Performance of chromID® CARBA medium for carbapenemases-producing Enterobacteriaceae detection during rectal screening

Use of a chromogenic medium with and without selective enrichment to screen for carbapenemase-producing Enterobacterales (CPE) from canine and feline fecal specimens during an outbreak of NDM-5-producing Escherichia coli

Carbapenemase-producing Enterobacterales (CPE) are one of the most urgent threats to human healthcare globally. Descriptions of CPE outbreaks in veterinary hospitals suggest the need for screening strategies for CPE from companion animals. Our aim was to optimize a chromogenic agar method with and without selective enrichment to isolate CPE from companion animal feces in an ongoing outbreak of New Delhi metallo-β-lactamse-5 Escherichia coli. A limit of detection (LOD) assay for spiked canine and feline feces was performed for both methods using a carbapenamase-producing E. coli (24213-18); the LOD (1.5 × 103 cfu/g of feces) was equivalent to that reported for human fecal specimens. We screened 1,247 companion animal fecal specimens for carriage of CPE by 1) direct plating to chromogenic agar and 2) plating to chromogenic agar following selective enrichment. Twenty-one specimens were positive for CPE by both direct culture and enrichment culture. No specimens were positive with selective enrichment and negative by direct culture. A selective enrichment step did not result in any increased recovery of CPE from companion animals, which suggests that enrichment broth may not be necessary for outbreak surveillance testing. It is important to continue to validate methods for the detection of CPE in companion animals as outbreaks become more common in veterinary facilities.

Increasing Trends of Association of 16S rRNA Methylases and Carbapenemases in Enterobacterales Clinical Isolates from Switzerland, 2017–2020

Aminoglycosides (AGs) in combination with β-lactams play an important role in antimicrobial therapy in severe infections. Pan-resistance to clinically relevant AGs increasingly arises from the production of 16S rRNA methylases (RMTases) that are mostly encoded by plasmids in Gram-negative bacteria. The recent emergence and spread of isolates encoding RMTases is worrisome, considering that they often co-produce extended-spectrum β-lactamases (ESBLs) or carbapenemases. Our study aimed to retrospectively analyze and characterize the association of carbapenem- and aminoglycoside-resistant clinical isolates in Switzerland during a 3.5-year period between January 2017 and June 2020. A total of 103 pan-aminoglycoside- and carbapenem-resistant clinical isolates were recovered at the NARA (Swiss National Reference Center for Emerging Antibiotic Resistance) during the 2017–2020 period. Carbapenemase and RMTase determinants were identified by PCR and sequencing. The characterization of plasmids bearing resistance determinants was performed by a mating-out assay followed by PCR-based replicon typing (PBRT). Clonality of the isolates was investigated by multilocus sequence typing (MLST). Over the 991 Enterobacterales collected at the NARA during this period, 103 (10.4%) of them were resistant to both carbapenems and all aminoglycosides. Among these 103 isolates, 35 isolates produced NDM-like carbapenemases, followed by OXA-48-like (n = 23), KPC-like (n = 21), or no carbapenemase (n = 13), OXA-48-like and NDM-like co-production (n = 7), and VIM-like enzymes (n = 4). The RMTases ArmA, RmtB, RmtC, RmtF, RmtG, and RmtB + RmtF were identified among 51.4%, 13.6%, 4.9%, 24.3%, 1%, and 1%, respectively. Plasmid co-localization of the carbapenemase and the RMTase encoding genes was found among ca. 20% of the isolates. A high diversity was identified in terms of the nature of associations between RMTase and carbapenemase-encoding genes, of incompatibility groups of the corresponding plasmids, and of strain genetic backgrounds, highlighting heterogeneous importations rather than clonal dissemination.

Mobile genetic elements-mediated Enterobacterales-associated carbapenemase antibiotic resistance genes propagation between the environment and humans: A One Health South African study

We, (1) studied carbapenem-resistant Enterobacterales (CRE) in the environment, humans, and animals, within the same geographical area and, (2) delineated the isolates' resistome, mobilome, virulome, and phylogeny. Following ethical approval, 587 samples (humans = 230, pigs = 345, and water = 12) were collected and cultured on CRE selective media. Confirmatory identification and antibiotic susceptibility testing were performed using the VITEK 2 automated platform. The resistomes, virulomes, mobilomes, and phylogenies were ascertained by whole genome sequencing. Nineteen (3.2%), i.e., 15/19 humans and 4/19 environmental, but no pig, CRE were obtained. CREs included Klebsiella pneumoniae 9/19 (47%), Enterobacter hormaechei 6/19 (32%), Klebsiella quasipneumoniae 2/19 (11%), a novel ST498 Citrobacter freundii 1/19 (5%) and Serratia marcescens 1/19 (5%). Eleven isolates were extensively drug-resistant; eight were multidrug-resistant. Sixteen CRE harbored the bla_OXA-181, bla_OXA-48, bla_OXA-484, bla_NDM-1, and bla_GES-5 genes. Multiple species/clones carried bla_OXA-48 and bla_NDM-1 carbapenemase-encoding genes with respective mobile genetic elements (MGEs). The IncFIB(K) plasmid replicon was found in most human K. pneumoniae strains (7/9) and all environmental K. quasipneumoniae isolates; most K. pneumoniae produced OXA-181 (5/9). The (Col440I) plasmid replicon, identified in 11 (26.82%) isolates, mainly E. hormaechei (n = 6), predominated both sectors. Most β-lactamase-encoding genes were associated with class 1 integrons IntI1, insertion sequences (IS) (IS91, IS5075, IS30, IS3000, IS3, IS19, ISKpn19, IS5075) and transposons (Tn3). The IncL/M(pMU407) and IncL/M(pOXA48) plasmid replicons were found exclusively in K. pneumoniae; all but one of these strains produced OXA-181. Also, the Klebsiella spp. harbored 80 virulence genes. Phylogenomic clustered identified isolates with other carbapenemase-producing K. pneumoniae, E. hormaechei, S. marcescens, and C. freundii from different South African sources (animals, environment, and humans). We delineated the resistome, mobilome, virulome, and phylogeny of carbapenemase-producing Enterobacterales in humans and environment, highlighting antibiotic resistance genes propagation via MGEs across sectors, emphasizing a One Health approach to AMR.

An Application of Imipenem Discs or P. aeruginosa ATCC 27853 Reference Strain Increases Sensitivity of Carbapenem Inactivation Method for Non-Fermenting Gram-Negative Bacteria

Non-fermenting Gram-negative rods are one of the most commonly isolated bacteria from human infections. These microorganisms are typically opportunistic pathogens that pose a serious threat to public health due to possibility of transmission in the human population. Resistance to beta-lactams, due to carbapenemases synthesis, is one of the most important antimicrobial resistance mechanisms amongst them. The aim of this study was to evaluate the usefulness of the Carbapenem Inactivation Method (CIM), and its modifications, for the detection of carbapenemase activity amongst non-fermenting Gram-negative rods. This research involved 81 strains of Gram-negative rods. Of the tested strains, 55 (67.9%) synthesized carbapenemases. For non-fermenting rods, 100% sensitivity and specificity was obtained in the version of the CIM test using imipenem discs and E. coli ATCC 25922 strain. The CIM test allows for differentiation of carbapenems resistance mechanisms resulting from carbapenemase synthesis from other resistance types. It is a reliable diagnostic method for the detection of carbapenemase activity amongst non-fermenting Gram-negative rods. Application of imipenem discs and P. aeruginosa ATCC 27853 reference strain increases CIM results sensitivity, while imipenem discs and E. coli ATCC 25922 strain use maintains full precision of the test for non-fermenting rods.

Isolation Procedure for CP E. coli from Caeca Samples under Review towards an Increased Sensitivity

Due to the increasing reports of carbapenemase-producing Enterobacteriaceae (CPE) from livestock in recent years, the European Reference Laboratory for Antimicrobial Resistances (EURL-AR) provided a protocol for their recovery from caecum and meat samples. This procedure exhibited limitations for the detection of CPE with low carbapenem MIC values. Therefore, it was modified by a second, selective enrichment in lysogeny broth with cefotaxime (CTX 1 mg/L) and with meropenem (MEM 0.125 mg/L) at 37 °C under microaerophilic conditions. By Real-time PCR, these enrichments are pre-screened for the most common carbapenemase genes. Another adaptation was the use of in-house prepared MacConkey agar with MEM and MEM+CTX instead of commercial selective agar. According to the EURL-method, we achieved 100% sensitivity and specificity using the in-house media instead of commercial agar, which decreased the sensitivity to ~75%. Comparing the method with and without the second enrichment, no substantial influence on sensitivity and specificity was detected. Nevertheless, this enrichment has simplified the CPE-isolation regarding the accompanying microbiota and the separation of putative colonies. In conclusion, the sensitivity of the method can be increased with slight modifications.

Guía de práctica clínica para la tamización de pacientes con riesgo de colonización por Enterobacterales productores de carbapenemasas y el manejo de infecciones causadas por estas bacterias

Las infecciones por Enterobacterales productores de carbapenemasas (EPC) han aumentado en los últimos años. Colombia se ha convertido en un país endémico para este grupo de microorganismos y las infecciones que causan tienen un impacto importante en términos de morbilidad y mortalidad. La identificación temprana de los portadores de EPC que ingresan como pacientes a las instituciones de salud es necesaria para implementar medidas de aislamiento y control de infecciones adecuadas que limiten la diseminación de este tipo de microorganismos en los hospitales. Además, el tratamiento de estas infecciones es difícil debido a las limitadas alternativas terapéuticas disponibles y la escasez de estudios que demuestren su efectividad en este escenario. Por lo anterior, el objetivo del presente trabajo es desarrollar una guía de práctica clínica (GPC) para la tamización de pacientes con riesgo de colonización por EPC y para el manejo de pacientes con   infecciones, ya sea sospechadas o confirmadas, causadas por este tipo de bacterias, mediante un proceso de adaptación de GPC basado en la metodología ADAPTE. Con este propósito en mente, se hacen recomendaciones informadas en evidencia para realizar la tamización y oportuna identificación de portadores de EPC admitidos en instituciones hospitalarias, así como para el adecuado manejo farmacológico de las infecciones por EPC en este escenario.

Surveillance of Extended-Spectrum β-Lactamase-, Cephalosporinase- and Carbapenemase-Producing Gram-Negative Bacteria in Raw Milk Filters and Healthy Dairy Cattle in Three Farms in Île-de-France, France

The aim of this work was to test a surveillance protocol able to detect extended-spectrum β-lactamase (ESBL)-, cephalosporinase (AmpC)- and carbapenemase (CP)-producing gram-negative bacteria in three conveniently chosen dairy farms with known prior occurrences of ESBL- and CP-producing strains. The protocol was applied monthly for a year. At each visit, 10 healthy lactating dairy cows were rectally swabbed, and raw milk filters (RMFs) were sampled in two of the three farms. Bacterial isolation was based on a first screening step with MacConkey agar supplemented with 1 mg/L cefotaxime and commercial carbapenem-supplemented media. We failed to detect CP-producing strains but showed that ESBL-Escherichia strains, found in one farm only (13 strains), were closely associated with multi-drug resistance (12 out of 13). The limited number of conveniently selected farms and the fact that RMFs could not be retrieved from one of them limit the validity of our findings. Still, our results illustrate that ESBL-status changes monthly based on fecal swabs and negative herds should be qualified as “unsuspected” as proposed by previous authors. Although surveillance of farm statuses based on RMF analysis could theoretically allow for a better sensitivity than individual swabs, we failed to illustrate it as both farms where RMFs could be retrieved were constantly negative. Determination of CP herd-level status based on RMFs and our surveillance protocol was hindered by the presence of intrinsically resistant bacteria or strains cumulating multiple non-CP resistance mechanisms which means our protocol is not specific enough for routine monitoring of CP in dairy farms.

Comparative Pathogenomics of Aeromonas veronii from Pigs in South Africa: Dominance of the Novel ST657 Clone

The pathogenomics of carbapenem-resistant Aeromonas veronii (A. veronii) isolates recovered from pigs in KwaZulu-Natal, South Africa, was explored by whole genome sequencing on the Illumina MiSeq platform. Genomic functional annotation revealed a vast array of similar central networks (metabolic, cellular, and biochemical). The pan-genome analysis showed that the isolates formed a total of 4349 orthologous gene clusters, 4296 of which were shared; no unique clusters were observed. All the isolates had similar resistance phenotypes, which corroborated their chromosomally mediated resistome (bla_CPHA3 and bla_OXA-12) and belonged to a novel sequence type, ST657 (a satellite clone). Isolates in the same sub-clades clustered according to their clonal lineages and host. Mobilome analysis revealed the presence of chromosome-borne insertion sequence families. The estimated pathogenicity score (P_score ≈ 0.60) indicated their potential pathogenicity in humans. Furthermore, these isolates carried several virulence factors (adherence factors, toxins, and immune evasion), in different permutations and combinations, indicating a differential ability to establish infection. Phylogenomic and metadata analyses revealed a predilection for water environments and aquatic animals, with more recent reports in humans and food animals across geographies, making A. veronii a potential One Health indicator bacterium.

ChromID® CARBA Agar Fails to Detect Carbapenem-Resistant Enterobacteriaceae With Slightly Reduced Susceptibility to Carbapenems

After first detections of carbapenemase-producing Enterobacteriaceae (CPE) in animals, the European Union Reference Laboratory for Antimicrobial Resistance has provided a protocol for the isolation of carbapenemase-producing Escherichia (E.) coli from cecum content and meat. Up to now, only few isolates were recovered using this procedure. In our experience, the choice of the selective agar is important for the efficacy of the method. Currently, the use of the prevailing method fails to detect CPE that exhibit a low resistance against carbapenems. Thus, this study aims to evaluate the suitability of selective media with antibiotic supplements and commercial ChromID^® CARBA agar for a reliable CPE detection. For comparative investigations, detection of freeze-dried carbapenemase-resistant bacteria was studied on different batches of the ChromID^® CARBA agar as well as on MacConkey agar supplemented with 1 mg/L cefotaxime and 0.125 mg/L meropenem (McC+CTX+MEM). The suitability of the different media was assessed within a time of 25 weeks, starting at least six weeks before expiration of the media. Carbapenem-resistant isolates exhibiting a serine-based hydrolytic resistance mechanism (e.g., bla _KPC genes) were consistently detected over 25 weeks on the different media. In contrast, carbapenemase producers with only slightly reduced susceptibility and exhibiting a zinc-catalyzed activity (e.g., bla _VIM, bla _NDM, and bla _IMP) could only be cultivated on long-time expired ChromID^® CARBA, but within the whole test period on McC+CTX+MEM. Thus, ChromID^® CARBA agar appears to be not suitable for the detection of CPE with slightly increased minimum inhibitory concentrations (MIC) against carbapenems, which have been detected in German livestock and thus, are of main interest in the national monitoring programs. Our data are in concordance with the results of eleven state laboratories that had participated in this study with their ChromID^® CARBA batches routinely used for the German CPE monitoring. Based on the determined CPE detection rate, we recommend the use of McC+CTX+MEM for monitoring purposes. This study indicates that the use of ChromID^® CARBA agar might lead to an underestimation of the current CPE occurrence in food and livestock samples.

Bacterial diversity of the green turtle (Chelonia mydas) nest environment

The green turtle is an endangered species that is highly sensitive to environmental pollution that can adversely affect the healthy development of eggs. Moreover, the presence of some bacteria in nests can be regarded as an indicator of the pollution level in nesting areas. In our study, nest sand and egg contents were collected from Sugözü Beaches (Turkey), in the Mediterranean. Phenotypic and genotypic identification of bacteria were carried out by using conventional phenotypic methods, 16S rRNA gene sequencing respectively. The extended-spectrum beta-lactamase presence and carbapenem resistance of bacteria isolated from egg contents were determined. This is the first report of carbapenem resistance in the eggs. All strains were evaluated in three different categories including growth promoters in agriculture and aquaculture, pathogens that are found in human and animal, and biomonitoring aquatic pollution. According to our analysis, 67 bacterial species were identified from samples. This study is the first record of Alcaligenes, Zobellella, Lysinibacillus, Sphingobacterium, Achromobacter, Acinetobacter, Alcanivorax, Ochrobactrum, Microbacterium, Rhodococcus, and Stenotrophomonas isolated from sea turtles. Pathogens detected in the bacterial flora can threaten both sea turtles and field workers. These data can contribute to the development of new conservation strategies on the treatment of sea turtles, nest protection, and pollution detection on nesting beaches.

Screening for carriage of carbapenem-resistant Enterobacteriaceae in settings of high endemicity: a position paper from an Italian working group on CRE infections

Introduction

A variety of national and international guidelines exist around the management of carbapenem resistant Enterobacteriaceae (CREs), but some of these are several years old and do not reflect current epidemiology and they also do not necessarily give pragmatic advice around active surveillance of CREs in countries with a high burden of cases and limited resources. This paper aims to provide a best practice position paper to guide active surveillance in a variety of scenarios in these settings, and discusses which patients should be screened, what methods could be used for screening, and how results might influence infection prevention interventions.

Methods

This paper was developed as a result of a series of meetings of expert opinion leaders representing the major infectious disease and infection prevention societies in Italy and having the endorsement of AMCLI (Italian Association of Clinical Microbiology) and SITA (Italian Society for Anti-infective Therapy). There was no attempt to undertake a full systematic review of the evidence, as it was felt that this was inadequate to inform a pragmatic view on the best way forward based on current epidemiology and infection rates.

Key recommendations

Key recommendations focus on the urgent need to promote measures to prevent transmission and infection, focusing on high risk patients and clinical areas, as well as outbreak situations. Active surveillance leading to appropriate infection prevention precautions plays a major role in this.

Conclusions

There are limited national or international guidelines giving pragmatic advice on the most appropriate measures for active surveillance and management of colonized patients in a high-burden setting such as Italy. While individual hospitals and regions will need to formulate their own policies based on local epidemiology, this position paper attempts to highlight current best practice in this area and provide pragmatic advice for clinicians, infection prevention staff, and healthcare managers.

A comparative evaluation of two chromogenic media for surveillance of carbapenem-resistant Enterobacterales with non-carbapenemase-producing or carbapenemase-producing strains other than blaKPC: blaGES-5, blaNDM-1 or blaVIM-2

Background

Infections caused by carbapenem-resistant Enterobacterales (CREs) are an emerging problem associated with high rates of morbidity and mortality. CREs are divided into two categories (carbapenemase-producing [CP] CRE and non-CP CRE). The most prevalent carbapenemase produced by Enterobacterales is Klebsiella pneumoniae carbapenemase (KPC) in Korea. Rapid identification of CREs is clinically important in infection control precaution. We compared the performance of two chromogenic media (chromID CARBA agar and CHROMagar KPC agar) for non-CP CREs or CP CREs with blaGES-5, blaNDM-1 or blaVIM-2 in a Korean hospital.

Methods

The study was carried out during a 3-month period from April to June 2017 during the surveillance program for CRE colonization. Antimicrobial susceptibility testing (AST) and polymerase chain reaction (PCR) were performed at the Korean Centers for Disease Control and Prevention.

Results

A total of 45 rectal swabs from 42 hospitalized patients were examined. Sensitivity of both chromID CARBA and CHROMagar KPC were 100% for CP CREs; and 50% and 100% for non-CP CREs, respectively. Specificity of chromID CARBA and CHROMagar KPC were 89.2% and 70.3% for CP CRE, respectively; and 76.9% and 66.7% for non-CP CRE, respectively.

Conclusions

The CHROMagar KPC is useful to monitor non-CP and CP CREs. The chromID CARBA is efficient for rapid detection of CP CREs requiring high contact precaution.

A PCR-based diagnostic testing strategy to identify carbapenemase-producing Enterobacteriaceae carriers upon admission to UK hospitals: early economic modelling to assess costs and consequences

BACKGROUND

Carbapenemase-producing Enterobacteriaceae (CPE), bacteria which are resistant to the carbapenem class of antibiotics, present an urgent public health risk. The objective of this study was to assess the potential costs and consequences of implementing a testing strategy involving a polymerase chain reaction (PCR)-based diagnostic test for CPE amongst high risk patients upon admission to UK hospitals, to replace the current culture-based testing strategy.

METHODS

A decision-analytic model was developed to estimate the expected medical care costs associated with a PCR testing strategy for CPE compared with the current culture testing strategy, and to consider the consequences, in terms of the diagnostic accuracy and associated cost implications, of each approach. The modelled population were patients admitted to hospital at high risk of colonisation with CPE, with model pathways for current practice based on those described in the Public Health England (PHE) toolkit for CPE testing. Costs were estimated from a UK National Health Service (NHS) perspective, with outcomes presented in terms of percentage of samples identified as true positive, false positive, true negative and false negative following each method of testing.

RESULTS

Results indicated that the PCR testing strategy led to an estimated cost saving of £462 per patient for a 5-day hospital stay. For all sensitivity analyses conducted, PCR testing resulted in an expected cost saving. Potential cost savings approached £850 per patient for the sensitivity analysis assuming a 15-day hospital stay, indicating that PCR testing results in greater cost savings as length of stay increases. Fewer false positive, and more true negative, cases were identified with the PCR testing strategy in all analyses conducted.

CONCLUSIONS

This economic analysis gives an insight into the potential cost savings that could be made by the UK NHS through the introduction of a PCR-based diagnostic testing strategy to replace current recommended culture-based methods for the detection of CPE. Savings are due primarily to a faster time to result with PCR, meaning that CPE-free patients are not isolated unnecessarily. Therefore, a PCR-based diagnostic may aid appropriate use of isolation resource.

A Large, Refractory Nosocomial Outbreak of Klebsiella pneumoniae Carbapenemase-Producing Escherichia coli Demonstrates Carbapenemase Gene Outbreaks Involving Sink Sites Require Novel Approaches to Infection Control

Carbapenem-resistant Enterobacteriaceae (CRE) represent a health threat, but effective control interventions remain unclear. Hospital wastewater sites are increasingly being highlighted as important potential reservoirs. We investigated a large Klebsiella pneumoniae carbapenemase (KPC)-producing Escherichia coli outbreak and wider CRE incidence trends in the Central Manchester University Hospital NHS Foundation Trust (CMFT) (United Kingdom) over 8 years, to determine the impact of infection prevention and control measures. Bacteriology and patient administration data (2009 to 2017) were linked, and a subset of CMFT or regional hospital KPC-producing E. coli isolates (n = 268) were sequenced. Control interventions followed international guidelines and included cohorting, rectal screening (n = 184,539 screens), environmental sampling, enhanced cleaning, and ward closure and plumbing replacement. Segmented regression of time trends for CRE detections was used to evaluate the impact of interventions on CRE incidence. Genomic analysis (n = 268 isolates) identified the spread of a KPC-producing E. coli outbreak clone (strain A, sequence type 216 [ST216]; n = 125) among patients and in the environment, particularly on 2 cardiac wards (wards 3 and 4), despite control measures. ST216 strain A had caused an antecedent outbreak and shared its KPC plasmids with other E. coli lineages and Enterobacteriaceae species. CRE acquisition incidence declined after closure of wards 3 and 4 and plumbing replacement, suggesting an environmental contribution. However, ward 3/ward 4 wastewater sites were rapidly recolonized with CRE and patient CRE acquisitions recurred, albeit at lower rates. Patient relocation and plumbing replacement were associated with control of a clonal KPC-producing E. coli outbreak; however, environmental contamination with CRE and patient CRE acquisitions recurred rapidly following this intervention. The large numbers of cases and the persistence of bla _KPC in E. coli, including pathogenic lineages, are of concern.

Utility of CHROMagar mSuperCARBA for surveillance cultures of carbapenemase-producing Enterobacteriaceae

Culture of carbapenemase-producing Enterobacteriaceae (CPE) as part of active surveillance is one of the most useful strategies for successful infection control programmes. Our objective was to compare the recently introduced CHROMagar mSuperCARBA agar for CPE detection in surveillance cultures from perineal swabs with the US Centers for Disease Control and Prevention method. Our results showed that this agar is a useful and affordable alternative (sensitivity 93.05%, specificity 96.21%, diagnostic accuracy 95.2%) to detect CPE in hospital settings.

A Decade of Development of Chromogenic Culture Media for Clinical Microbiology in an Era of Molecular Diagnostics

In the last 25 years, chromogenic culture media have found widespread application in diagnostic clinical microbiology. In the last decade, the range of media available to clinical laboratories has expanded greatly, allowing specific detection of additional pathogens, including Pseudomonas aeruginosa, group B streptococci, Clostridium difficile, Campylobacter spp., and Yersinia enterocolitica. New media have also been developed to screen for pathogens with acquired antimicrobial resistance, including vancomycin-resistant enterococci, carbapenem-resistant Acinetobacter spp., and Enterobacteriaceae with extended-spectrum β-lactamases and carbapenemases. This review seeks to explore the utility of chromogenic media in clinical microbiology, with particular attention given to media that have been commercialized in the last decade. The impact of laboratory automation and complementary technologies such as matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is also assessed. Finally, the review also seeks to demarcate the role of chromogenic media in an era of molecular diagnostics.

Current methods for the identification of carbapenemases

Detection of carbapenemases in clinical microbiology labs is a challenging issue. Comparison of the results of susceptibility testing with the breakpoint values of carbapenems is the first step in the screening of carbapenemase producers. To date, screening of carbapenemase-producing (CP) bacteria has been mostly performed by a selective medium. Although these media are practical for the detection of most CP isolates, the inoculated plates have to be incubated overnight. Subsequently, we need the confirmation of the carbapenemase producers present in the culture medium by additional testing [e.g. inhibition studies with liquid or solid media, modified Hodge test (MHT), or gradient strips], which can take up to another 48 hours. Despite the lack of discrimination between the three different classes of carbapenemases (KPC, MBL and OXA) and difficulties in the interpretation of the results, the MHT is usually deemed as the phenotypic reference method for the confirmation of carbapenemase production. Molecular techniques, such as real-time polymerase chain reaction (PCR) assays, in contrast to phenotypic methods that are very time consuming, are faster and allow for the quick identification of carbapenemase genes. These techniques can detect and characterize carbapenemases, including NDM- and KPC-mediated resistance, which is critical for epidemiological investigations. The aim of this review is to gather a summary of the available methods for carbapenemase detection and describe the strengths and weaknesses of each method.

Screening for carbapenem-resistant Enterobacteriaceae: Who, When, and How?

The global spread of carbapenem-resistant Enterobacteriaceae (CRE) has been fostered by the lack of preemptive screening of patients in healthcare facilities that could prevent patient-to-patient transmission. Outbreaks of CRE infections have led some institutions to implement rigorous screening programs, although controlled comparative data are frequently lacking. Resource limitations and uncertainty regarding the optimal approach has kept many facilities from enacting more active routine surveillance policies that could reduce the prevalence of CRE. The ideal population to target for screening, the frequency of testing, and the preferred test method are components of surveillance programs that remain open to debate. This review discusses the rationale for different screening policies in use and the performance characteristics of laboratory methods available to detect CRE carriage.

Contemporary challenges and opportunities in the diagnosis and outbreak detection of multidrug-resistant infectious disease

INTRODUCTION

The dissemination of multi-drug resistant bacteria (MDRB) has become a major public health concern worldwide because of the increase in infections caused by MDRB, the difficulty in treating them, and expenditures in patient care. Areas covered: We have reviewed challenges and contemporary opportunities for rapidly confronting infections caused by MDRB in the 21st century, including surveillance, detection, identification of resistance mechanisms, and action steps. Expert commentary: In this context, the first critical point for clinical microbiologists is to be able to rapidly detect an abnormal event, an outbreak and/or the spread of a MDRB with surveillance tools so that healthcare policies and therapies adapted to a new stochastic event that will certainly occur again in the future can be implemented.

Intestinal Carriage of Carbapenemase-Producing Organisms: Current Status of Surveillance Methods

Carbapenemases have become a significant mechanism for broad-spectrum β-lactam resistance in Enterobacteriaceae and other Gram-negative bacteria such as Pseudomonas and Acinetobacter spp. Intestinal carriage of carbapenemase-producing organisms (CPOs) is an important source of transmission. Isolation of carriers is one strategy that can be used to limit the spread of these bacteria. In this review, we critically examine the clinical performance, advantages, and disadvantages of methods available for the detection of intestinal carriage of CPOs. Culture-based methods (Centers for Disease Control and Prevention [CDC] protocols, chromogenic media, specialized agars, and double-disk synergy tests) for detecting carriage of CPOs are convenient due to their ready availability and low cost, but their limited sensitivity and long turnaround time may not always be optimal for infection control practices. Contemporary nucleic acid amplification techniques (NAATs) such as real-time PCR, hybridization assays, loop-mediated isothermal amplification (LAMP), or a combined culture and NAAT approach may provide fast results and/or added sensitivity and specificity compared with culture-based methods. Infection control practitioners and clinical microbiologists should be aware of the strengths and limitations of available methods to determine the most suitable approach for their medical facility to fit their infection control needs.

Performance of the BD MAX™ instrument with Check-Direct CPE real-time PCR for the detection of carbapenemase genes from rectal swabs, in a setting with endemic dissemination of carbapenemase-producing Enterobacteriaceae

Carbapenemase-producing Enterobacteriaceae (CPE) represent an increasing public health issue and the early detection of colonization by CPE can help the implementation of infection control measures among inpatients. In this study, BD MAX Check-Direct CPE screen, with two different Master Mixes (BDMix and CPMix), using the automatic BD MAX(™) instrument, was evaluated for the detection of blaKPC, blaOXA-48, blaVIM and blaNDM genes, in comparison to selective broth enrichment and direct culture from rectal swabs. Among a total of 557 rectal swabs samples, 29 (5.2%) tested positive for CPE (23 for blaKPC, 5 for blaVIM and one for blaOXA-48). The sensitivity, specificity, positive and negative likelihood ratios values were 93.1%, 97.3%, 34.5 and 0.07, for BMix, and 100%, 97.1 %, 34.5 and 0 for CPMix, respectively. Five samples were positive with molecular methods only. The turn-around time was reduced from 18-24 hours (direct culture), or 48 h (broth enrichment) to only 3 h.

Evaluation of Multiple Methods for Detection of Gastrointestinal Colonization of Carbapenem-Resistant Organisms from Rectal Swabs

Rectal swabs from high-risk patients were screened for carbapenem-resistant organisms (CROs) using several methods. The direct MacConkey plate method was the most sensitive for CROs (95%), while chromID CARBA and the Check-Direct CPE screen assay were the most sensitive for the detection of carbapenemase-producing organisms (CPOs) (100%; all blaKPC). All methods had a specificity of >90% for CROs, and for CPOs, the specificity ranged from 85 to 98%. Broth enrichment methods performed poorly compared to direct inoculation methods, negating the need for the broth enrichment step.

Evaluation of Remel Spectra CRE Agar for Detection of Carbapenem-Resistant Bacteria from Rectal Swabs Obtained from Residents of a Long-Term-Care Facility

We compared the Remel Spectra CRE agar plate to CDC standard methodology for the isolation of carbapenem-resistant Enterobacteriaceae (CRE) from 300 rectal swab specimens obtained from patients residing in a long-term-care facility (LTCF). Multiplex PCR experiments were performed on isolates to identify specific Klebsiella pneumoniae carbapenemases (KPC) and additional β-lactamases. Of the 300 patients, 72 (24%) harbored CRE and were PCR positive for KPC enzymes. The Remel Spectra CRE plates detected KPC-type CRE in isolates from 70 of 72 patients (97.2%), while the CDC method detected CRE in 56 of 72 (77.8%). CRE identification results were available in 18 h compared to 36 h for the CDC method. Remel Spectra CRE agar plates can provide useful means for a fast and reliable method for detecting KPC-type CRE and for accelerated institution of appropriate infection control precautions.

Faecal carriage of carbapenemase-producing Gram-negative bacilli in hospital settings in southern France

The emergence of carbapenemase-producing Gram-negative bacilli is a worldwide problem. To date, no study has evaluated the prevalence of faecal carriage of carbapenemase-producing and carbapenem-resistant Gram-negative bacilli (CR GNB) in France. From 1 February to 30 April 2012, we conducted a prospective, multicentre study in three University Hospitals and four General Hospitals in the south of France. The carriage of carbapenemase-producing Enterobacteriaceae (CPE) and other CR GNB was screened by both cultivation on chromID® CARBA and chromID® OXA-48 media (bioMérieux) and molecular tools [multiplex polymerase chain reaction (PCR) and NucliSENS EasyQ® KPC (bioMérieux)]. The genetic relationship between isolates was assessed by rep-PCR (DiversiLab, bioMérieux) or multilocus sequence typing (MLST). The prevalences of CR GNB and carbapenemase-producing bacteria were 2.4 % (27/1,135) and 0.4 % (n = 5), respectively. Two strains corresponded to OXA-23-producing Acinetobacter baumannii and belonged to the widespread sequence type (ST) 2/international clone II, whereas one strain was an ST15 OXA-48-producing Klebsiella pneumoniae. Two OXA-48-producers were detected exclusively by PCR. This first French study revealed the very low dissemination of carbapenemase-producing bacteria in patients attending hospitals in southern France during a non-outbreak situation. However, the increasing description of epidemic cases in this area must reinforce the use of hygiene procedures to prevent diffusion of these multidrug-resistant microorganisms.

Comparison of chromogenic media for recovery of carbapenemase-producing enterobacteriaceae (CPE) and evaluation of CPE prevalence at a tertiary care academic medical center

We evaluated the performance characteristics of chromID CARBA and HardyCHROM Carbapenemase for the detection of carbapenemase-producing Enterobacteriaceae (CPE). A CPE prevalence study was conducted using chromID CARBA; this demonstrated that in low-prevalence settings, CPE screening agars may lack specificity, and confirmation of putative isolates is necessary.

Evaluation of carbapenemase screening and confirmation tests with Enterobacteriaceae and development of a practical diagnostic algorithm

Reliable identification of carbapenemase-producing members of the family Enterobacteriaceae is necessary to limit their spread. This study aimed to develop a diagnostic flow chart using phenotypic screening and confirmation tests that is suitable for implementation in different types of clinical laboratories. A total of 334 clinical Enterobacteriaceae isolates genetically characterized with respect to carbapenemase, extended-spectrum β-lactamase (ESBL), and AmpC genes were analyzed. A total of 142/334 isolates (42.2%) were suspected of carbapenemase production, i.e., intermediate or resistant to ertapenem (ETP) and/or meropenem (MEM) and/or imipenem (IPM) according to EUCAST clinical breakpoints (CBPs). A group of 193/334 isolates (57.8%) showing susceptibility to ETP, MEM, and IPM was considered the negative-control group in this study. CLSI and EUCAST carbapenem CBPs and the new EUCAST MEM screening cutoff were evaluated as screening parameters. ETP, MEM, and IPM with or without aminophenylboronic acid (APBA) or EDTA combined-disk tests (CDTs) and the Carba NP-II test were evaluated as confirmation assays. EUCAST temocillin cutoffs were evaluated for OXA-48 detection. The EUCAST MEM screening cutoff (<25 mm) showed a sensitivity of 100%. The ETP APBA CDT on Mueller-Hinton agar containing cloxacillin (MH-CLX) displayed 100% sensitivity and specificity for class A carbapenemase confirmation. ETP and MEM EDTA CDTs showed 100% sensitivity and specificity for class B carbapenemases. Temocillin zone diameters/MIC testing on MH-CLX was highly specific for OXA-48 producers. The overall sensitivity, specificity, positive predictive value, and negative predictive value of the Carba NP-II test were 78.9, 100, 100, and 98.7%, respectively. Combining the EUCAST MEM carbapenemase screening cutoff (<25 mm), ETP (or MEM), APBA, and EDTA CDTs, and temocillin disk diffusion on MH-CLX promises excellent performance for carbapenemase detection.