. Even though the East Coast is considered the epicenter of KPC infections in the United States, outbreaks in health care facilities as close as Chicago have been documented.17 Prompted by reports of outbreaks and the high case-fatality rates of patients with KPC-positive isolates, the Minnesota Department of Health began tracking CRE, specifically KPC, in early 2009. To date, the health department has tested more than 70 unique modified Hodge test-positive isolates for blaKPC, of which 25 (36%) had the blaKPC gene. Although the Department of Health has been alert to other carbapenemases such as NDM-1 and VIM, it currently tests only for blaKPC by PCR. Only a handful of isolates from Minnesota have been sent to the CDC for blaNDM-1 or blaVIM characterization by PCR. All have tested negative.
Long-term care facilities and long-term acute care hospitals play a major role in multidrug-resistant Enterobacteriaceae transmission. Residents of these facilities are frequently hospitalized for prolonged periods, during which they may be exposed to multidrug-resistant Enterobacteriaceae and often receive multiple courses of broad-spectrum antibiotics. These are ideal conditions for colonization with these organisms. A study looking at long-term care facilities documented a significant rise in infections caused by multidrug-resistant GNB over a two-year period, during which the prevalence surpassed that of methicillin-resistant Staphylococcus aureus and vancomycin-resistant enterococcus.18 Given their increasing presence, it is important that all health care facilities pay attention to infection prevention and control measures and communicate the history of colonization or recent infection with multidrug-resistant Enterobacteriaceae when patients are transferred between facilities.
As we witness CRE flow in and out of hospitals with increasing prevalence, it is no surprise that we also see movement between countries. Medical tourism is a particularly concerning means by which patients are exposed to resistant bacteria. Travel to India and Pakistan has been linked to recent identification of the NDM-1 enzyme in Europe, the United States, and Canada.7,8,19
Treatment Limitations and Morbidity
With the plethora of antibiotics available, it is difficult to accept that certain infections are untreatable. The carbapenems (ertapenem, imipenem, meropenem, and doripenem) have typically been the last-line, broad-spectrum antibiotic of choice for resistant organisms. The emergence of CRE presents new challenges. Clinicians have been forced to use alternative antibiotics such as tigecycline and the polymixins (polymixin B or colistin) to treat infections caused by CRE. Tigecycline, which is FDA-approved for the treatment of complicated skin and skin structure infections, intra-abdominal infections, and certain types of community-acquired pneumonia, has been used off-label for the treatment of CRE infections. One concern with tigecycline is that poor serum levels are achieved, which may make it insufficient for treating certain infections. The polymixins, which were introduced decades ago, are nephrotoxic, which limits their use. Concerns about toxicity have eased as we have become more knowledgeable about the pharmacokinetics of polymixins.20
Unfortunately, new resistance mechanisms and antibiotic misuse are making CRE a major public health threat. An increased risk of mortality associated with CRE has been well- documented.21-23 In locations where CRE are not endemic, empiric treatment typically does not include coverage for CRE. Thus, delays in diagnosis and inexperience with treatments for CRE can increase the likelihood of poor outcomes. Even in areas where CRE are common, mortality has increased. A case-control study of patients with invasive K. pneumoniae infections in a large tertiary care hospital in New York City showed an increased mortality rate (48% versus 20%) in patients with a carbapenem-resistant K. pneumoniae infection. This study also noted an average of 3.2 days between specimen collection and initiation of antibiotics with in vitro activity against the carbapenem-resistant K. pneumoniae isolate, compared with 0.8 days for control patients.22
Identification Challenges
The challenge of confronting multidrug-resistant Enterobacteriaceae is not only one of antibiotic resistance but also one of definitions and identification. Although we are familiar with the ß-lactamases, the nomenclature surrounding the hundreds of different enzymes that exist can be overwhelming. Multidrug-resistant Enterobacteriaceae constitute an entire family of bacteria. The ß-lactamases vary from chromosomally to plasmid-mediated, and can be induced or constitutively expressed; they also have a spectrum of antibiotic targets. It is not uncommon for highly resistant organisms to carry more than one ß-lactamase or other resistance mechanisms such as decreased porin production that enhance the resistance phenotype. Labeling such bacteria is difficult. Terms such as “multidrug-resistant,” “KPC-producing,” or “CRE” can be confusing and nonspecific.
The ability of laboratories to detect carbapenem resistance is limited, as many of the common screening methods have been shown to have poor sensitivity to KPC producers.24,25 The modified Hodge test, an agar/antibiotic disk-based test, has been used as a confirmatory test with good sensitivity and specificity for detecting blaKPC when compared with PCR testing.24 The limitations of this test are that it is subject to reader interpretation and that it does not distinguish between different mechanisms of carbapenem resistance. Also, the test adds another step to the identification process, delaying the time until clinicians receive a final result, and requiring extra time and resources that some laboratories do not have.
Molecular testing such as PCR seems to be the ideal way to detect these enzymes, but PCR testing is often only available at reference laboratories. Even more promising is the development of microarray technology for the rapid identification of multiple-resistance genes from a single isolate, although the clinical utility of this technique needs to be assessed.26,27
Shifting Breakpoints
Microbiology laboratories in the United States follow guidelines issued by the Clinical and Laboratory Standards Institute (CLSI) for interpreting and reporting susceptibility data to clinicians. Susceptibility breakpoints for Enterobacteriaceae were revised in 2010 for cephalosporins (Table 1) and carbapenems (Table 2). Along with these changes came new recommendations for reporting resistance and conducting confirmatory tests for ß-lactamase production. Previously, laboratories were instructed to perform ESBL screening and confirmatory tests on appropriate isolates and, if positive, change the susceptibility results of penicillin, cephalosporins, and aztreonam from susceptible to resistant. The new recommendations lower the breakpoints for several cephalosporins, and the CLSI no longer recommends supplementary testing for ESBL. Instead, the CLSI recommends that laboratories report susceptibility results without applying resistance rules based on confirmatory test results. These changes were made in response to availability of additional data that conferred a better understanding of ß-lactamases and of pharmacokinetic and pharmacodynamic properties of cephalosporins.28 The carbapenem breakpoints were also lowered and the CLSI no longer recommends performing a modified Hodge test for carbapenemase during routine testing. The changes for carbapenem breakpoints were made for similar reasons, in addition to reports showing deficiencies of common laboratory methods to detect carbapenem resistance using the previous breakpoints.24,25
The logistics involved in the CLSI changes further add to the complexity of dealing with multidrug-resistant Enterobacteriaceae. This is because the Food and Drug Administration must approve breakpoint recommendations on automated kits and devices, and approval has not yet been granted. Laboratories are able to follow either recommendation to remain in good standing. A validation study using disk diffusion can help laboratories convert to the new CLSI breakpoints (see IDSA alert at www.idsociety.org/Content.aspx?id=17429).
During this transition period, there will be inconsistencies between laboratories regarding labeling of ESBLs and CREs. Different laboratory interpretations of minimum inhibitory concentration (MIC) values will lead to confusion among clinicians about when it is appropriate to use an extended spectrum cephalosporin, a carbapenem, or neither. Since these determinations are also linked to infection prevention and control practices, there may be discordant practices among clinicians. The hospital pharmacist also will need to be aware of these issues so that he or she can provide advice on the appropriate antibiotic choice. Improved interdepartmental communication within hospitals during this transition period is necessary.
Effective Prevention Measures
Amidst the failure of antibiotics and the confusion generated by resistant organisms, there has been some success in combating this growing problem. Using infection prevention and control strategies, hospitals have been able to prevent the spread of CREs. In one report, a New York hospital with endemic KPC-producing bacteria was able to significantly reduce the incidence of patients with carbapenem-resistant K. pneumoniae in the ICU through active surveillance with rectal swabs of all patients on admission and weekly throughout their ICU stay; contact precautions and cohorting of patients with positive cultures; and regular cleaning of environmental surfaces. In addition, members of the infection prevention service regularly participated in medical rounds and held meetings with the nursing staff to encourage adherence to contact precautions and other infection prevention measures. The decreased incidence of carbapenem-resistant K. pneumoniae was independent of the incidence of other resistant non-Enterobacteriaceae organisms.29
A similar scenario was reported in a Chicago-area long-term acute care hospital that demonstrated control of a KPC-producing K. pneumoniae outbreak. This facility’s infection prevention program included patient decolonization, improved cleaning methods, active surveillance, and pre-emptive isolation with contact precautions.17 In this case, active surveillance cultures were taken on admission and once a month to obtain point prevalence data. Admission surveillance cultures were taken from the rectum, nares, wounds, central vascular catheter insertion sites, and gastrostomy tube sites. Patients were placed in isolation if they were considered to be at high risk for carrying multidrug-resistant organisms until surveillance culture results returned. Within two months, their point prevalence data decreased from 21% to zero percent.
Conclusion
Multidrug-resistant Enterobacteriaceae are a growing concern. Controlling the spread of these highly resistant bacteria requires a multidisciplinary team approach that involves clinicians, laboratory staff, infection prevention specialists, and pharmacists. Seamless communication among these professionals within and between health care facilities is needed if we are to ensure that appropriate care is provided. In addition, facilities should have protocols in place for antimicrobial stewardship,30 surveillance, and the prevention of transmission and control of infection with multidrug-resistant organisms. Information about identification and prevention and control measures can be found on the CDC and Minnesota Department of Health websites (www.cdc.gov and www.health.state.mn.us).31,32
Health care providers now need to work closely with one another if we are to ensure that we do not again face a time when we have no useful tools against bacterial infections. MM
Edwin Pereira is an assistant professor in the department of medicine at the University of Minnesota. Kristin Shaw is an epidemiologist in the Infection Control and Antimicrobial Resistance Unit at the Minnesota Department of Health. Paula Snippes Vagnone supervises the Clinical Microbiology Laboratory at the Minnesota Department of Health’s Public Health Laboratory. Jane Harper supervises the Infection Control and Antimicrobial Resistance Unit at the Minnesota Department of Health. Ruth Lynfield is Minnesota’s state epidemiologist.
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