Evaluation of Two Phenotypic Screening Tests for Carbapenemase-Producing Enterobacteriaceae

Evaluation of biosynthesized silver nanoparticles effects on expression levels of virulence and biofilm-related genes of multidrug-resistant Klebsiella pneumoniae isolates

The emergence of multidrug-resistant (MDR) strains of Klebsiella pneumoniae is associated with high morbidity and mortality due to limited treatment options. This study attempts to biologically synthesize silver nanoparticles (AgNPs) and investigate their effect on expression levels of virulence and biofilm-related genes in clinically isolated K. pneumoniae. In this study, biofilm formation ability, antibiotic resistance pattern, extended-spectrum β-lactamases (ESBLs), and carbapenemases production were investigated for 200 clinical isolates of K. pneumoniae using phenotypic methods. Polymerase chain reaction (PCR) was used to detect virulence and biofilm-related genes, ESBL-encoding genes, and carbapenem resistance genes. AgNPs were synthesized using the bio-reduction method. The antibacterial effects of AgNPs were investigated by microdilution broth. In addition, the cytotoxic effect of AgNPs on L929 fibroblast cell lines was determined. The effects of AgNPs on K. pneumoniae virulence and biofilm-related genes (fimH, rmpA, and mrkA) were determined using quantitative real-time PCR. Thirty percent of the isolates produced a strong biofilm. The highest and lowest levels of resistance were observed against amoxicillin/clavulanic acid (95.4%) and tigecycline (96%), respectively. About 31% of isolates were considered positive for carbapenemases, and 75% of the isolates produced an ESBLs enzyme. Different frequencies of mentioned genes were observed. The synthesized AgNPs had a spherical morphology and varied in size. AgNPs inhibited the growth of MDR K. pneumoniae at 128 µg/ml. In addition, AgNPs downregulated the expression of fimH, rmpA, and mrkA genes by 10, 7, and 14-fold, respectively (p < 0.05), also exerted no cytotoxic effect on L929 fibroblast cell lines. It was revealed that AgNPs lead to a decrease in expression levels of virulence and biofilm-related genes; therefore, it was concluded that AgNPs had an excellent antibacterial effect on MDR K. pneumoniae.

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.

Systematic Comparison of Three Commercially Available Combination Disc Tests and the Zinc-Supplemented Carbapenem Inactivation Method (zCIM) for Carbapenemase Detection in Enterobacterales Isolates

Detection of carbapenemases in Enterobacterales is crucial for patient treatment and infection control. Among others, combination disc tests (CDTs) with different inhibitors (e.g., EDTA) and variations of the carbapenem inactivation method (CIM) are recommended by EUCAST or the CLSI and are used by many laboratories as they are relatively inexpensive. In this study, we compare three commercially available CDTs, faropenem disc testing (FAR), and the zinc-supplemented CIM (zCIM) test for the detection of carbapenemase-producing Enterobacterales (CPE). The Rosco KPC/MBL and OXA-48 Confirm kit (ROS-CDT), the Liofilchem KPC&MBL&OXA-48 disc kit (LIO-CDT), Mastdiscs Combi Carba plus (MAST-CDT), FAR, and zCIM were challenged with 106 molecularly characterized CPE and 47 non-CPE isolates. The sensitivities/specificities were 86% (confidence interval [CI], 78 to 92%)/98% (CI, 89 to 100%) for MAST-CDT and ROS-CDT, 96% (CI, 91 to 99%)/87% (CI, 74 to 95%) for LIO-CDT, and 99% (CI, 95 to 100%)/81% (CI, 67 to 91%) for FAR compared to 98% (CI, 93 to 100%)/100% (CI, 92 to 100%) for zCIM. The CDTs showed great performance differences depending on the carbapenemase class, with MAST-CDT and LIO-CDT best detecting class B, ROS-CDT best detecting class A, and LIO-CDT best detecting class D carbapenemases. The overall performance of commercially available CDTs was good but varied greatly for different carbapenemases and between manufacturers, compared with FAR and zCIM, which performed well for all carbapenemase types. For reliable carbapenemase detection, CDTs should preferably not be used as the sole test but can be part of a diagnostic strategy when combined with other assays (e.g., CIM-based, immunochromatographic, or molecular tests).

Genomic Analysis of two NDM-1 Providencia stuartii Strains Recovered from a Single Patient

In the last years, an increasing number of untreatable infections caused by drug-resistant microbes have impacted the health care system. Worldwide, infections caused by carbapenem-resistant (CR) Gram-negative bacilli have dramatically increased. Among the CR-Gram-negative bacilli, those producing carbapenemases, such as NDM-1, are the main concern. Different Enterobacterales harboring NDM-1 have been reported lately. Providencia stuartii, a member of the Morganellaceae family, is ubiquitous in the environment, but is also known to cause nosocomial infections. Here we describe the genomic analysis of two NDM-1- producing P. stuartii strains recovered from the same patient as well as other carbapenem resistant strains recovered from the same hospital. As a result of the genomic analysis thirteen resistance genes, including three to β-lactams (bla_OXA-1, bla_TEM-1, bla_NDM-1), four to aminoglycosides (aphA6, aac(3)-IId, aac(2')-Ia, aac(6')-Ib-cr5), one to sulfonamides (sul1), two to chloramphenicol (catB3, catA3), one to rifampicin, one to bleomycin (ble), and one to tetracycline (tet(B)) were found. Moreover, a variety of mobile genetic elements, such as insertion sequences, plasmids and phage- related sequences, were found within P. stuartii genomes. The spread of carbapenem-resistant isolates remains a significant clinical and public health concern. Therefore, we considered that the detection of CR isolates is an essential step in addressing this problem.

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.

Comparative evaluation of in-house Carba NP test with other phenotypic tests for rapid detection of carbapenem-resistant Enterobacteriaceae

BACKGROUND

The prevalence of carbapenem-resistant Enterobacteriaceae (CRE) is alarming worldwide causing serious infections. Rapid and accurate identification of CRE is crucial to reduce the mortality and morbidity. In this study, we tried to develop an in-house Carba NP test for detection of CRE and evaluate its performance with others.

METHODS

A prospective study was conducted with 40 nonrepeating Enterobacteriaceae isolates over a period of 3 months. All the isolates were screened for carbapenem resistance as per CLSI 2016 guidelines followed by PCR for blaNDM-1, blaOXA-48, blaKPC, blaVIM, and blaIMP genes. All the isolates were subjected to five phenotypic tests, that is, in-house Carba NP (iCarba NP), commercial Carba NP (cCarba NP), Blue-Carba, modified Hodge test (MHT), and CHROMagar.

RESULTS

Among the 40 isolates, 87.5% were identified as Escherichia coli, 7.5% were Klebsiella pneumoniae, 2.5% were Enterobacter cloacae, and 2.5% were Citrobacter freundii. Thirty-three of 40 (82.5%) isolates were found to harbor one or more resistant genes. Considering PCR to be the gold standard test, sensitivity of the phenotypic methods for CRE detection ranged from 63.6% (MHT) to 96.9% (CHROMagar). Both cCarba NP and iCarba NP observed to have highest specificity. The performance of iCarba NP was found comparable with cCarba NP by kappa score 1 and found approximately 10 times less expensive than cCarba NP.

CONCLUSION

CHROMagar was observed most sensitive assay for detection of CRE followed by both Carba NP tests. iCarba NP was proved cheaper and equally good as cCarba NP for detection of CRE.

Evaluation of modified carbapenem inactivation method for suspected carbapenemase among Enterobacteriaceae clinical isolates

Modified carbapenem inactivation method (mCIM) testing was currently recommended by Clinical and Laboratory Standards Institute (CLSI) for detection of carbapenemase among Enterobacteriaceae clinical isolates. In this study, a panel of 145 clinical strains were collected for evaluating the mCIM for detection of carbapenemase. Antimicrobial susceptibility testing were performed by microbroth dilution and the results were interpreted according to CLSI guidelines. All strains were resistant to ertapenem with high MIC₅₀ and MIC₉₀ (64 mg/L –>128 mg/L). For bla_NDM-1-positive or bla_OXA-232-positive strains, the zone of inhibition of meropenem were all 6 mm despite the incubation time of 6 h, 18 h or 24 h. For 6 h, the zone of meropenem inhibition for most of carbapenemase-positive isolates were meet the positive criteria 6–15 mm. However, for carbapenemase-negative isolates, the zone of meropenem inhibition were 16–18 mm after 6 h incubation which should be considered indeterminate for standard incubating time such as 18 h or 24 h. After incubating for 18 h or 24 h, the zone of meropenem inhibition were 22–25 mm for carbapenemase-negative isolates and meet the negative criteria. Our study indicate mCIM is a simple and effective method to identify the carbapenemases producers among Enterobacteriaceae clinical isolates.

Clinical and laboratory considerations for the rapid detection of carbapenem-resistant Enterobacteriaceae

Carbapenem resistance among the Enterobacteriaceae has become a significant clinical and public health dilemma. Rapid administration of effective antimicrobials and implementation of supplemental infection control practices is required to both improve patient outcomes and limit the spread of these highly resistant organisms. However, carbapenem-resistant Enterobacteriaceae (CRE)-infected patients are predominantly identified by routine culture methods, which take days to perform. Rapid genomic and phenotypic methods are currently available to accelerate the identification of carbapenemase-producing CRE. Effective use of these technologies is reliant on close collaboration between clinical microbiology, infection prevention, antimicrobial stewardship and infectious diseases specialists. This review discusses the performance characteristics of these technologies to date, and describes strategies for their optimal implementation.