Carbapenem-Resistant Enterobacteriaceae: Laboratory Detection and Infection Control Practices

An Overview on Phenotypic and Genotypic Characterisation of Carbapenem-Resistant Enterobacterales

Improper use of antimicrobials has resulted in the emergence of antimicrobial resistance (AMR), including multi-drug resistance (MDR) among bacteria. Recently, a sudden increase in Carbapenem-resistant Enterobacterales (CRE) has been observed. This presents a substantial challenge in the treatment of CRE-infected individuals. Bacterial plasmids include the genes for carbapenem resistance, which can also spread to other bacteria to make them resistant. The incidence of CRE is rising significantly despite the efforts of health authorities, clinicians, and scientists. Many genotypic and phenotypic techniques are available to identify CRE. However, effective identification requires the integration of two or more methods. Whole genome sequencing (WGS), an advanced molecular approach, helps identify new strains of CRE and screening of the patient population; however, WGS is challenging to apply in clinical settings due to the complexity and high expense involved with this technique. The current review highlights the molecular mechanism of development of Carbapenem resistance, the epidemiology of CRE infections, spread of CRE, treatment options, and the phenotypic/genotypic characterisation of CRE. The potential of microorganisms to acquire resistance against Carbapenems remains high, which can lead to even more susceptible drugs such as colistin and polymyxins. Hence, the current study recommends running the antibiotic stewardship programs at an institutional level to control the use of antibiotics and to reduce the spread of CRE worldwide.

Routine detection of carbapenem-resistant gram-negative bacilli in clinical laboratories. A review of current challenge

The detection of carbapenem-resistant organisms (CROs) represents a substantial challenge for many clinical laboratories. In this review, several phenotypic and non-phenotypic methods for detecting CROs are discussed. However, no consensus has yet been reached with regards to the single most optimal method. Due to differences in carbapenem-resistant activity between carbapenemases, the simultaneous use of 2 or more phenotypic detection methods can improve the detection of CROs compared with a single technique. Molecular methods are currently favored because the majority can be performed rapidly with a high level of accuracy. Whole-genome sequencing (WGS) yields unambiguous data pertaining to complete analysis of the entire genome and may ultimately become a highly powerful tool in routine clinical settings. However, WGS is still relatively expensive and requires an automated data interpretation system. The routine implementation of this technique in clinical laboratories may not occur for several years, particularly in developing countries.

CHROMagar mSuperCARBA and RAPIDEC® Carba NP test for detection of carbapenemase-producing Enterobacteriaceae

A novel chromogenic medium CHROMagar mSuperCARBA was evaluated to detect carbapenem-resistant Gram-negatives. This medium is as sensitive and as specific as the SUPERCARBA medium for detecting KPC, MBL and OXA-48-type producers (100% and 100%, respectively) and is compatible with subsequent testing of carbapenemase activity using the RAPIDEC^® CARBA NP.

Infection control implications of heterogeneous resistance mechanisms in carbapenem-resistant Enterobacteriaceae (CRE)

The Centers for Disease Control and Prevention (CDC) defines carbapenem-resistant Enterobacteriaceae (CRE) based upon a phenotypic demonstration of carbapenem resistance. However, considerable heterogeneity exists within this definitional umbrella. CRE may mechanistically differ by whether they do or do not produce carbapenemases. Moreover, patients can acquire CRE through multiple pathways: endogenously through antibiotic selective pressure on intestinal microbiota, exogenously through horizontal transmission or through a combination of these factors. Some evidence suggests that non-carbapenemase-producing CRE may be more frequently acquired by antibiotic exposure and carbapenemase-producing CRE via horizontal transmission, but definitive data are lacking. This review examines types of CRE resistance mechanisms, antibiotic exposure and horizontal transmission pathways of CRE acquisition, and the implications of these heterogeneities to the development of evidence-based CRE healthcare epidemiology policies. In our Expert Commentary & Five-Year View, we outline specific nosocomial CRE knowledge gaps and potential methodological approaches for their resolution.

The pros, cons, and unknowns of search and destroy for carbapenem-resistant enterobacteriaceae

Antibiotic drug discovery has not kept pace with the development of microbial resistance to these agents. There are ever increasing reports where the causative agents of serious infections are multi-drug resistant and in some cases resistant to all known antibiotics. The emergence and spread of carbapenemase-producing Enterobacteriaceae has heightened awareness regarding antibiotic stewardship programs and infection prevention and control measures. There has been much controversy regarding the utility of the "search and destroy" strategy to prevent the spread of carbapenem-resistant Enterobacteriaceae. These controversies center on screening and management of carriers, including decontamination and isolation. It is however clear that a functional infection prevention and control program is fundamental to any strategy that serves to address the spread of microbes within a healthcare facility.

Carbapenem-resistant Enterobacteriaceae: biology, epidemiology, and management

Introduced in the 1980s, carbapenem antibiotics have served as the last line of defense against multidrug-resistant Gram-negative organisms. Over the last decade, carbapenem-resistant Enterobacteriaceae (CRE) have emerged as a significant public health threat. This review summarizes the molecular genetics, natural history, and epidemiology of CRE and discusses approaches to prevention and treatment.

Carbapenemase-producing Klebsiella pneumoniae

The continuing emergence of infections due to multidrug resistant bacteria is a serious public health problem. Klebsiella pneumoniae, which commonly acquires resistance encoded on mobile genetic elements, including ones that encode carbapenemases, is a prime example. K. pneumoniae carrying such genetic material, including both bla_KPC and genes encoding metallo-β-lactamases, have spread globally. Many carbapenemase-producing K. pneumoniae are resistant to multiple antibiotic classes beyond β-lactams, including tetracyclines, aminoglycosides, and fluoroquinolones. The optimal treatment, if any, for infections due to these organisms is unclear but, paradoxically, appears to often require the inclusion of an optimally administered carbapenem.

Rapid time to results and high sensitivity of the CarbaNP test on early cultures

For rapid results, we adapted the CarbaNP test by using 5-hour-old cultures; the sensitivity and specificity for detection of carbapenemase production were 100% for non-OXA-producing organisms. The sensitivity from early cultures was 94% for detection of carbapenemase production in Enterobacteriaceae strains. Utilizing younger cultures allows the test to be incorporated into a single day's workflow, facilitating timely patient care and antimicrobial stewardship.

A method for de novo nucleic acid diagnostic target discovery

MOTIVATION

A proper target or marker is essential in any diagnosis (e.g. an infection or cancer). An ideal diagnostic target should be both conserved in and unique to the pathogen. Currently, these targets can only be identified manually, which is time-consuming and usually error-prone. Because of the increasingly frequent occurrences of emerging epidemics and multidrug-resistant 'superbugs', a rapid diagnostic target identification process is needed.

RESULTS

A new method that can identify uniquely conserved regions (UCRs) as candidate diagnostic targets for a selected group of organisms solely from their genomic sequences has been developed and successfully tested. Using a sequence-indexing algorithm to identify UCRs and a k-mer integer-mapping model for computational efficiency, this method has successfully identified UCRs within the bacteria domain for 15 test groups, including pathogenic, probiotic, commensal and extremophilic bacterial species or strains. Based on the identified UCRs, new diagnostic primer sets were designed, and their specificity and efficiency were tested by polymerase chain reaction amplifications from both pure isolates and samples containing mixed cultures.

AVAILABILITY AND IMPLEMENTATION

The UCRs identified for the 15 bacterial species are now freely available at http://ucr.synblex.com. The source code of the programs used in this study is accessible at http://ucr.synblex.com/bacterialIdSourceCode.d.zip

CONTACT

yazhousun@synblex.com

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Rapid ertapenem susceptibility testing and Klebsiella pneumoniae carbapenemase phenotype detection in Klebsiella pneumoniae isolates by use of automated microscopy of immobilized live bacterial cells

We evaluated detection of ertapenem (ETP) resistance and Klebsiella pneumoniae carbapenemase (KPC) in 47 Klebsiella pneumoniae isolates using a novel automated microscopy system. Automated microscopy correctly classified 22/23 isolates as ETP resistant and 24/24 as ETP susceptible and correctly classified 21/21 isolates as KPC positive and 26/26 as KPC negative.