Evaluation of the K-SeT R.E.S.I.S.T. immunochromatographic assay for the rapid detection of KPC and OXA-48-like carbapenemases

Companion Animals—An Overlooked and Misdiagnosed Reservoir of Carbapenem Resistance

The dissemination of antimicrobial-resistance is a major global threat affecting both human and animal health. Carbapenems are human use β-lactams of last resort; thus. the dissemination of carbapenemase-producing (CP) bacteria creates severe limitations for the treatment of multidrug-resistant bacteria in hospitalized patients. Even though carbapenems are not routinely used in veterinary medicine, reports of infection or colonization by carbapenemase-producing Enterobacterales in companion animals are being reported. NDM-5 and OXA-48-like carbapenemases are among the most frequently reported in companion animals. Like in humans, Escherichia coli and Klebsiella pneumoniae are the most represented CP Enterobacterales found in companion animals, alongside with Acinetobacter baumannii. Considering that the detection of carbapenemase-producing Enterobacterales presents several difficulties, misdiagnosis of CP bacteria in companion animals may lead to important animal and public-health consequences. It is of the upmost importance to ensure an adequate monitoring and detection of CP bacteria in veterinary microbiology in order to safeguard animal health and minimise its dissemination to humans and the environment. This review encompasses an overview of the carbapenemase detection methods currently available, aiming to guide veterinary microbiologists on the best practices to improve its detection for clinical or research purposes.

Blood culture surveillance in a secondary care hospital in Benin: epidemiology of bloodstream infection pathogens and antimicrobial resistance

BACKGROUND

Although global surveillance of antimicrobial resistance (AMR) is considered key in the containment of AMR, data from low- and middle-income countries, especially from sub-Saharan Africa, are scarce. This study describes epidemiology of bloodstream infections and antimicrobial resistance rates in a secondary care hospital in Benin.

METHODS

Blood cultures were sampled, according to predefined indications, in BacT/ALERT FA Plus and PF Plus (bioMérieux, Marcy-l'Etoile, France) blood culture bottles (BCB) in a district hospital (Boko hospital) and to a lesser extent in the University hospital of Parakou. These BCB were incubated for 7 days in a standard incubator and twice daily inspected for visual signs of growth. Isolates retrieved from the BCB were processed locally and later shipped to Belgium for reference identification [matrix-assisted laser desorption/ionization time-of-flight spectrometry (MALDI-TOF)] and antibiotic susceptibility testing (disk diffusion and E-tests).

RESULTS

From October 2017 to February 2020, 3353 BCB were sampled, corresponding to 3140 blood cultures (212 cultures consisting of  > 1 BCB) and 3082 suspected bloodstream infection (BSI) episodes. Most of these cultures (n = 2471; 78.7%) were sampled in children < 15 years of age. Pathogens were recovered from 383 (12.4%) cultures, corresponding to 381 confirmed BSI. 340 of these pathogens were available and confirmed by reference identification. The most common pathogens were Klebsiella pneumoniae (n = 53; 15.6%), Salmonella Typhi (n = 52; 15.3%) and Staphylococcus aureus (n = 46; 13.5%). AMR rates were high among Enterobacterales, with resistance to third-generation cephalosporins in 77.6% of K. pneumoniae isolates (n = 58), 12.8% of Escherichia coli isolates (n = 49) and 70.5% of Enterobacter cloacae isolates (n = 44). Carbapenemase production was detected in 2 Escherichia coli and 2 Enterobacter cloacae isolates, all of which were of the New Delhi metallo-beta lactamase type. Methicillin resistance was present in 22.4% of S. aureus isolates (n = 49).

CONCLUSION

Blood cultures were successfully implemented in a district hospital in Benin, especially among the pediatric patient population. Unexpectedly high rates of AMR among Gram-negative bacteria against commonly used antibiotics were found, demonstrating the clinical and scientific importance of clinical bacteriology laboratories at this level of care.

Evaluation of the Performances of the Rapid Test RESIST-5 O.O.K.N.V Used for the Detection of Carbapenemases-Producing Enterobacterales

Background: The emergence of carbapenemase-producing Enterobacterales (CPE) is a public health problem, requiring rapid and reliable diagnostic methods. The aim is to compare the new rapid immunochromatographic (IC) test: RESIST-5 O.O.K.N.V with PCR and the predictive model of EUCAST algorithm for the detection of CPE. Methods: A longitudinal cross-sectional study was carried out in the bacteriology-virology laboratory of the Ibn Rochd-Casablanca University Hospital, from 1 February 2019 to 28 February 2020, concerning strains with reduced sensitivity to Ertapenem. The identification of bacterial species was carried out according to the standard criteria of microbiology and antibiogram according to CASFM-EUCAST 2019 recommendations. The sensitivity and specificity of the rapid IC test were calculated. Results: The results of the new IC test showed a sensitivity and specificity of 100% for the detection of OXA-48 and NDM. These carbapenemases were detected simultaneously with a sensitivity and specificity of 100%. OXA-48 was the most common carbapenemas found (36%), followed by NDM (24%) and (13.4%) cases of OXA-48 and NDM coexistence. Conclusion: The rapid IC test could be a rapid and effective diagnostic tool for detecting the most common carbapenemases in our context, and to accelerate the implementation of adequate antibiotic therapy and infection control measures in patients with CPE infections

Evaluation of the Immunochromatographic NG-Test Carba 5, RESIST-5 O.O.K.N.V., and IMP K-SeT for Rapid Detection of KPC-, NDM-, IMP-, VIM-type, and OXA-48-like Carbapenemase Among Enterobacterales

Background

Enterobacterales are the most common pathogens for nosocomial infections. The emergence and spread of KPC, NDM, and OXA-48-like carbapenemase-producing Enterobacterales with their extensively drug-resistant characteristics have posed great threats to public health. This study aimed to evaluate the performance of NG-test Carba 5, RESIST-5 O.O.K.N.V., and IMP K-SeT for rapid detection of five carbapenemases (KPC, NDM, VIM, IMP, and OXA-48-like) among Enterobacterales.

Methods

A total of 186 carbapenem-resistant Enterobacterales clinical isolates and 29 reference strains were used in this study. Carbapenemase genes were confirmed by PCR and DNA sequencing. The sensitivities and specificities of these assays were calculated utilizing the VassarStats software.

Results

For clinical isolates, the NG-test Carba 5 detected KPC, NDM, OXA-48-like, IMP, and VIM in less than 15 min with the sensitivity and specificity of 100% and 100%, respectively. The RESIST-5 O.O.K.N.V. detected KPC, NDM, OXA-48-like, and VIM with the sensitivity and specificity of 99.4 and 100%. The IMP K-SeT detected all of the IMP producers (6/6). For reference strains, the sensitivity and specificity of NG-test Carba 5, RESIST-5 O.O.K.N.V., and IMP K-SeT were all 100 and 100%, respectively.

Conclusion

As efficient, rapid, and convenient diagnostic methods, NG-test Carba 5, RESIST-5 O.O.K.N.V., and IMP K-SeT could help to simplify the complex routine workflow for detecting carbapenemases. Rapid and accurate identification of carbapenemase is of significance for both epidemiological and infection control purposes.

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.

A multiplex lateral flow immunoassay for the rapid identification of NDM-, KPC-, IMP- and VIM-type and OXA-48-like carbapenemase-producing Enterobacteriaceae

Objectives

The global spread of carbapenemase-producing Enterobacteriaceae represents a substantial challenge in clinical practice and rapid and reliable detection of these organisms is essential. The aim of this study was to develop and validate a lateral flow immunoassay (Carba5) for the detection of the five main carbapenemases (KPC-, NDM-, VIM- and IMP-type and OXA-48-like).

Methods

Carba5 was retrospectively and prospectively evaluated using 296 enterobacterial isolates from agar culture. An isolated colony was suspended in extraction buffer and then loaded on the manufactured Carba5.

Results

All 185 isolates expressing a carbapenemase related to one of the Carba5 targets were correctly and unambiguously detected in <15 min. All other isolates gave negative results except those producing OXA-163 and OXA-405, which are considered low-activity carbapenemases. No cross-reaction was observed with non-targeted carbapenemases, ESBLs, AmpCs or oxacillinases (OXA-1, -2, -9 and -10). Overall, this assay reached 100% sensitivity and 95.3% (retrospectively) to 100% (prospectively) specificity.

Conclusions

Carba5 is efficient, rapid and easy to implement in the routine workflow of a clinical microbiology laboratory for confirmation of the five main carbapenemases encountered in Enterobacteriaceae.

Phenotypic and Genotypic Characterization of Enterobacteriaceae Producing Oxacillinase-48-Like Carbapenemases, United States

Oxacillinase (OXA)-48-like carbapenemases remain relatively uncommon in the United States. We performed phenotypic and genotypic characterization of 30 Enterobacteriaceae producing OXA-48-like carbapenemases that were recovered from patients during 2010-2014. Isolates were collected from 12 states and not associated with outbreaks, although we could not exclude limited local transmission. The alleles β-lactamase OXA-181 (bla_OXA-181) (43%), bla_OXA-232 (33%), and bla_OXA-48 (23%) were found. All isolates were resistant to ertapenem and showed positive results for the ertapenem and meropenem modified Hodge test and the modified carbapenem inactivation method; 73% showed a positive result for the Carba Nordmann-Poirel test. Whole-genome sequencing identified extended-spectrum β-lactamase genes in 93% of isolates. In all bla_OXA-232 isolates, the gene was on a ColKP3 plasmid. A total of 12 of 13 isolates harboring bla_OXA-181 contained the insertion sequence ΔISEcp1. In all isolates with bla_OXA-48, the gene was located on a TN1999 transposon; these isolates also carried IncL/M plasmids.

Rapid detection of NDM, KPC and OXA-48 carbapenemases directly from positive blood cultures using a new multiplex immunochromatographic assay

Bloodstream infections caused by carbapenemase-producing Enterobacteriaceae (CPE) are associated with treatment failure and increased mortality. Detection of CPE from blood cultures (BC) by standard methods takes 16–72 hours, which can delay the initiation of appropriate antimicrobial therapy and compromise patient outcome. In the present study, we developed and evaluated a new method for the rapid detection of carbapenemases directly from positive BC using a new multiplex immunochromatographic test (ICT). The new ICT was assessed using 170 molecularly characterized Enterobacteriaceae clinical isolates including 126 CPE (OXA-48-like (N = 79), KPC (N = 18) and NDM (N = 29)). After spiking with bacteria and incubation in a BC system, blood from positive BC bottles was hemolyzed, bacteria concentrated by centrifugation and lysed. The lysate was transferred to the RESIST-3 O.K.N. ICT (Coris BioConcept, Gembloux, Belgium), which detects OXA-48-like, KPC and NDM carbapenemases. The final results of the ICT were read when they became positive, at the latest after 15 min. All CPE isolates (126/126) were correctly detected with the new protocol (100% sensitivity, 100% specificity). There was perfect concordance between ICT results and molecular characterization. Total time to result was 20–45 min.

Conclusions: This proof-of-principle study demonstrates that with the newly developed method, OXA-48-like, KPC and NDM carbapenemases can be reliably detected directly from positive BC bottles. The new method is more rapid than other currently available assays and can be performed in any routine microbiology laboratory. This can help to rapidly identify patients with CPE BSI and optimize the management of patients with these difficult-to-treat infections. Further studies are needed to assess the performance of the ICT in routine diagnostics.

Prospective evaluation of the OKN K-SeT assay, a new multiplex immunochromatographic test for the rapid detection of OXA-48-like, KPC and NDM carbapenemases

Objectives: There is an urgent need for accurate and fast diagnostic tests capable of identifying carbapenemase producers. Here, we assessed the performance of a new multiplex lateral flow assay (OKN K-SeT) for the rapid detection of OXA-48-like, KPC and NDM carbapenemase-producing Enterobacteriaceae from culture colonies.

Methods: Two hundred collection isolates with characterized β-lactamase content and 183 non-duplicate consecutive isolates referred to two National Reference Centres over a 2 month period in 2016 were used to evaluate the OKN K-SeT assay.

Results: The assay correctly detected all 42 OXA-48-like-, 27 KPC- and 30 NDM-producing isolates from the collection panel, including 7 isolates that co-produced NDM and OXA-181 carbapenemases. No cross-reactivity was observed with non-targeted carbapenemases (n = 41) or with non-carbapenemase producers (n = 60). Prospectively, all OXA-48-like (n = 69), KPC (n = 9) and NDM (n = 19) carbapenemase-producing Enterobacteriaceae isolates were correctly detected, while 11 carbapenemase producers not targeted by the assay went undetected [VIM (n = 8) and OXA-23/OXA-58-like (n = 3)]. Overall, the sensitivity and specificity of the assay were 100%.

Conclusions: The OKN assay is efficient, rapid and easy to implement in the workflow of a clinical microbiology laboratory for the confirmation of OXA-48, NDM and KPC carbapenemases. This test represents a powerful diagnostic tool as it enables the rapid detection of the most clinically important carbapenemases without the need for more costly and less frequently available molecular assays.

Multiplex Immunochromatographic Detection of OXA-48, KPC, and NDM Carbapenemases: Impact of Inoculum, Antibiotics, and Agar

For the rapid detection of carbapenemase-producing Enterobacteriaceae (CPE), immunochromatographic lateral flow tests (ICT) have recently been developed. The aim of this study was to assess the new multiplex ICT Resist-3 O.K.N. and to investigate if it can be performed directly from susceptibility testing plates. Additionally, the impact of the inoculum and carbapenem disks on sensitivity and specificity was evaluated. The new ICT was challenged using 63 carbapenem-resistant Enterobacteriaceae (CRE) isolates, including 51 carbapenemase producers. It was assessed under five different conditions directly from Mueller-Hinton agar (MHA): 1 μl or 10 μl of inoculum harvested in the absence of antibiotic pressure or 1 μl taken from the inhibition zone of either an ertapenem, imipenem, or meropenem disk. The sensitivity of the ICT was 100% for OXA-48-like and KPC carbapenemases and 94.4% for the NDM carbapenemase with the 1-μl inoculum. When harvested adjacent to a carbapenem disk, the sensitivity increased to 100%. Additionally, with zinc-supplemented MHA, both the sensitivity increased and the NDM band became visible faster (mean time, 8 ± 3.9 min for MHA compared to 1.9 ± 1.5 min for MHA plus zinc; P = 0.0016). The specificity of the ICT was 100%. The Resist-3 O.K.N. ICT is a sensitive and rapid test for the detection of three highly prevalent carbapenemases. However, false-negative results for NDM can occur. We recommend an inoculum of 1 μl that is harvested adjacent to an ertapenem or meropenem disk and the use of agars with sufficient zinc content to achieve the best performance.

Multicentre evaluation of the BYG Carba v2.0 test, a simplified electrochemical assay for the rapid laboratory detection of carbapenemase-producing Enterobacteriaceae

Rapid detection of carbapenemase-producing Enterobacteriaceae (CPE) represents a major challenge for microbiology laboratories. We evaluated the BYG Carba v2.0 using a simplified protocol, which detects CPE in less than 30 minutes. This new procedure reduces the hands-on-time from 5 to one minute and only requires a limited amount of material (one to three colonies) thereby preventing the need for subculturing bacterial isolates to reach a larger amount of pure biomass. This multicentre study involved four European reference laboratories. For the 1181 isolates tested across four centres, BYG Carba v2.0 yielded overall sensitivity and specificity of 96.3% (CI95: 94.5–97.5) and 99.7% (CI95: 98.6–100) respectively. Considering only the 670 consecutive isolates tested prospectively, the BYG Carba v2.0 displayed overall positive and negative predictive values of 99.7% (CI95: 95.4–98.9) and 97.5% (CI95: 94.9–98.8). Regarding time to positivity, 85% of CPE detected were positive within ten minutes. The BYG Carba v2.0 is a new highly simplified, rapid and accurate electrochemical assay discriminating between CPE and non-CPE in less than 30 min. The real-time quantified signal allows objective and traceable interpretation of the results.

Evaluation of a rapid immunochromatographic test for detection of distinct variants of Klebsiella pneumoniae carbapenemase (KPC) in Enterobacteriaceae

The rapid detection of KPC-producing Enterobacteriaceae by microbiology laboratories has been required for infectious control programs. Herein we evaluated the performance of a novel immunochromatographic test for detecting KPC-2-, KPC-3-, KPC-4-, KPC-6-, KPC-7-, KPC-8-, and KPC-11-producing isolates and the influence of different growth media on the test performance.

Multicenter evaluation of the RAPIDEC® CARBA NP test for rapid screening of carbapenemase-producing Enterobacteriaceae and Gram-negative nonfermenters from clinical specimens

The rapid diagnosis of carbapenemase-producing (CP) bacteria is essential for the management of therapy and infection control. In this study, RAPIDEC® CARBA NP (RCNP) was evaluated for the rapid screening of CP Enterobacteriaceae, Acinetobacter baumannii complex, and Pseudomonas aeruginosa from clinical specimens collected at five Italian hospitals. Firstly, each site tested 20 well-characterized strains in a blinded fashion. Secondly, each center prospectively tested 25 isolates from blood cultures processed with a rapid workflow (6h after subculture) and 25 isolates from other specimens processed after an overnight culture. The presence of carbapenemases was confirmed by multiplex real-timePCRs targeting carbapenemase genes. RCNP presented an overall sensitivity, specificity, positive predictive value, and negative predictive value of 70%, 94%, 82%, and 89%, respectively, with a higher performance in detection of CP Enterobacteriaceae and a poorer performance in detection of CP A. baumannii complex. With isolates from blood cultures, RCNP could significantly reduce the time required for identification of CP Enterobacteriaceae (less than 9h since the positivization of blood cultures).

Comparison of Phenotypic Tests and an Immunochromatographic Assay and Development of a New Algorithm for Detection of OXA-48-like Carbapenemases

OXA-48 is the most prevalent carbapenemase in Enterobacteriaceae in Europe and the Middle East, but it is frequently missed because many isolates display low MICs for carbapenems. Furthermore, in contrast to metallo-β-lactamases or Klebsiella pneumoniae carbapenemases (KPC), no specific inhibitor is available for the phenotypic detection of OXA-48. Molecular detection of bla_OXA-48 is the "gold standard" but is not available in many laboratories. A few phenotypic assays have been described but have not been independently evaluated. The aim of this study was the systematic comparison of phenotypic tests and an immunochromatographic assay (ICT) for the detection of OXA-48/OXA-48-like carbapenemases and the development of an algorithm for reliable phenotypic detection of OXA-48. Four phenotypic tests (temocillin disk test, faropenem disk test, OXA-48 disk test, and high-inoculum [HI] OXA-48 disk test) and a new ICT (OXA-48 K-SeT) were compared by using a set of 166 Enterobacteriaceae isolates, including isolates producing OXA-48/OXA-48-like carbapenemases (n = 84) or Ambler class A and B carbapenemases (n = 41) and carbapenemase-negative isolates (n = 41). The sensitivity and specificity for the different assays were 100% and 43.9% for temocillin, 57.1% and 98.8% for faropenem, 53.6% and 100% for the OXA-48 disk test, 98.8% and 97.6% for the HI OXA-48 disk test, and 100% and 100% for the ICT, respectively. The ICT displayed the highest sensitivity and specificity and was the most rapid assay, but it is more costly than phenotypic assays. Based on these results, a new algorithm incorporating temocillin, faropenem, and ICT which allows cost-effective detection of OXA-48 with 100% sensitivity and specificity was developed.

Evaluation of a rapid immunochromatographic test for the detection of OXA-48 carbapenemase

We evaluated the OXA-48K-Set, a rapid immunochromatographic test for the detection of Oxacillinase-48 (OXA-48) carbapenemases, among 37 strains expressing OXA-48 and OXA-48-like carbapenemases and 20 additional strains harboring other β-lactamases. The test showed 100% sensitivity and specificity and the results were obtained in 15minutes.

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

Objectives

Evaluation of the LightMix^® modular carbapenemase kits for the rapid detection of carbapenemase-producing Enterobacteriaceae (CPE) and the application of these kits to the direct detection of colonized patients and bacteraemias.

Methods

The modular multiplex PCR kits targeting bla_KPC, bla_NDM, bla_VIM, bla_IMP and bla_OXA-48-like carbapenem resistance genes were evaluated in terms of sensitivity and specificity for carbapenemase resistance in a set of 118 labelled clinical isolates. Among these, 96 were CPE genotypically characterized by PCR and sequencing. The limits of detection were calculated for the different carbapenem resistance genes in terms of cfu/mL. In addition, the kits were used to evaluate colonization of patients by CPE by comparing this assay with the Xpert^® Carba-R Kit on 127 rectal, perirectal and pharyngeal samples. Blood cultures from bacteraemias (4) and spiked blood cultures (23) with genotypically characterized isolates were also evaluated.

Results

The overall sensitivity and specificity of the multiplex PCR assay was 99% and 100%, respectively. The limit of detection for bla_KPC, bla_VIM, bla_IMP and bla_OXA-48-like is 60 cfu/mL and for bla_NDM 500 cfu/mL. The colonization and bacteraemia studies revealed a 100% agreement between the results obtained by this assay and the ones obtained by GeneXpert^®.

Conclusions

The LightMix^® modular carbapenemase kits are highly reliable and utilizable assays for both colonized and septic patients, and can help in the improvement of infection control. Their modular design facilitates cost-effective detection of CPE in hospital settings.

Rapid Identification of OXA-48 and OXA-163 Subfamilies in Carbapenem-Resistant Gram-Negative Bacilli with a Novel Immunochromatographic Lateral Flow Assay

We assessed a novel immunochromatographic lateral flow assay for direct identification of OXA-48-like carbapenemases and accurate differentiation of allele variants with distinct substrate profiles (OXA-48 or OXA-163 subfamilies). The assay allowed rapid (less than 4 min) and reliable direct confirmation of OXA-163- and/or OXA-48-like enzymes (with 100% sensitivity and 100% specificity) from cultured colonies that were recovered from both solid medium and spiked blood culture bottles.