Evaluation of a novel procedure for rapid detection of carbapenemase-producing Enterobacteriaceae (CPE) using the LightMix® modular carbapenemase kits

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.

Carbapenem resistance determinants in Klebsiella pneumoniae strains isolated from blood cultures-comparative analysis of molecular and phenotypic methods

Introduction: This study provides data on carbapenemases identified in carbapenem-resistant Klebsiella pneumoniae (CR-KP) isolated from blood-cultures by the multiplex molecular method.

Material and method: Between October 2016 and September 2017, 47 non-duplicate Klebsiella pneumoniae (KP) were isolated from blood cultures, from hospitalized patients in the Regional Institute of Gastroenterology and Hepathology, Cluj-Napoca, Romania. Identification and antimicrobial susceptibility tests (AST) were performed by Vitek 2 Compact. The combination disks test (CDT) was used for phenotypic analysis and the LightCycler® Multiplex DNA assay was used to detect and identify the carbapenemases by the LightCycler®z 480 Instrument. The following targets were chosen: blaKPC, blaNDM, blaGES, blaIMP and blaOXA-48 genes and the Cobas® 4800 software variant 2.2.0 was used for the results interpretation.

Results: Taking into consideration the meropenem minimum inhibitory concentration (MIC), 29 KP were susceptible and 18 were not-susceptible (MIC≥0.5 µg ml-1). In the CR-KP group, the CDT identified OXA-48 (10/18) and KPC (7/18) producers. One isolate showed a noninterpretable profile. The multiplex molecular analyses confirmed the carbapenemases production as: 9 CR-KP were KPC and OXA-48 co-producers, 8 were OXA-48 and one was KPC producing strains. In CR-KP group, we found a significant correlation between the CDT and RT-PCR tests results, concerning KPC (p = 0.671). Eight phenotypic results were confirmed by molecular Light-Cycler® Multiplex DNA assay. For CR-KP co-producers (KPC and OXA-48), the CDT could indicate only one carbapenem-hydrolyzing enzyme.

Conclusion: This study highlights the CR-KP co-producers (OXA-48 and KPC). OXA-48-like is more frequently encountered in our area than other carbapenemases.

Improved diagnosis of antibiotic-associated haemorrhagic colitis (AAHC) in faecal specimens by a new qualitative real-time PCR assay detecting relevant toxin genes of Klebsiella oxytoca sensu lato

OBJECTIVE

Toxin-producing Klebsiella oxytoca causes antibiotic-associated haemorrhagic colitis (AAHC). The disease-relevant cytotoxins tilivalline and tilimycine produced by certain K. oxytoca isolates are encoded by the non-ribosomal peptide synthetase genes A (npsA) and B (npsB). In this study, the new LightMix® Modular kit for the detection of relevant K. oxytoca sensu lato (s.l.) toxin genes was evaluated.

METHODS

DNA was extracted on the automated EMAG® platform. Amplification was done on the Light Cycler® 480 II instrument. In total, 130 residual faecal specimens collected from patients with antibiotic-associated diarrhoea were studied to determine the clinical sensitivity and specificity. Toxigenic culture served as reference method.

RESULTS

With the new kit, the limit of detection was 15 CFU/mL for all targets. For the pehX target specific to K. oxytoca s.l., 65 of 130 clinical specimens were positive, while toxin-specific targets (npsA/npsB) were positive in 47 of 130. The npsA/npsB PCR targets showed a clinical sensitivity of 100% (95%CI 80.5-100%) and a specificity of 73.5% (95%CI 64.3-81.3%) with a positive predictive value of 16.5% (95%CI 12.7-21.2%) and a negative predictive value of 100%.

CONCLUSION

Compared with culture, additional clinical specimens positive for K. oxytoca s.l. were detected with real-time PCR. The specificity of the toxin targets appears moderate due to the inferior sensitivity of the culture-based reference method. Since the developed assay is highly sensitive, it may be used as first-line method to improve the diagnosis of AAHC.

Multiplex Real-Time PCR Assay for Six Major Carbapenemase Genes

The global dissemination of carbapenemase-producing Enterobacteriaceae (CPE) is a major concern in public health. Due to the existence of the diversity of carbapenemases, development of an easily available, cost-effective multiplex detection assay for CPE is required worldwide. Using clinically available and reliable equipment, COBAS^® z480 (Roche Diagnostics K.K., Tokyo, Japan), we developed a multiplex real-time PCR assay for the detection of two combinations of carbapenemases; first, bla_NDM, bla_KPC, and bla_IMP (Set 1), and second, bla_GES, bla_OXA-48, and bla_VIM (Set 2). We constructed standard curves for each carbapenemase gene using serial dilutions of DNA standards, then applied reference or clinical isolates with each carbapenemase gene to this assay. The multiplex assay showed satisfactory accuracy to detect CPE genes, with the correlation coefficients of greater than 0.99 for all genotypes. The assay appropriately differentiated the reference or clinical strains harboring each carbapenemase gene without cross reactivity. Lastly, the assay successfully detected multiple genes without false-positive reactions by applying six clinical isolates carrying both NDM and OXA-48-like carbapenemase genes. Major advantages of our assay include multiplicity, simple operation, robustness, and speed (1 h). We believe that the multiplex assay potentially contributes to early diagnosis of CPE with a diverse genetic background.

Diagnostic tools for bacterial infections in travellers: Current and future options

International travel has increased dramatically over the past 50 years, and travel destinations have diversified. Although physicians are more familiar with the panel of aetiological agents responsible for illnesses of returning travellers, thanks to regular epidemiological studies, the spectrum of pathogens potentially encountered in various travel destinations is nevertheless increasing. In addition, the wide array of approaches currently available and addressed in this paper could render the procedures for microbiological analyses increasingly complex. As the time to result is crucial to adequately manage patients, modern approaches have been developed to shorten diagnosis delays. The syndromic approach, which consists of simultaneously testing a wide panel of microorganisms, substantially increases the diagnostic yield with significant time savings, particularly when coupled with point-of-care laboratories. The tools commonly used for this purpose are immunochromatographic tests, mainly targeting bacterial antigens, and multiplex real-time PCR. The emergence of next-generation sequencing technologies, which enable random amplification of genetic material of any microbe present in a clinical specimen, provides further exciting perspectives in the diagnosis of infectious diseases.

Carbapenemase-producing Enterobacteriaceae in animals and methodologies for their detection

Carbapenemase-producing bacteria are difficult to treat and pose an important threat for public health. Detecting and identifying them can be a challenging and time-consuming task. Due to the recent rise in prevalence of infections with these organisms, there is an increased demand for rapid and accurate detection methods. This review describes and contrasts current methods used for the identification and detection of carbapenemase-producing bacteria to help control their spread in animal populations and along the food chain. The methods discussed include cultures used for screening clinical samples and primary isolation, susceptibility testing, culture-based and molecular confirmation tests. Advantages and disadvantages as well as limitations of the methods are discussed.

Active Surveillance of Carbapenemase-Producing Organisms (CPO) Colonization With Xpert Carba-R Assay Plus Positive Patient Isolation Proves to Be Effective in CPO Containment

Background: Rapid screening of patients for colonization with carbapenemase-producing organisms (CPO), coupled with implementation of infection prevention strategies, has the potential to contain the spread of CPO.

Methods: We first evaluated the performance of Xpert Carba-R assay (in comparison with other phenotypic methods) for carbapenemase detection using clinical isolates, and then used it to determine the intestinal CPO colonization in hospitalized patients. We then assessed the effectiveness of patient isolation in controlling the spread of CPO in a medical intensive care unit.

Results: The Xpert Carba-R assay required the least processing time to reveal results and showed a 94.5% sensitivity and specificity in carbapenemase detection, except for IMP-8 (n = 4). During a 6-month study period, 134 patients in one ward were studied for CPO colonization and infection. Fifteen patients (11.2%) were colonized by CPO as detected by Xpert Carba-R assay, including three NDM, three IMP, and nine KPC possessing strains. The overall colonization and CPO infection rates were both 11.2% each. Isolation of patients with CPO led to a reduction in both colonization (from 28.6 to 5.6%) and infection rates (from 35.7 to 2.8%) during the study period (p < 0.05).

Conclusion: Active surveillance of CPO utilizing the Xpert Carba-R assay supplemented with immediate patient isolation, proved to be an effective strategy to limit the spread of CPO in a health care setting.

High Prevalence of Multidrug-Resistant Bacteria in Libyan War Casualties Admitted to a Tertiary Care Hospital, Germany

The ongoing Libyan conflict constantly causes victims among the military and civilian population. Cross-border transfer of patients represents a high risk of introducing multidrug-resistant organisms (MDROs), for example, methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant enterococci, and carbapenem-resistant gram-negative organisms (CROs), into the country of destination. This study assessed the MDRO status in Libyan war casualties (n = 67) admitted to Northwest Medical Centre in Frankfurt/Main, Germany, from August 2016 till January 2017. Identified multidrug-resistant nonfermenters and Enterobacteriaceae were subjected to molecular detection of β-lactamases and further mechanisms of resistance. All isolates were typed by enzymatic macrorestriction and subsequent pulsed-field gel electrophoresis. MDROs were found in 40 (60%) patients, including 25 (37%) positive for at least one CRO and 11 (16%) patients with MRSA. A total of 37 isolates of Klebsiella pneumoniae, Acinetobacter baumannii, Escherichia coli, Enterobacter cloacae, and Serratia marcescens produced carbapenemases: NDM (n = 17), OXA-48 (n = 15), and OXA-23 (n = 9) in addition to other β-lactamases (with bla_{CTX-M-group-1} being most frequent) and plasmid-mediated quinolone resistance genes (qnrB, aac(6')Ib-cr). Bacterial strain typing revealed the presence of various clones. This high MDRO rate in Libyan war casualties demands awareness, appropriate screening, and containment measures for medical institutions involved in medical care to avoid patient-to-patient transmission.