Rapid Screening for Carbapenem Resistant Organisms: Current Results and Future Approaches

Validation of a rapid molecular detection test for gram-negative multidrug-resistant bacteria in rectal swabs upon admission of patients to the intensive care unit

In ICU settings, screening patients upon admission for potential multiresistant bacteria (BMR) carriers is crucial. Traditionally, clinical decisions relied on delayed culture results, but a rapid PCR molecular test called RealCycler-Rezero-U/G (Progenie-molecular©), emerged as an alternative. This study aimed to validate its effectiveness in detecting gram-negative BMR in rectal swabs at ICU admission. Over 24 months, an observational study was conducted on 1,234 admitted patients, with 217 meeting isolation criteria and undergoing both PCR and culture tests. Results showed a 17.5 % positive rate for screening. The PCR test exhibited impressive accuracy at 98.6 % and a strong negative predictive value of 99.4 %. The area under the ROC curve (AUC) was 0.98, indicating high reliability. Notably, PCR results were available 44.5 h earlier than culture. In conclusion, PCR-based molecular testing for gram-negative BMR offers excellent diagnostic performance and a valuable negative predictive value, making it a suitable screening tool for ICU admissions.

Xpert Carba-R Assay on Flagged Blood Culture Samples: Clinical Utility in Intensive Care Unit Patients with Bacteremia Caused by Enterobacteriaceae

Introduction and background

Rapid molecular diagnostics to predict carbapenem resistance well before the availability of routine drug sensitivity testing (DST) can serve as an antimicrobial stewardship tool in the context of high rates of Carbapenem-resistant Enterobacteriaceae (CRE).

Materials and methods

A retrospective observational study of patients more than 18 years of age on whom Xpert Carba-R (FDA approved for rectal swab specimen) was done on gram-negative bacteria (GNB) flagged blood culture samples, in an Indian intensive care unit between January 2015 and November 2018. We analyzed the performance of Xpert Carba-R in comparison with routine DST.

Results

A total of 164 GNBs were isolated from 160 patients. Klebsiella pneumoniae and Escherichia coli were the predominant isolates. Carba-R was positive in 35.36% of samples and 45.34% were carbapenem-resistant (CR) on routine DST. The distribution of the CR gene was: Oxacillinase (OXA) (50%), NDM (32.7%) followed by OXA and NDM co-expression (15.51%). The sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, positive predictive value, and negative predictive value of Carba-R were 90.74, 93.15, 13.25, 0.10, 83.58 and 96.31% for Enterobacteriaceae. The median time to obtain the Carba-R report was 30 hours 34 minutes vs 74 hours and 20 minutes for routine DST. Based on the Carba-R report, 9.72% of patients had escalation and 27.08% had de-escalation of antibiotics.

Conclusion

Xpert Carba-R serves as a rapid diagnostic tool for predicting carbapenem resistance in intensive care unit patients with bacteremia caused by Enterobacteriaceae.

How to cite this article

Rajendran S, Gopalakrishnan R, Tarigopula A, Kumar DS, Nambi PS, Sethuraman N, et al. Xpert Carba-R Assay on Flagged Blood Culture Samples: Clinical Utility in Intensive Care Unit Patients with Bacteremia Caused by Enterobacteriaceae. Indian J Crit Care Med 2023;27(9):655-662.

Laboratory automation, informatics, and artificial intelligence: current and future perspectives in clinical microbiology

Clinical diagnostic laboratories produce one product-information-and for this to be valuable, the information must be clinically relevant, accurate, and timely. Although diagnostic information can clearly improve patient outcomes and decrease healthcare costs, technological challenges and laboratory workflow practices affect the timeliness and clinical value of diagnostics. This article will examine how prioritizing laboratory practices in a patient-oriented approach can be used to optimize technology advances for improved patient care.

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.

Development of Loop-Mediated Isothermal Amplification Rapid Diagnostic Assays for the Detection of Klebsiella pneumoniae and Carbapenemase Genes in Clinical Samples

Klebsiella pneumoniae is an important pathogenic bacterium commonly associated with human healthcare and community-acquired infections. In recent years, K. pneumoniae has become a significant threat to global public and veterinary health, because of its high rates of antimicrobial resistance (AMR). Early diagnosis of K. pneumoniae infection and detection of any associated AMR would help to accelerate directed therapy and reduce the risk of the emergence of multidrug-resistant isolates. In this study, we identified three target genes (yhaI, epsL, and xcpW) common to K. pneumoniae isolates from both China and Europe and designed loop-mediated isothermal amplification (LAMP) assays for the detection of K. pneumoniae in clinical samples. We also designed LAMP assays for the detection of five AMR genes commonly associated with K. pneumoniae. The LAMP assays were validated on a total of 319 type reference strains and clinical isolates of diverse genetic backgrounds, in addition to 40 clinical human sputum samples, and were shown to be reliable, highly specific, and sensitive. For the K. pneumoniae–specific LAMP assay, the calculated sensitivity, specificity, and positive and negative predictive values (comparison with culture and matrix-assisted laser desorption/ionization–time of flight mass spectrometry) were all 100% on clinical isolates and, respectively, of 100%, 91%, and 90%, and 100% when tested on clinical sputum samples, while being significantly faster than the reference methods. For the bla_KPC and other carbapenemases’ LAMP assays, the concordance between the LAMP results and the references methods (susceptibility tests) was 100%, on both pure cultures (n = 125) and clinical samples (n = 18). In conclusion, we developed highly sensitive and specific LAMP assays for the clinical identification of K. pneumoniae and detection of carbapenem resistance.

One-Step Detection and Classification of Bacterial Carbapenemases in 10 Minutes Using Fluorescence Identification of β-Lactamase Activity

Rapid and accurate diagnosis of bacterial carbapenemases remains a major challenge for clinical laboratories. A novel assay was developed here using fluorescence identification of β-lactamase activity (FIBA) to permit rapid detection and classification of bacterial carbapenemases. By mixing a fluorogenic β-lactamase substrate, β-LEAF (β-lactamase enzyme-activated fluorophore), with bacterial isolates plus the respective inhibitor (imipenem for noncarbapenemase β-lactamases, clavulanic acid for type A carbapenemases, and EDTA for type B carbapenemases), objective results with 95% to 100% sensitivity and specificity were generated in 10 min. FIBA is ≈$1/test and consists of only a single mixing step. Given the combination of rapidity, accuracy, low cost, and simplicity, this novel carbapenemase detection and classification assay is well positioned to be applied in clinical microbiology laboratories to provide guidance for the choice of proper treatment and control of globally prevalent carbapenemase-positive infections.

Performance of a loop-mediated isothermal amplification assay (Isoplex CRE-ART) to detect common carbapenemase-encoding genes in Gram-negative bacteria

Carbapenem-resistant Gram-negative bacteria (CR-GNB) are a major source of nosocomial infections worldwide. In this study, the ability of a loop-mediated isothermal amplification (LAMP)-based method (Isoplex CRE-ART) to rapidly detect carbapenemase-encoding genes bla _OXA-48-like, bla _OXA-23-like, bla _OXA-24-like, bla _KPC, bla _VIM, bla _NDM and bla _IMP in 231 carbapenem-resistant Enterobacterales, Pseudomonas aeruginosa and Acinetobacter baumannii isolates was investigated. The accuracy of the LAMP test was compared to results of molecular isolate characterization using a Laboratory Developed Test multiplex carbapenemase PCR assay. The LAMP test correctly identified the presence of on-panel carbapenemases with a sensitivity of 99.16 % [95 % confidence interval (CI): 95.39-99.96 %] and a specificity of 98.21 % (95 % CI: 93.72-99.68 %) in 60 min. Our findings suggest that the Isoplex CRE-ART assay is able to rapidly identify carbapenemase genes in CR-GNB and improves options for pathogen characterization in the context of clinical microbiological and infection control diagnostics.

Therapeutic Options for the Treatment of Carbapenem-resistant Enterobacteriaceae Infections: Hope in the Times of Hype and Despair

How to cite this article: Ansari AS. Therapeutic Options for the Treatment of Carbapenem-resistant Enterobacteriaceae Infections: Hope in the Times of Hype and Despair. Indian J Crit Care Med 2021;25(7):752-753.

Evaluation of Xpert Carba-R Assay for the Detection of Carbapenemase Genes in Gram-Negative Bacteria

Introduction

High mortality associated with carbapenemase-producing Gram-negative bacteria (CP-GNB) has evolved into a global health threat. Rapid and accurate detection as well as prompt treatment are of great significance in this case. Xpert Carba-R, a multiple qualitative analysis designed to detect five clinically relevant carbapenem-resistant gene families within one hour, is regarded as reliable, accurate, and easy-to-operate. This study is to present a systematic evaluation of the performance of Xpert Carba-R in detecting carbapenemase genes in GNB suspected for carbapenemase production.

Methods

We searched and screened the literature on “Xpert Carba-R” in the database of PubMed, Web of Science, Embase, and Cochrane Library, employing two independent evaluators to collect data, respectively. Then, statistical analysis of the data obtained was performed by the Stata 12.0 software to measure the accuracy of Xpert Carba-R assay in detecting the carbapenemase genes in GNB.

Results

We screened a total of 1767 Gram-negative bacillus isolates documented in 9 articles. The precision of the detection of OXA-48 carbapenemase genes was 100%; that of NDM = 100%; that of VIM = 100%. When it came to KPC, the precision rate was 100%; that of IMP = 99%. The overall accuracy of the detection of carbapenemase genes was 100%.

Conclusions

Xpert Carba-R assay demonstrates a 100% precision in identifying carbapenemase genes in GNB. It can be seen that Xpert Carba-R method is an effective tool for early clinical detection, which is suitable for the detection of carbapenase gene in GNB.

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.

Epidemiology of Carbapenem-Resistant Enterobacteriaceae at a Long-term Acute Care Hospital

Background

Residents of long-term acute care hospitals (LTACHs) are considered important reservoirs of multidrug-resistant organisms, including Carbapenem-resistant Enterobacteriaceae (CRE). We conducted this study to define the characteristics of CRE-infected/colonized patients admitted to an LTACH and the molecular characteristics of the CRE isolates.

Methods

This retrospective study was conducted to collect information on demographic and comorbid conditions in CRE-colonized/infected patients admitted to a 77-bed LTACH in Detroit between January 2011 and July 2012. Data pertaining to hospital-related exposures were collected for 30 days before positive CRE culture. Polymerase chain reaction (PCR) gene amplification, repetitive sequence–based PCR, and multilocus sequence typing (MLST) were performed on 8 of the CRE isolates.

Results

The study cohort included 30 patients with CRE-positive cultures, 24 (80%) with infections, and 6 (20%) with colonization. The mean age of cohort was 69 ±12.41 years; 19 (63%) patients were ventilator-dependent, and 20 (67%) were treated with at least 1 antibiotic. Twenty-three (77%) patients had CRE detected following LTACH admission, and the median days from admission to CRE detection in these patients (interquartile range) was 25 (11–43). Seven more patients were already positive for CRE at the time of LTACH admission. Molecular genotyping and MLST of 8 CRE isolates demonstrated that all isolates belonged to the same strain type (ST258) and contained the bla_KPC-3 sequence.

Conclusions

The majority of patients with CRE presented several days to weeks after LTACH admission, indicating possible organism acquisition in the LTACH itself. The genetic similarity of the CRE isolates tested could further indicate the occurrence of horizontal transmission in the LTACH or simply be representative of the regionally dominant strain.

Molecular detection of blaNDM-1 (New Delhi metallobetalactamase-1) in nosocomial Enterobacteriaceae isolates by nested, multiplex polymerase chain reaction

BACKGROUND

Carbapenems are considered "drugs of last resort" in many life-threatening infections. Advent of carbapenemases like KPC, OXA-48, VIM, IMP, and NDM have greatly affected the efficacy of these drugs, posing serious threat to global health and infection control. NDM bears special significance to the India subcontinent, labeled as place of origin and reservoir. NDM tends to escape detection by routine phenotypic methods, requiring molecular confirmation. This study utilizes nested, multiplex polymerase chain reaction (PCR) for reliable detection of bla_NDM-1 in nosocomial Enterobacteriaceae isolates.

METHODS

This study was conducted to detect prevalence of bla_NDM-1, bla_IMP, bla_VIMand bla_KPC genes by multiplex PCR among multidrug/carbapenem-resistant nosocomial Enterobacteriaceae isolates. From March 2013 to April 2014, 100 consecutive non-repeat isolates of Enterobacteriaceae from various inpatient clinical samples were analyzed. Imipenem-resistant isolates identified by Kirby Bauer disk diffusion method with Clinical and Laboratory Standards Institute guidelines were further subjected to nested, multiplex PCR to simultaneously detect bla_NDM-1, bla_IMP, bla_VIMand bla_KPC genes.

RESULTS

Out of 100 isolates, 17 (17%) were found to be imipenem-resistant. bla_NDM-1 was detected in all 17 isolates by nested, multiplex PCR. bla_VIM was co-carried in 4 isolates while one isolate co-harbored bla_IMP with bla_NDM-1. Imipenem resistance and NDM-1 carriage was predominant amongst Klebsiella isolates. Maximum NDM-1 producers were isolated from the intensive care unit (70.6%).

CONCLUSION

NDM-1 prevalence in nosocomial Enterobacteriaceae isolates in our hospital was found to be 17%. A nested, multiplex PCR was used for rapid detection of various carbapenemase genes with high sensitivity and specificity which is essential not only for favorable patient outcome but also for timely implementation of appropriate infection control practices to prevent further spread of such organisms.

Evaluation of two commercial real-time PCR assays for detection of carbapenemase genes in Enterobacteriaceae

The implementation of PCR for the detection of carbapenemase genes enables rapid results with significant epidemiological implications. Two commercial real-time PCR assays, the Hylabs Hy-CRE and Sacace MDR MBL+KPC/OXA, were evaluated for the detection of the genes blaKPC, blaVIM, blaNDM, blaIMP and blaOXA-48-carbapenemasein a collection of 96 carbapenem-resistant Enterobacteriaceae strains with different resistant mechanisms. Both assays exhibited excellent diagnostic performance, with 100 % sensitivity and specificity.

Carbapenem resistant Klebsiella pneumoniae isolated from bloodstream infection: Indian experience

Increased incidence of multidrug resistant (MDR) Gram negative infection has resulted in high rates of morbidity and mortality. Klebsiella pneumoniae is one of the commonest MDR pathogens causing bacteraemia with limited therapeutic options such as colistin and tigecycline. Present study focused on molecular characterisation of MDR K. pneumoniae from bloodstream infection and their clinical outcome. A total of 115 K. pneumoniae from January 2015 to September 2016 were included in the study which comprised of phenotypically identified ESBL and carbapenem resistant (CR) isolates. Multiplex PCR was performed for detection of resistance genes encoding β-lactam resistance. This includes bla_SHV, bla_TEM, bla_VEB, bla_PER, bla_CTX-M, bla_DHA, bla_CIT, bla_FOX, bla_ACC, bla_ACT, bla_NDM, bla_OXA48-like, bla_VIM and bla_KPC. Co-expression of bla_SHV, bla_TEM and bla_CTX-M was predominant with 64% (74/115) prevalence. CTX-M-1 was the variant produced by all the isolates producing CTX-M. AmpC was uncommon, seen in 5% of the isolates (6/115). Among the carbapenemases co-expression of bla_NDM and bla_OXA48-like was observed in 28% (32/115) and bla_NDM in 19% (22/115) and bla_OXA48-like in 13% (15/115). bla_KPC was absent. Overall mortality was observed to be 57% (64/113) and mortality among CR K. pneumoniae (Kp) was 68% (50/73). The antibiotics that were administered for treatment of CRKp were colistin in 90% (66/73) and tigecycline in 7% (5/73) and in 99% combined with meropenem (72/73). Prevalence of community acquired and nosocomial infections were 5% (4/73) and 95% (69/73) respectively among CRKp. Minocycline and meropenem susceptibilities were comparable and hence minocycline can be a carbapenem sparing agent. The resistance to β-lactam antibiotics is steadily increasing and are plasmid mediated, their containment in healthcare setting is a challenge.

Antibiotic resistance: What is so special about multidrug-resistant Gram-negative bacteria?

In the past years infections caused by multidrug-resistant Gram-negative bacteria have dramatically increased in all parts of the world. This consensus paper is based on presentations, subsequent discussions and an appraisal of current literature by a panel of international experts invited by the Rudolf Schülke Stiftung, Hamburg. It deals with the epidemiology and the inherent properties of Gram-negative bacteria, elucidating the patterns of the spread of antibiotic resistance, highlighting reservoirs as well as transmission pathways and risk factors for infection, mortality, treatment and prevention options as well as the consequences of their prevalence in livestock. Following a global, One Health approach and based on the evaluation of the existing knowledge about these pathogens, this paper gives recommendations for prevention and infection control measures as well as proposals for various target groups to tackle the threats posed by Gram-negative bacteria and prevent the spread and emergence of new antibiotic resistances.

Comparison of clinical methods for detecting carbapenem-resistant Enterobacteriaceae

We evaluated detection of carbapenem-resistant Enterobacteriaceae (CRE) by routine minimal inhibitory concentration (MIC) testing, polymerase chain reaction (PCR) using Xpert® Carba-R assay, hydrolysis of ertapenem and imipenem detected by matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS), and hydrolysis by colorimetry using the EPI-CRE assay. Ninety-six Enterobacteriaceae isolates possessing carbapenemase genes and 29 carbapenem-susceptible Enterobacteriaceae were available for testing. The sensitivity and specificity of each assay was determined. For sensitivity, discrepant results from each assay compared to reference genotype were arbitrated with MIC and/ or PCR testing to assess loss of plasmid-mediated resistance. Xpert Carba-R was evaluated for resistance genes in their FDA claim (i.e., the genes encoding KPC; NDM; VIM; IMP; and OXA-48). The sensitivity for the assays was: MIC (N=96), 96.8%, (discrepant analysis to 98.9% [2 cured plasmids]); Xpert Carba-R (N=85), 97.6% (discrepant analysis to 100% % [2 cured plasmids]); EPI-CRE (N=96), 91.7% (discrepant analysis to 91.7%); MALDI-TOF MS (N=96) ertapenem hydrolysis using Compass software for interpretation (2 h incubation), 92.7% (discrepant analysis to 94.7% % [2 cured plasmids]); MALDI-TOF MS (N=96) imipenem hydrolysis (1 h incubation), 97.9% (discrepant analysis to 98.9% % [1 cured plasmid]). The specificity for each assay was: MIC (N=29), 100%; EPI-CRE (N=29), 96.6%; MALDI-TOF MS ertapenem hydrolysis (N=29), 100%; MALDI-TOF MS imipenem hydrolysis (N=29), 96.6%. All isolates tested to ensure specificity demonstrated susceptible MIC results for carbapenems and did not qualify for testing with Xpert Carba-R. No single assay detected all of the known genetic markers of carbapenem hydrolysis.

Molecular Mechanisms of Colistin Resistance in Klebsiella pneumoniae Causing Bacteremia from India-A First Report

Colistin has long been a reserve drug used for the treatment of carbapenem resistant Klebsiella pneumoniae. Carbapenem resistance in K. pneumoniae has been increasing and is as high as 44% in India. Although a reserve agent, with rise in rates of resistance to carbapenems, the usage of colistin has increased over the years leading to slow emergence of resistance. Colistin resistance is mainly mediated by the alteration in the LPS of bacterial outer membrane with the addition of L-Ara4-N and PEtN molecules. These alterations are mediated by mutations in several genes involved in lipidA modifications and most commonly mutations in mgrB gene has been reported. Recently there is emergence of plasmid mediated resistance due to mcr-1 and mcr-2 genes which poses a threat for the rapid global spread. This study aims at characterizing eight colistin resistant K. pneumoniae from bacteremia by whole genome sequencing. Eight K. pneumoniae were isolated from blood culture during 2013 and 2014 at the Department of Clinical Microbiology, Christian Medical College, India. Antimicrobial susceptibility testing was performed and minimum inhibitory concentration (MIC) was determined for colistin and polymyxin B by broth-micro dilution method. Whole genome sequencing was performed using Ion Torrent and the genome of all eight isolates was analyzed. The eight isolates were resistant to all the antimicrobials expect tigecycline. MIC of colistin and polymyxin B were ranged from 4 to 1024 μg/ml and 0.5 to 2048 μg/ml respectively. Multiple mutations were observed in the chromosomal genes involved in lipid A modifications. mcr-1 and mcr-2 gene was absent in all the isolates. The most significant were mutations in mgrB gene. Among the eight isolates, four, three and one were belonged to sequence types ST 231, ST14 and ST147 respectively. Seven isolates had bla_{OXA-48 like}, one co-expressed bla_NDM-1 and bla_{OXA-48 like} genes leading to carbapenem resistance. Overall, multiple numbers of alterations have been observed. This includes silent mutations, point mutations, insertions and/or deletions. Mutations in mgrB gene is responsible for resistance to colistin in this study. Due to emergence of resistance to reserve drugs, there is a need for combination therapies for carbapenem resistant K. pneumoniae and colistin must be judiciously used.

Global Dissemination of Carbapenemase-Producing Klebsiella pneumoniae: Epidemiology, Genetic Context, Treatment Options, and Detection Methods

The emergence of carbapenem-resistant Gram-negative pathogens poses a serious threat to public health worldwide. In particular, the increasing prevalence of carbapenem-resistant Klebsiella pneumoniae is a major source of concern. K. pneumoniae carbapenemases (KPCs) and carbapenemases of the oxacillinase-48 (OXA-48) type have been reported worldwide. New Delhi metallo-β-lactamase (NDM) carbapenemases were originally identified in Sweden in 2008 and have spread worldwide rapidly. In this review, we summarize the epidemiology of K. pneumoniae producing three carbapenemases (KPCs, NDMs, and OXA-48-like). Although the prevalence of each resistant strain varies geographically, K. pneumoniae producing KPCs, NDMs, and OXA-48-like carbapenemases have become rapidly disseminated. In addition, we used recently published molecular and genetic studies to analyze the mechanisms by which these three carbapenemases, and major K. pneumoniae clones, such as ST258 and ST11, have become globally prevalent. Because carbapenemase-producing K. pneumoniae are often resistant to most β-lactam antibiotics and many other non-β-lactam molecules, the therapeutic options available to treat infection with these strains are limited to colistin, polymyxin B, fosfomycin, tigecycline, and selected aminoglycosides. Although, combination therapy has been recommended for the treatment of severe carbapenemase-producing K. pneumoniae infections, the clinical evidence for this strategy is currently limited, and more accurate randomized controlled trials will be required to establish the most effective treatment regimen. Moreover, because rapid and accurate identification of the carbapenemase type found in K. pneumoniae may be difficult to achieve through phenotypic antibiotic susceptibility tests, novel molecular detection techniques are currently being developed.

Multisite Evaluation of Cepheid Xpert Carba-R Assay for Detection of Carbapenemase-Producing Organisms in Rectal Swabs

Rapid identification of patients who are colonized with carbapenemase-producing organisms (CPO) is included in multiple national guidelines for containment of these organisms. In a multisite study, we evaluated the performance of the Cepheid Xpert Carba-R assay, a qualitative diagnostic test that was designed for the rapid detection and differentiation of the bla_KPC, bla_NDM, bla_VIM, bla_OXA-48, and bla_IMP-1 genes from rectal swab specimens. A double rectal swab set was collected from 383 patients admitted at four institutions (2 in the United States, 1 in the United Kingdom, 1 in Spain). One swab was used for reference culture (MacConkey broth containing 1 mg/liter of meropenem and subcultured to a MacConkey agar plate with a 10-μg meropenem disk) and for sequencing of DNA obtained from carbapenem-nonsusceptible isolates for carbapenemase identification. The other swab was used for the Xpert Carba-R assay. In addition to the clinical rectal swabs, 250 contrived specimens (108 well-characterized CPO and 142 negative controls spiked onto negative rectal swabs) were tested. Overall, 149/633 (23.5%) samples were positive by the Xpert Carba-R assay. In 6 samples, multiple targets were detected (4 VIM/OXA-48, 1 IMP-1/NDM, and 1 NDM/KPC). The Xpert Carba-R assay detected 155 targets (26 IMP-1, 30 VIM, 27 NDM, 33 KPC, 39 OXA-48) within a time range of 32 to 48 min. The sensitivity, specificity, and positive and negative predictive values of the Xpert Carba-R assay compared to those of the reference culture and sequencing results were 96.6% (95% confidence interval [CI], 92.2% to 98.9%), 98.6% (95% CI, 97.1% to 99.4%), 95.3%, and 99.0%, respectively. The Cepheid Xpert Carba-R assay is an accurate and rapid test to identify rectal colonization with CPO, which can guide infection control programs to limit the spread of these organisms.

The Problem of Carbapenemase-Producing-Carbapenem-Resistant-Enterobacteriaceae Detection

The emergence and spread of carbapenemase-producing carbapenem-resistant Enterobacteriaceae (CP-CRE) are a significant clinical and public health concern. Reliable detection of CP-CRE is the first step in combating this problem. There are both phenotypic and molecular methods available for CP-CRE detection. There is no single detection method that is ideal for all situations.