Evaluation of the CRE and ESBL ELITe MGB® kits for the accurate detection of carbapenemase- or CTX-M-producing bacteria

Intestinal colonization with multidrug-resistant Enterobacterales: screening, epidemiology, clinical impact, and strategies to decolonize carriers

The clinical impact of infections due to extended-spectrum β-lactamase (ESBL)- and/or carbapenemase-producing Enterobacterales (Ent) has reached dramatic levels worldwide. Infections due to these multidrug-resistant (MDR) pathogens-especially Escherichia coli and Klebsiella pneumoniae-may originate from a prior asymptomatic intestinal colonization that could also favor transmission to other subjects. It is therefore desirable that gut carriers are rapidly identified to try preventing both the occurrence of serious endogenous infections and potential transmission. Together with the infection prevention and control countermeasures, any strategy capable of effectively eradicating the MDR-Ent from the intestinal tract would be desirable. In this narrative review, we present a summary of the different aspects linked to the intestinal colonization due to MDR-Ent. In particular, culture- and molecular-based screening techniques to identify carriers, data on prevalence and risk factors in different populations, clinical impact, length of colonization, and contribution to transmission in various settings will be overviewed. We will also discuss the standard strategies (selective digestive decontamination, fecal microbiota transplant) and those still in development (bacteriophages, probiotics, microcins, and CRISPR-Cas-based) that might be used to decolonize MDR-Ent carriers.

Evaluation of the EasyScreen™ ESBL/CPO Detection Kit for the Detection of ß-Lactam Resistance Genes

Early detection of multidrug resistant bacteria is of paramount importance for implementing appropriate infection control strategies and proper antibacterial therapies. We have evaluated a novel real-time PCR assay using fluorescent probes and 3base^® technology, the EasyScreen^TM ESBL/CPO Detection Kit (Genetic Signatures, Newtown, Australia), for the detection of 15 β-lactamase genes (bla_VIM, bla_NDM, bla_IMP, bla_OXA-48, bla_KPC, bla_OXA-23, bla_OXA-51, bla_SME,bla_IMI, bla_GES,bla_TEM,bla_SHV, bla_CTX-M,bla_CMY, bla_DHA) and colistin resistance mcr-1 gene from 341 bacterial isolates (219 Enterobacterales, 66 P. aeruginosa and 56 A. baumannii) that were grown on Mueller–Hinton (MH) agar plates. One colony was suspended in provided extraction buffer, which lyses and converts the nucleic acids into a 3base^®-DNA form (cytosines are converted into uracil, and subsequently thymine during PCR). The converted bacterial DNA is then added to the 6 PCR mixes, with primers for three targets plus one internal control. The EasyScreen^TM ESBL/CPO Detection Kit was able to detect the 5-major (NDM, VIM, IMP, KPC, OXA-48) and 2-minor (IMI, Sme) carbapenemases and their variants irrespective of the species expressing them with nearly 100% sensitivity and specificity. With cephalosporinases CMY (82% of sensitivity) and DHA (87% of sensitivity) detection of chromosomally encoded variants was less efficient. Similarly, the chromosomally encoded OXA-51 variants were not consistently detected in A. baumannii. Despite being capable of efficiently detecting bla_CTX-M-, bla_TEM-, bla_SHV- and bla_GES-like genes, the EasyScreen™ ESBL/CPO Detection Kit was not able to distinguish between penicillinases and ESBL-variants of TEM and SHV and between GES-ESBLs and GES-carbapenemases. As GES enzymes are still rare, their detection as an ESBL or a carbapenemase remains important. Detection of mcr-1 was efficient, but none of the other mcr-alleles were detected in the 341 bacterial isolates tested. The EasyScreen^TM ESBL/CPO Detection Kit is adapted for the detection of the most prevalent carbapenemases encountered in Gram-negatives isolated worldwide.

Rapid detection of CTX-M-type ESBLs and carbapenemases directly from biological samples using the BL-DetecTool

BACKGROUND

Lateral flow immunoassays (LFIA) have shown their usefulness for detecting CTX-M- and carbapenemase-producing Enterobacterales (CPEs) in bacterial cultures. Here, we have developed and validated the BL-DetecTool to detect CTX-M enzymes and carbapenemases directly from clinical samples.

METHODS

The BL-DetecTool is an LFIA that integrates an easy sample preparation device named SPID (Sampling, Processing, Incubation and Detection). It was evaluated in three University hospitals on urine, blood culture (BC) and rectal swab (RS) specimens either of clinical origin or on spiked samples. RS evaluation was done directly and after a 24 h enrichment step.

RESULTS

The CTX-M BL-DetecTool was tested on 485 samples (154 BC, 150 urines, and 181 RS) and revealed a sensitivity and specificity of 97.04% (95% CI 92.59%-99.19%) and 99.43% (95% CI 97.95%-99.93%), respectively. Similarly, the Carba5 BL-DetecTool was tested on 382 samples (145 BC, 116 urines, and 121 RS) and revealed a sensitivity and specificity of 95.3% (95% CI 89.43%-98.47%) and 100% (95% CI 98.67%-100%), respectively. While with the Carba5 BL-DetecTool five false negatives were observed, mostly in RS samples, with the CTX-M BL-DetecTool, in addition to four false-negatives, two false-positives were also observed. Direct testing of RS samples revealed a sensitivity of 78% and 86% for CTX-M and carbapenemase detection, respectively.

CONCLUSIONS

BL-DetecTool showed excellent biological performance, was easy-to-use, rapid, and could be implemented in any microbiology laboratory around the world, without additional equipment, no need for electricity, nor trained personnel. It offers an attractive alternative to costly molecular methods.

Phenotypic and genotypic detection methods for antimicrobial resistance in ESKAPE pathogens (Review)

Antimicrobial resistance (AMR) represents a growing public health problem worldwide. Infections with such bacteria lead to longer hospitalization times, higher healthcare costs and greater morbidity and mortality. Thus, there is a greater need for rapid detection methods in order to limit their spread. The ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.) are a series of epidemiologically-important microorganisms of great concern due to their high levels of resistance. This review aimed to update the background information on the ESKAPE pathogens as well as to provide a summary of the numerous phenotypic and molecular methods used to detect their AMR mechanisms. While they are usually linked to hospital acquired infections, AMR is also spreading in the veterinary and the environmental sectors. Yet, the epidemiological loop closes with patients which, when infected with such pathogens, often lack therapeutic options. Thus, it was aimed to give the article a One Health perspective.

Multiplex Lateral Flow Immunoassay for the Detection of Expanded-Spectrum Hydrolysis and CTX-M Enzymes

Background: Early detection of expanded-spectrum cephalosporinase (ESC) hydrolyzing ß-lactamases is essential for antibiotic stewardship. Here we have developed a multiplex lateral flow immunoassay (LFIA) that detects cefotaxime-hydrolyzing activity as well as the most prevalent ESC-hydrolyzing ß-lactamases: the CTX-M-like. Methods: The Rapid LFIA ESC test was evaluated retrospectively on 188 (139 Enterobacterales, 30 Pseudomonas spp. and 14 Acinetobacter spp.) agar-grown bacterial isolates with well-characterized ß-lactamase content. One single colony was resuspended in 150 µL extraction buffer containing cefotaxime, incubated at room temperature for 30 min prior to loading on the LFIA for reading within 10 min. Results: Out of the 188 isolates, all 17 that did not express a β-lactamase hydrolyzing cefotaxime gave negative results, and all 171 isolates expressing a β-lactamase known to hydrolyze cefotaxime, gave a positive test result. In addition, all 86 isolates expressing a CTX-M-variant belonging to one of the five CTX-M-subgroups were correctly identified. The sensitivity and specificity was 100% for both tests. Conclusions: The results showed that the multiplex LFIA was efficient, fast, low cost and easy to implement in routine laboratory work for the confirmation of ESC hydrolyzing activity and the presence of CTX-M enzymes.

Direct detection of extended-spectrum-β-lactamase-producers in Enterobacterales from blood cultures: a comparative analysis

Accurate detection of extended-spectrum-β-lactamase (ESBL)-producing Enterobacterales from bloodstream infection (BSI) is of paramount importance for both epidemiological and clinical purposes, especially for optimization of antibiotic stewardship interventions. Three phenotypic methods for the detection of ESBL phenotype in Klebsiella pneumoniae and Escherichia coli BSI were compared over a 4-month period (May-August 2021) in a main University Hospital from Northern Italy. The methods were the biochemical Rapid ESBL NP®, the immunological NG-Test CTX-M MULTI®, and the E-test technique based on ESBL E-test®. One hundred forty-two blood cultures (BCs) positive for K. pneumoniae or E. coli were included. ESBL and carbapenemase phenotype were detected in 26.1% (n = 37) and 16.9% (n = 24), respectively. The Rapid ESBL NP®, NG-Test CTX-M MULTI®, and direct ESBL E-test® positive and negative predictive values with 95% confidence intervals were 1 (0.87-1) and 0.97 (0.92-0.99), 1 (0.87-1) and 0.97 (0.92-0.99), and 1 (0.88-1) and 1 (0.96-1), respectively. The three phenotypic methods evaluated showed good performance in the detection of ESBL phenotype from K. pneumoniae- or E. coli-positive BCs. Rapid ESBL NP® and NG-test CTX-M® offer the important advantage of a turnaround time of 15 to 45 min, and the Rapid ESBL NP test in addition detects any type of ESBL producers.

Detection of Multidrug-Resistant Enterobacterales-From ESBLs to Carbapenemases

Multidrug-resistant Enterobacterales (MDRE) are an emerging threat to global health, leading to rising health care costs, morbidity and mortality. Multidrug-resistance is commonly caused by different β-lactamases (e.g., ESBLs and carbapenemases), sometimes in combination with other resistance mechanisms (e.g., porin loss, efflux). The continuous spread of MDRE among patients in hospital settings and the healthy population require adjustments in healthcare management and routine diagnostics. Rapid and reliable detection of MDRE infections as well as gastrointestinal colonization is key to guide therapy and infection control measures. However, proper implementation of these strategies requires diagnostic methods with short time-to-result, high sensitivity and specificity. Therefore, research on new techniques and improvement of already established protocols is inevitable. In this review, current methods for detection of MDRE are summarized with focus on culture based and molecular techniques, which are useful for the clinical microbiology laboratory.

Genetic Diversity, Biochemical Properties, and Detection Methods of Minor Carbapenemases in Enterobacterales

Gram-negative bacteria, especially Enterobacterales, have emerged as major players in antimicrobial resistance worldwide. Resistance may affect all major classes of anti-gram-negative agents, becoming multidrug resistant or even pan-drug resistant. Currently, β-lactamase-mediated resistance does not spare even the most powerful β-lactams (carbapenems), whose activity is challenged by carbapenemases. The dissemination of carbapenemases-encoding genes among Enterobacterales is a matter of concern, given the importance of carbapenems to treat nosocomial infections. Based on their amino acid sequences, carbapenemases are grouped into three major classes. Classes A and D use an active-site serine to catalyze hydrolysis, while class B (MBLs) require one or two zinc ions for their activity. The most important and clinically relevant carbapenemases are KPC, IMP/VIM/NDM, and OXA-48. However, several carbapenemases belonging to the different classes are less frequently detected. They correspond to class A (SME-, Nmc-A/IMI-, SFC-, GES-, BIC-like…), to class B (GIM, TMB, LMB…), class C (CMY-10 and ACT-28), and to class D (OXA-372). This review will address the genetic diversity, biochemical properties, and detection methods of minor acquired carbapenemases in Enterobacterales.

A Lateral Flow Immunoassay for the Rapid Identification of CTX-M-Producing Enterobacterales from Culture Plates and Positive Blood Cultures

We have developed a lateral flow immunoassay (LFIA), named NG-Test CTX-M MULTI (NG-Test), to detect group 1, 2, 8, 9, 25 CTX-M producers from agar plates and from positive blood cultures in less than 15 min. The NG-Test was validated retrospectively on 113 well-characterized enterobacterial isolates, prospectively on 102 consecutively isolated ESBL-producers from the Bicêtre hospital and on 100 consecutive blood cultures positive with a gram-negative bacilli (GNB). The NG-Test was able to detect all CTX-M producers grown on the different agar plates used in clinical microbiology laboratories. No false positive nor negative results were observed. Among the 102 consecutive ESBL isolates, three hyper mucous isolates showed an incorrect migration leading to invalid results (no control band). Using an adapted protocol, the results could be validated. The NG-Test detected 99/102 ESBLs as being CTX-Ms. Three SHV producers were not detected. Among the 100 positive blood cultures with GNB tested 10/11 ESBL-producers were detected (8 CTX-M-15, 2 CTX-M-27). One SHV-2-producing-E. cloacae was missed. The NG-Test CTX-M MULTI showed 100% sensitivity and specificity with isolates cultured on agar plates and was able to detect 98% of the ESBL-producers identified in our clinical setting either from colonies or from positive blood cultures.

Detection of Carbapenemase and CTX-M Encoding Genes Directly from Bronchoalveolar Lavage Using the CRE and ESBL ELITe MGB Assays: Toward Early and Optimal Antibiotic Therapy Management of Critically Ill Patients with Pneumonia

The detection of carbapenemase extended-spectrum β-lactamase (ESBL)-producing Enterobacterales (EB) has become a major issue among critically ill patients, especially due to their impact on appropriate antimicrobial therapy. This study aimed at evaluating the potential contribution of molecular assays to early optimization of empirical antibiotic therapy among critically ill patients with carbapenemase- and/or CTX-M-producing EB pneumonia. The CRE and ESBL ELITe MGB^® assays were evaluated directly on 197 bronchoalveolar lavage (BAL) samples obtained from 120 patients. Molecular results were then compared to routine culture-based diagnostic results, and a retrospective analysis of the therapeutic antimicrobial management was performed. Among the 197 clinical specimens, bla_KPC-like and bla_CTX-M-like were detected in 20 (10.2%) and 12 (6.1%) specimens belonging to 15 and 11 patients, respectively. Positive predictive value (PPV) and negative predictive value (NPV) of the CRE ELITe MGB Kit were 85% [95% confidence interval [CI]: 64.9-94.6] and 100%, respectively. PPV and NPV of the ESBL ELITe MGB Kit were 75% [95% CI: 49.4-90.2] and 100%, respectively. Retrospective analysis of the therapeutic antimicrobial management at the time of BAL collection showed that in ∼50% of patients with carbapenemase- and CTX-M-producing EB pneumonia empirical antibiotic therapy could have been optimized at least 48-72 hr earlier if positive molecular data had been used. The CRE and ESBL ELITe MGB assays might be an interesting tool for expediting optimization of empirical antibiotic therapy in critically ill patients with pneumonia, depending on local epidemiology of antibiotic resistance, patient risk stratification for EB infection, and availability of an antimicrobial stewardship team.

A profile of the GenePOC Carba C assay for the detection and differentiation of gene sequences associated with carbapenem-non-susceptibility

The novel GenePOC/Revogene Carba C assay (GenePOC, Québec, Canada; now Meridian Bioscience, Cincinnati, OH, USA) is a CE-IVD marked, FDA-approved qualitative in vitro diagnostic test for the detection of genes associated with carbapenem-non-susceptibility. Colonies of Enterobacterales can be directly tested without prior DNA isolation. The test consists of a fluorescent-based real-time PCR assay that runs on the centripetal microfluidic revogene platform, providing results within 70 minutes. The assay was evaluated in two studies comprising a total of 294 molecularly characterized clinical Enterobacterales isolates. The overall sensitivity for the detection of carbapenemase gene sequences with the GenePOC assay was 100% (95% CI, 98.4% to 100). Besides the common KPC, VIM, NDM and OXA-48-like carbapenemase genes, also the very variable IMP variants were all detected. The specificity of the assay was 100% (95% CI, 98.8% to 100%). In this article the performance of the GenePOC/Revogene Carba C assay is evaluated and other currently available methods for the detection of carbapenemases are reviewed.

Evaluation of the Revogene Carba C Assay for Detection and Differentiation of Carbapenemase-Producing Gram-Negative Bacteria

The Revogene Carba C assay (formerly GenePOC Carba assay) is a multiplex nucleic acid-based in vitro diagnostic test intended for the detection of carbapenemase-producing Enterobacterales (CPE) from cultured colonies. This assay was evaluated directly on colonies of 118 well-characterized Enterobacterales with reduced susceptibility to carbapenems and on 49 multidrug-resistant (MDR) Pseudomonas aeruginosa and 40 MDR Acinetobacter baumannii isolates. The Revogene Carba C assay's performance was high, as it was able to detect the five major carbapenemases (NDM, VIM, IMP, KPC, and OXA-48). In Enterobacterales, sensitivity and specificity were 100%. When extrapolating the results to the French CPE epidemiology between 2012 and 2018, this assay would have detected 99.28% of the 9,624 CPE isolates sent to the French NRC, missing 69 CPE isolates (2 GES-5, 10 OXA-23, 2 TMB-1, 1 SME-4, 53 IMI, and 1 FRI). The overall sensitivity and specificity for CP P. aeruginosa were 93.7 and 100%, respectively, as two rare IMP variants (IMP-31 and -46) were not detected. Extrapolating these results to the French epidemiology of CP P. aeruginosa in 2017, 93.3% would have been identified, missing only 1 DIM and 10 GES variants. The Revogene Carba C assay accurately identified the targeted carbapenemase genes in A. baumannii, but when extrapolating these results to the French CP A. baumannii epidemiology of 2017, only 12.50% of them could be detected, as OXA-23 is the most prevalent carbapenemase in CP A. baumannii The Revogene Carba C assay showed excellent sensitivity and specificity for the five most common carbapenemases regardless of the bacterial host. It is well adapted to the CPE and CP P. aeruginosa epidemiology of many countries worldwide, which makes it suitable for use in the routine microbiology laboratory, with a time to result of ca. 85 min for eight isolates simultaneously.

Accuracy of the ELITe MGB assays for the detection of carbapenemases, CTX-M, Staphylococcus aureus and mecA/C genes directly from respiratory samples

INTRODUCTION

Bacterial lower respiratory tract infections (BLRTI) may represent serious clinical conditions which can lead to respiratory failure, intensive care unit admission and high hospital costs. The detection of carbapenemase- and extended-spectrum β-lactamase (ESBL)-producing Enterobacterales, as well as meticillin-resistant Staphylococcus aureus (MRSA), has become a major issue, especially in healthcare-associated infections. This study aimed to determine whether molecular assays could detect genes encoding carbapenemases, ESBL and MRSA directly from respiratory samples in order to expedite appropriate therapy and infection control for patients with BLRTI.

METHODS

The carbapenem-resistant enterobacterales (CRE), ESBL and MRSA/SA ELITe MGB assays were performed directly on 354 respiratory specimens sampled from 318 patients admitted with BLRTI. Molecular results were compared with routine culture-based diagnostics results.

RESULTS

Positive (PPV) and negative (NPV) predictive values of the CRE ELITe MGB kit were 75.9% [95% confidence interval (CI) 60.3-86.7] and 100%, respectively. PPV and NPV of the ESBL ELITe MGB kit were 80.8% (95% CI 63.6-91.0) and 99.1% (95% CI 96.6-99.8), respectively. PPV and NPV of the MRSA/SA ELITe MGB kit were 91.7% (95% CI 73.7-97.7)/100% and 98.3% (95% CI 89.8-99.3)/96.8% (95% CI 81.6-99.5), respectively.

DISCUSSION

Validity assessment of molecular assays detecting the main antibiotic resistance genes directly from respiratory samples showed high accuracy compared with culture-based results. Molecular assays detecting the main carbapenemase, ESBL, S. aureus and meticillin resistance encoding genes provide an interesting tool with potential to expedite optimization of antibiotic therapy and infection control practices in patients with BLRTI.

Evaluation of the ELITe InGenius PCR Platform for Detection of Mycoplasma pneumoniae

Mycoplasma pneumoniae is the leading cause of bacterial community-acquired pneumonia in persons of all ages. Due to the fastidious nature of this bacterium and the necessary specialized growth media, nucleic acid amplification testing is currently the most reliable means for patient diagnostics. Analytical sensitivity, specificity, reproducibility, and clinical performance of the ELITe InGenius automated PCR platform with its MGB Alert M. pneumoniae real-time PCR research use only reagents (ELITechGroup, Inc., Bothell, WA) were compared with those of a laboratory-developed real-time PCR assay targeting repMp1 for detection of M. pneumoniae The ELITe InGenius PCR assay successfully detected 31 distinct M. pneumoniae clinical isolates and reference strains, and there was no cross-reactivity with other mollicutes, Gram-positive bacteria, or Gram-negative bacteria. In testing 223 clinical samples, the ELITe InGenius PCR showed 95.79% and 99.22% positive and negative agreement with the repMp1 assay, respectively. Additionally, the ELITech platform showed 98.91% positive and 96.95% negative predictive values, and there was no significant difference detected between the two assays (McNemar's test, P = 0.375). The ELITe InGenius PCR assay limit of detection was 0.16 CFU/PCR test or 4.16 genome copies (GCs)/test. Accuracy, instrument ease-of-use, and decreased hands-on time make the ELITe InGenius platform suitable for detection of M. pneumoniae directly from clinical specimens.