Comparison of the Performance of Phenotypic Methods for the Detection of Carbapenem-Resistant Enterobacteriaceae (CRE) in Clinical Practice

REL/DPA/AVI method: a novel approach for rapid detection of carbapenemase-producing Enterobacterales directly from positive blood cultures based on optical density

The high mortality rate associated with carbapenem-resistant Enterobacterales (CRE), particularly for bloodstream infections (BSI), underscores the urgent need for early identification and differentiation of its resistance mechanisms. In China, traditional phenotypic detection methods for carbapenemases, including the modified Carbapenem Inactivation Method (mCIM), EDTA Carbapenemase Inactivation Method (eCIM), and the carbapenemase inhibitor 3-aminophenylboronic acid (APB) and EDTA enhancement method (APB-EDTA method), are widely used; however, they are time consuming. The relebactam, dipicolinic acid, and avibactam sodium (REL/DPA/AVI) method is a novel phenotypic test for carbapenemase targeting to address these challenges. This method exploits the growth status differences of enzyme-producing bacteria under the combined action of imipenem and enzyme inhibitors (REL, DPA, and AVI) to identify Class A, B, and D carbapenemases at an early stage through optical density (OD) measurements. The REL/DPA/AVI method was optimized and evaluated using 213 contrived (seeded) blood cultures and compared to mCIM/eCIM and APB-EDTA methods. The REL/DPA/AVI method achieved results within 1.5 h (OD measurement) or 2 h (visual observation or OD measurement) from blood culture positivity. Sensitivities of detection of class A, B, D, and A + B carbapenemases at 1.5 h were 97.56% (40/41), 100% (82/82), 71.43% (5/7), and 100% (7/7), respectively. After 2 h, the sensitivity for detecting class D carbapenemases increased to 85.71% (6/7). Conversely, the sensitivities of mCIM/eCIM were 95.83% (46/48) and 97.56% (80/82) for serine β-lactamases and metallo-β-lactamases, respectively. However, the APB-EDTA method demonstrated a sensitivity of 95.1% (39/41), 87.8% (72/82), and 71.43% (5/7) for classes A, B, and A + B carbapenemases, respectively.

IMPORTANCE

The relebactam, dipicolinic acid, and avibactam sodium (REL/DPA/AVI) method has demonstrated significant success in identifying and differentiating carbapenemase-producing Enterobacterales (CPE) from positive blood cultures, exhibiting superior performance compared with existing technologies. Although numerous advanced technologies such as mNGS, Filmarray, Verigene, and NG-Test CARBA 5 DetecTool have been developed for carbapenemase typing of CPE in positive blood cultures, our method is distinguished by a significant economic advantage, with a cost of less than $1 USD per test. This substantial cost-effectiveness underscores the immense potential for widespread clinical applications.

Phenotype Detection and Drug Resistance Analysis of Carbapenem-Resistant Gram-Negative Bacilli

BACKGROUND

The increasing prevalence of infections caused by carbapenem-resistant organisms (CRO) represents a global health issue. Therefore, a rapid and accurate method for detecting these microbes in any clinical microbiology laboratory is crucial for the prevention and control of their transmission, as well as for clinical treatment. This study aimed to evaluate the phenotypic detection methods, PBA-EDTA, mCIM, PCR, and immunocolloidal gold kit for CRO.

METHODS

We collected 99 samples from the inpatients in Sun Yat-Sen University Cancer Center (SYSUCC) from March 2019 to February 2022 and classified the drug resistance and genotype of various strains by various enzyme-type experiments.

RESULTS

Out of 99 multidrug-resistant Gram-negative bacilli resistant to carbapenems, 58 (58.59%) were identified as carbapenemase-positive using the mCIM test. The carbapenemase genotypes included 19 NDM strains, 4 KPC strains, 1 IMP strain, and 5 OXA-23 strains. Enzyme detection revealed 21 strains positive for metallo-β-lactamase, 50 for serine-β-lactamase, and 2 positive for both, with a total positive rate of 73.74%. 26 strains were negative for enzyme detection, and mCIM showed limited effectiveness in detecting strains coproducing NDM and KPC. The immunocolloidal gold assay had a sensitivity of 96.9% and specificity of 98.5%.

CONCLUSION

This study used an immunocolloidal gold kit for carbapenemase detection, providing results within 15 min. This cost-effective method can quickly assist in identifying carbapenemase genotypes and holds potential as a new rapid detection and diagnostic tool for CRE in clinical and lab settings.

Evaluation of the NG-Test Carba 5 for the clinical detection of carbapenemase-producing gram-negative bacteria

Background

Currently, the spread and prevalence of carbapenem-resistant gram-negative bacteria cause a worldwide health problem, significantly affecting patients' prognosis. Therefore, reliable detection of carbapenemases is crucial for managing and controlling infections. Numerous investigations have shown that the innovative immunochromatographic assay NG-Test Carba 5 has great sensitivity and specificity for carbapenemase typing. This meta-analysis aimed to comprehensively assess the efficacy of the NG-Test Carba 5 in the clinical detection of carbapenemase-producing gram-negative bacteria.

Methods

Previously published articles were systematically reviewed, relevant data were extracted, and the results were pooled and analyzed using Meta-DiSk 1.4 and Stata 12.0 software.

Results

The sensitivity, specificity, positive LR value, and negative LR value for the identification of carbapenemase-type KPC, NDM, VIM, IMP, and OXA-48-like by immunochromatographic NG-Test Carba 5 using PCR as gold standard were 0.97 [95% CI (0.97, 0.98)], 0.99 [95% CI (0.99, 1.00)], 65.38 [95% CI (36.73, 116.39)], and 0.03 [95% CI (0.02, 0.05)], respectively, and the combined diagnostic odds ratio was 2,734.42 [95% CI (1,464.05, 5,107.12)]. The AUC of the SROC curve was 0.9976.

Conclusion

In summary, the NG-Test Carba 5 is a clinical test that can identify and quickly detect five major carbapenemases, thus offering valuable insights for clinical decision-making and infection control.

Evaluating the Performance of Two Rapid Immunochromatographic Techniques for Detecting Carbapenemase in Carbapenem-Resistant Enterobacterales Clinical Isolates

Introduction

The rapid and accurate identification of carbapenemases in Enterobacterales isolates is of paramount importance for the selection of effective antibiotics and the control of hospital-acquired infections.

Methods

This study aimed to evaluate the performance of two immunochromatographic methods, NG-Test Carba 5 (Carba 5) and Goldstream Carbapenem-resistant K.N.I.V.O. Detection K-Set (K-Set) for detecting five major carbapenemase (KPC, NDM, IMP, OXA-48-like, and VIM). Carbapenemase genes were confirmed by PCR.

Results

In this study, a total of 245 carbapenem-resistant Enterobacterales (CRE) isolates were encompassed, with an overwhelming 96.7% of these strains exhibiting the ability to produce carbapenemase. A total of 58.2% of Klebsiella pneumoniae strains that produce KPC carbapenemase were the most prevalent among carbapenem-resistant Enterobacteriaceae (CRE). NDM-producing Klebsiella pneumoniae accounted for 30.4%. Importantly, NDM-type carbapenemase emerges as the predominant form in Escherichia coli and Enterobacter cloacae strains, accounting for 46 (93.9%) and 20 (83.3%) cases, respectively. The performance of the two methods in carbapenemase detection has demonstrated remarkable outcomes, exhibiting overall specificity and sensitivity exceeding 99%. Specifically, the K-Set accurately detected a unique KPC-carbapenemase in K. pneumoniae, whereas Carba 5 was unable to identify it. This was due to the presence of a novel bla KPC gene, which harbored a specific point mutation (A to G) at nucleotide position 787, differentiating it from the bla KPC-33 gene.

Conclusion

These two methods, characterized by their simplicity, rapidity, and accuracy, are ideally suited for detecting carbapenemases in routine microbiology laboratories. They serve as a vital foundation for the rational selection of antibiotics in clinical practice.

Next-Gen Nano Biosensor Technologies to Monitor Carbapenem Resistance for Personalized Medicine

Carbapenem resistance represents a pressing public health concern, posing significant challenges due to limited treatment options and escalating mortality rates. In India, the prevalence of carbapenem resistance among Enterobacteriaceae ranges between 18 to 31%, causing severe infections such as bloodstream infections, pneumonia, urinary tract infections, and intra-abdominal infections. Accurate and timely diagnosis, particularly for Enterobacteriaceae producing carbapenemase, is crucial for effective clinical prophylaxis of critical care patients as they are considered as a last resort of therapy. Various genotypic and non-genotypic detection methods have been developed over the past decade, their limitations in terms of sensitivity and specificity have led the exploration of innovative technologies. Advanced opportunities for carbapenem resistance detection using microfluidic-based biosensors have miniaturized various biomedical devices. This enables the use of less sample and reagents, cheap pricing, automation, screening, and improved detection. Despite ongoing research and development, the adoption of these biosensors in healthcare settings is limited due to the lack of awareness and understanding of their efficiency. Therefore, this review primarily focuses on the advantages and limitations of all biosensor-based devices over existing methods for the detection of carbapenem resistance in gram negative bacilli. These biosensors represent substantial advancements in combating carbapenem resistance, providing promise for more reliable and accurate diagnostic techniques that may eventually improve patient care and infection control.

Exploring New Delhi Metallo Beta Lactamases in Klebsiella pneumoniae and Escherichia coli: genotypic vs. phenotypic insights

BACKGROUND

Carbapenemase-producing Enterobacterales pose a serious clinical threat, particularly in high-burden settings of carbapenem-resistant Escherichia coli and Klebsiella pneumoniae (CREK), where rapid detection tools are essential to aid patient management. In this study, we focused on blaNDM, the most frequently reported carbapenemase in the region, and evaluated a combined phenotypic (lateral flow) and genotypic (PCR and WGS) approach for its detection. This research underscores the utility of lateral flow assays as a practical alternative to resource-intensive genotypic methods, offering a scalable solution for settings with limited laboratory capacity.

METHOD

One hundred seventy-seven extensively drug-resistant strains were characterized using MALDI-TOF. Isolates were analyzed to detect Carbapenem-resistant Escherichia coli and Klebsiella pneumoniae (CREK) using disk diffusion, MIC test, and PCR targeting blaNDM. Antibiotic susceptibility patterns were analyzed and visualized using single-linkage hierarchical clustering, with results displayed on a permuted heat map. Immunochromatographic assay, RESIST-5 O.K.N.V.I (Coris Bioconcept®) was used for CREK isolates [(n = 17), positive and negative)] and Oxford Nanopore Sequencing was conducted on subsets [(n = 5) blaNDM-positive co-producers of blaNDM and blaOXA, and (n = 2) blaNDM-negative blaOXA producers) to evaluate the reliability of phenotypic and genotypic tests.

RESULT

Most of the XDR strains (90%) were CREK, with K. pneumoniae (71.2%) more prevalent than E. coli (28.7%) (p < 0.05). All CREK strains exhibited complete resistance (100%) to multiple antibiotics with 66% showing sensitivity to levofloxacin. Furthermore, K. pneumoniae (57.8%) had higher blaNDM gene prevalence than E. coli (36.9%). Among blaNDM-positive CREK, lateral flow assay revealed approximately half of each bacteria type co-produced blaOXA (E.coli, 52.9%), and (K. pneumoniae, 47%). For blaNDM-negative strains, blaOXA was more prevalent in K. pneumoniae (82.35%) than E. coli (41%) (p < 0.05). Comparing phenotypic to genotypic assays, E. coli showed 100% (CI 80.49 - 100%) sensitivity and specificity with a high Kappa agreement coefficient (0.91) (CI 95% 0.661-1, p < 0.01), whereas K. pneumoniae assays had lower sensitivity and specificity (40%) (CI 5.27 - 85.34%), with a lower Kappa agreement coefficient (0.20) (CI 95% 0.104-0.298, p < 0.01).

CONCLUSION

This study demonstrates the value of the RESIST-5 O.K.N.V.I. lateral flow assay as a rapid and reliable diagnostic tool for detecting blaNDM in Escherichia coli, with strong agreement to PCR and WGS. While performance for Klebsiella pneumoniae was lower, the assay offers a practical alternative in resource-limited settings, aiding antimicrobial stewardship and improving diagnostic capacities in high-burden regions.

Detection and molecular characterization of carbapenem-resistant gram-negative bacterial isolates

Antimicrobial-resistant bacteria (ARB) are responsible for increased mortality and morbidity. Therefore, this study focuses on evaluating traditional and molecular diagnostic tools of carbapenem-resistant gram-negative bacteria (CRGNB). In order to achieve this, 94 samples, from different patients' specimens, and surrounding environment, were collected from intensive care units (ICUs) at Ain Shams University Specialized Hospital and the National Cancer Institute, Cairo, Egypt. The swabs were cultured on appropriate media, including Chromogenic medium (HiCrome KPC Agar Base "HIMEDI AM1831"), and MacConkey-10 µg imipenem disc resulting in 136 isolates with different culture characteristics. Next, the selected isolates were subjected to VITEK 2 machine and 16SrRNA (16 S ribosomal RNA) sequencing. The sensitivity of HiCROME KPC agar for CRGNB detection was 99.3% and 94.7%, in reference to the MacConkey-disc and VITEK-2 methods, respectively. The HiCrome KPC agar assumptions for bacterial identification were not as consistent as those of VITEK 2 (with only 47.4% agreement) and 16SrRNA gene sequencing analysis. The approaches discussed in this study facilitate providing rapid diagnosis and treatment of CRGNB, which helps increase survival rates. HiCrome KPC agar is considered a relatively accurate and easy method that can be used in any laboratory. In addition, the selected strains were deposited in the gene bank with the accession numbers OR553657, OR553658, and OR553659. It is noteworthy that Genus Acinetobacter is the major CRGNB isolated from the patients and environmental surfaces in the hospitals. This highlights the importance of proper environmental and terminal cleaning procedures in healthcare facilities and applying control measures to ensure infection prevention.

Methodological Evaluation of Carbapenemase Detection by Different Methods

The global proliferation of carbapenemase-producing bacteria (CPB) has garnered significant attention worldwide. Early diagnosis of CPB and accurate identification of carbapenemases are crucial for preventing the spread of CPB and ensuring targeted antibiotic therapy. Therefore, efficient and accurate identification of carbapenemases is paramount in clinically treating diseases associated with CPB. In this study, 58 CPB strains were collected and detected using the DNA endonuclease-targeted CRISPR trans reporter (DETECTR) method, a rapid detection platform based on CRISPR-Cas12a gene editing and isothermal amplification. Additionally, four conventional methods (the APB/EDTA method, PCR, NG-test Carba 5, and GeneXpert Carba-R) were employed and compared against whole genome sequencing (WGS) results, considered the gold standard, to evaluate their efficacy in detecting carbapenemases. Detection by the APB/EDTA method revealed that 29 strains were positive for Class A serine endopeptidases, while 29 strains were positive for Class B metalloenzymes. The classification of these zymotypes was consistent with the sequencing result. All target carbapenemases for KPC were identified with 100% sensitivity using NG-test Carba 5, PCR, DETECTR, and GeneXpert Carba-R. In the case of NDM, both Xpert Carba-R and DETECTR showed a sensitivity of 100%. In contrast, NG-test Carba 5 and PCR had a slightly lower sensitivity of 96.7%, each missing one target carbapenemase. n this study, the APB/EDTA method is capable of identifying the zymotype classification but not the specific resistant genes, while Xpert Carba-R and DETECTR are able to detect all target carbapenemases.

Diagnostic Test Precision of Modified Carbapenem Inactivation Method and Carbapenemase Nordmann-Poirel Test for Phenotypic Detection of Carbapenemase Production in Enterobacterales: A Systematic Review

Carbapenem-resistant Enterobacterales, particularly those that produce carbapenemases, pose a significant public health concern due to very limited treatment options. The timely identification of carbapenemase-producing Enterobacterales (CPE) is essential for putting in place efficient infection control measures and selecting appropriate antimicrobial therapies, thereby improving the clinical outcome of the patient. The purpose of this systematic review is to compare the diagnostic accuracy and practicality between two phenotypic tests, namely the modified carbapenem inactivation method (mCIM) and carbapenemase Nordmann-Poirel (Carba NP) test, in detecting carbapenemase production by Enterobacterales and thereby aiding the clinician in making a decision to choose an appropriate test for their phenotypic detection. This systematic review involved combining sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), accuracy, diagnostic odds ratio with 95% confidence interval (CIs), Forest plot for sensitivity and specificity, and plotting suitable summary receiver operating characteristic curve with the area under the curve. Of the 20 studies included in this review, the overall effect sizes of Carba NP and mCIM with 95% CIs were as follows: sensitivity, 91% (86-96%) and 97% (95-99%); specificity, 93% (88-97%) and 97% (93-100%); PPV, 97% and 98%; NPV, 79% and 90%; accuracy, 93% and 97%; diagnostic odds ratio, 1487.8879 and 8527.5541; and AUC, 0.85 and 1, respectively. In conclusion, the mCIM method showed superior sensitivity (97%), specificity (97%), and accuracy compared to the Carba NP test in detecting carbapenemase production, even though both these methods had a few technical limitations. The Carba NP test is rapid, affordable, and dependable, whereas mCIM is more accurate and cost-effective but time-consuming. We propose that both tests can be reliably used for screening of carbapenemase production in Enterobacterales, as endorsed by the Clinical and Laboratory Standards Institute even in resource-limited clinical laboratories, in the order of prioritizing the mCIM method first and then followed by the Carba NP test when situation demands expedited results.

Molecular characteristics and evaluation of the phenotypic detection of carbapenemases among Enterobacterales and Pseudomonas via whole genome sequencing

Background/purposes

The continuously increasing carbapenem resistance within Enterobacterales and Pseudomonas poses a threat to public health, nevertheless, the molecular characteristics of which in southern China still remain limited. And carbapenemase identification is a key factor in effective early therapy of carbapenem-resistant bacteria infections. We aimed to determine the molecular characteristics of these pathogens and compare commercial combined disc tests (CDTs) with the modified carbapenem inactivation method (mCIM) and EDTA-CIM (eCIM) in detecting and distinguishing carbapenemases using whole genome sequencing (WGS).

Methods

A total of 78 Enterobacterales, 30 Pseudomonas were obtained from two tertiary hospitals in southern China. Susceptibility tests were conducted using an automated VITEK2 compact system with confirmation via the Kirby-Bauer method. The WGS was conducted on all clinical isolates and the molecular characteristics were analyzed by screening the whole genome sequences. CDTs with or without cloxacillin, mCIM, and eCIM, were performed and compared by taking WGS results as the benchmark.

Results

A total of 103 carbapenem non-susceptible and 5 carbapenem susceptible bacteria were determined, with Klebsiella pneumoniae (42.7%), Pseudomonas aeruginosa (23.3%) and Escherichia coli (18.4%) being most prevalent. Carbapenemase genes were detected in 58 (56.3%) of the 103 carbapenem-non-susceptible clinical isolates, including 46 NDM, 6 KPC, 3 IMP, 1 IPM+VIM,1NDM+KPC, and 1 OXA-181. Carbapenemase-producing isolates were detected more frequently in Enterobacterales (76.3%). Among K. pneumoniae, the major sequence types were st307 and st11, while among E. coli and P. aeruginosa, the most prevalent ones were st410 and st242 respectively. For carbapenemase detection in Enterobacterales, the mCIM method achieved 100.00% (95% CI, 92.13-100.00%) sensitivity and 94.44% (70.63-99.71%) specificity (kappa, 0.96); for Pseudomonas, detection sensitivity was 100% (5.46-100.00%), and 100% (84.50-100.00%) specificity (kappa, 0.65). Commercial CDT carbapenemase detection sensitivity for Enterobacterales was 96.49% (86.84-99.39%), and 95.24% (74.13-99.75%) specificity (kappa, 0.90); for Pseudomonas, carbapenemase detection sensitivity was 100.00% (5.46-100.00%) and 37.93% (21.30-57.64%) specificity (kappa, 0.04). When cloxacillin testing was added, CDT specificity reached 84.61% (64.27-94.95%).

Conclusion

The molecular epidemiology of carbapenem-non-susceptible isolates from pediatric patients in Southern China exhibited distinctive characteristics. Both the mCIM-eCIM combination and CDT methods effectively detected and differentiated carbapenemases among Enterobacterales isolates, and the former performed better than CDT among Pseudomonas.

A comparative evaluation of five phenotypic methods for identification of carbapenemase-producing Enterobacteriaceae: a modified carbapenemase detection test

Rapid detection of carbapenemase-producing Enterobacteriaceae (CPE) is urgently needed to prevent their spread in healthcare settings. Here, we have evaluated the performance of the phenotypic methods for detection of carbapenemase production directly from bacterial cultures. A total of 99 clinical and rectal Enterobacteriaceae isolates were included (81 carrying known carbapenemase-encoding genes and 18 without carbapenemase production). All isolates were subjected to the five phenotypic tests including in-house Carba NP (iCarba NP), modified-Carba NP, E-Test MBL, modified Hodge test (MHT), and commercial combination disk test. Test results were read at different time points for iCarba NP and modified-Carba (1 min, 5 min, 15 min, 1 h and 2 h). The sensitivity and specificity of the iCarba NP were 78.87% and 100%, respectively, whereas those of the modified-Carba NP test were 95.06% and 94.44%, respectively. False-negative results were detected in four OXA-48 isolates with the use of modified-Carba NP, whereas one non-carbapenemase isolate had false-positive results. The sensitivity/specificity was 91.30%/100% and 80.25%/83.33% for the E-Test MBL and MHT, respectively. The sensitivity and specificity of the aminophenylboronic acid synergy test were 100% and 97.94%, respectively, whereas those of the dipicolinic acid synergy test were 82.61% and 96.23%, respectively. Rapid, simple, and reliable methods are needed for laboratory detection of CPE isolates to improve the detection and surveillance of these clinically relevant pathogens in an epidemiological context. We conclude that the modified-Carba NP test can be one of the reliable tests for the prediction of carbapenemase-producing bacteria.IMPORTANCEThe emergence of carbapenem resistance among Gram-negative bacteria is a serious global health threat. Here, we investigate the performance of the five phenotypic assays against carbapenemase-producing and carbapenemase-non-producing Enterobacteriaceae. Accurate and rapid detection of CPE isolates is critically required for clinical management and treatment of infections caused by these organisms. Among the five evaluated phenotypic tests, the mCNP test presented the highest sensitivity (95.06%) and, therefore, can be considered the best test to be used as a screening phenotypic methodology.

Molecular epidemiology and antimicrobial resistance profiles of Klebsiella pneumoniae isolates from hospitalized patients in different regions of China

Introduction

The increasing incidence of Klebsiella pneumoniae and carbapenem-resistant Klebsiella pneumoniae (CRKP) has posed great challenges for the clinical anti-infective treatment. Here, we describe the molecular epidemiology and antimicrobial resistance profiles of K. pneumoniae and CRKP isolates from hospitalized patients in different regions of China.

Methods

A total of 219 K. pneumoniae isolates from 26 hospitals in 19 provinces of China were collected during 2019-2020. Antimicrobial susceptibility tests, multilocus sequence typing were performed, antimicrobial resistance genes were detected by polymerase chain reaction (PCR). Antimicrobial resistance profiles were compared between different groups.

Results

The resistance rates of K. pneumoniae isolates to imipenem, meropenem, and ertapenem were 20.1%, 20.1%, and 22.4%, respectively. A total of 45 CRKP isolates were identified. There was a significant difference in antimicrobial resistance between 45 CRKP and 174 carbapenem-sensitive Klebsiella pneumoniae (CSKP) strains, and the CRKP isolates were characterized by the multiple-drug resistance phenotype.There were regional differences among antimicrobial resistance rates of K. pneumoniae to cefazolin, chloramphenicol, and sulfamethoxazole,which were lower in the northwest than those in north and south of China.The mostcommon sequence type (ST) was ST11 (66.7% of the strains). In addition, we detected 13 other STs. There were differences between ST11 and non-ST11 isolates in the resistance rate to amikacin, gentamicin, latamoxef, ciprofloxacin, levofloxacin, aztreonam, nitrofurantoin, fosfomycin, and ceftazidime/avibactam. In terms of molecular resistance mechanisms, the majority of the CRKP strains (71.1%, 32/45) harbored blaKPC-2, followed by blaNDM (22.2%, 10/45). Strains harboring blaKPC or blaNDM genes showed different sensitivities to some antibiotics.

Conclusion

Our analysis emphasizes the importance of surveilling carbapenem-resistant determinants and analyzing their molecular characteristics for better management of antimicrobial agents in clinical use.

Emergence of pandrug-resistant carbapenemase-producing Enterobacterales in dogs and cats: a cross-sectional study in Egypt

One of the most important emerging health problems is the increasing role of animals in the rapid global rise in resistance to last-resort antibiotics, such as carbapenems. However, there is limited information on the role of pet animals in harboring and spreading pandrug-resistant (PDR) carbapenemase-producing Enterobacterales (CPE), especially in Egypt. This cross-sectional study was conducted to screen for CPE in healthy and diseased pets using phenotypic and molecular methods and the NG-Test CARBA 5 immunochromatographic assay. Rectal swabs were collected from 62 dogs and 48 cats, incubated overnight in tryptic soy broth containing 10 μg of meropenem disc and subsequently cultured on MacConkey agar supplemented with meropenem (1 mg/L). Sixty-six isolates (60.6%), including 56 Klebsiella pneumoniae, seven Escherichia coli, and three K. oxytoca isolates, were confirmed to be carbapenem-resistant Enterobacterales (CRE) by the disc diffusion method, broth microdilution test, CNPt-direct, and PCR assay targeting carbapenemase genes. Forty-three (65.2%) dogs and 23 (34.8%) cats carried CPE. Of these, 35 (70.0%) were healthy (including 27 dogs and 8 cats) and 31 (52.5%) were diseased (including 16 dogs and 15 cats). bla OXA-181 was the most common gene detected (42/66, 63.6%), followed by bla IMP (40/66, 60.6%), bla OXA-48-like (29/66, 43.9%), bla KPC and bla VIM (20/66, 30.3% each), and bla NDM (17/66, 25.8%). The identified genotypes were bla KPC-2, bla IMP-1, bla VIM-1, bla NDM-1, and bla NDM-5. The CARBA 5 assay showed higher sensitivity and specificity for the detection of NDM, OXA and KPC than that for VIM and IMP genes. Antimicrobial resistance profiles of CRE isolates revealed 20 PDR, 30 extensively drug-resistant (XDR), and 16 multidrug-resistant (MDR) phenotypes. This study provides evidence of colonization with PDR CPE in dogs and cats. To manage the infection or colonization of pets in veterinary clinical settings, extended surveillance systems should be considered, and the use of critical antibiotics should be strictly controlled.

Comparison of the NG-Test Carba 5, Colloidal Gold Immunoassay (CGI) Test, and Xpert Carba-R for the Rapid Detection of Carbapenemases in Carbapenemase-Producing Organisms

Carbapenem-resistant Enterobacterales (CRE) are increasingly recognized as an urgent public health concern. The rapid and accurate identification of carbapenemases could provide insights into antimicrobial therapy and infection control. In this study, we evaluated the efficacy of three different methods, including the NG-test Carba 5, colloidal gold immunoassay (CGI) test, and Xpert Carba-R assay, for the rapid detection of five carbapenemases (KPC, NDM, IMP, OXA-48, and VIM). A total of 207 Gram-negative strains collected from patients and hospital sewages were tested. The presence or absence of carbapenemase genes in the whole-genome sequences was used as the gold standard for evaluating the accuracy of the above-mentioned three methods. Among the 192 strains carrying only one carbapenemase gene, the accuracies of the NG-Test Carba 5, CGI test, and Xpert Carba-R were 96.88% (95% CI, 93.01-98.72%), 96.88% (95% CI, 93.01-98.72%), and 97.92% (95% CI, 94.41-99.33%), respectively. Xpert Carba-R was able to detect all 13 types of KPC variants, including KPC-2, KPC-3, KPC-25, KPC-33, KPC-35, KPC-51, KPC-52, KPC-71, KPC-76, KPC-77, KPC-78, KPC-93, and KPC-123, with a detection sensitivity of 100.00% (95% CI, 96.50-100.00%), a specificity of 100.00% (95% CI, 92.38-100.00%), and a κ index of 1.00. For IMP, Carba 5 was superior to the other two methods, with a sensitivity of 100% (95% CI, 71.66-100.00%), a specificity of 100% (95% CI, 97.38-100.00%), and a κ index of 1.00. For the remaining 15 strains carrying two or three kinds of carbapenemase genes, Carba 5 performed the best, which accurately identified all the target genes, followed by Xpert Carba-R (12/15, 80.00%) and the CGI test (10/15, 66.67%). Therefore, all three assays demonstrated reliable performances in carbapenemase detection, and Xpert Carba-R should be recommended for the detection of KPC variants, especially for patients at a high risk of infections caused by ceftazidime/avibactam-resistant strains. IMPORTANCE: CRE was listed as one of the top three pathogens that are in critical need of new antibiotics by the WHO. The rapid and accurate identification of carbapenemases is important for antimicrobial therapy and infection control. In recent years, new beta-lactam/beta-lactamase inhibitor combinations such as ceftazidime/avibactam (CZA) have been approved by the Food and Drug Administration (FDA) to cope with CRE challenges. CZA was effective against class A, class C, and some class D enzymes such as OXA-48-like. However, CZA-resistant KPC variants emerged at an alarming speed, which posed a new challenge for the accurate identification of KPC variants. In this study, we evaluated the performance of two lateral flow immunochromatographic assays, namely, NG-test Carba 5 and the CGI test, and the automated real-time quantitative PCR Xpert Carba-R in the rapid detection of carbapenemases. Notably, 13 types of KPC variants were enrolled in this study, which covered most KPC variants discovered in China. Carba-R was superior to NG-teat Carba 5 and the CGI test; it was able to detect all of the included KPC variants, including KPC-2, KPC-3, KPC-25, KPC-33, KPC-35, KPC-51, KPC-52, KPC-71, KPC-76, KPC-77, KPC-78, KPC-93, and KPC-123.

Insights on the performance of phenotypic tests versus genotypic tests for the detection of carbapenemase-producing Gram-negative bacilli in resource-limited settings

Background:

Carbapenemase-producing Gram-negative (CPGN) bacteria impose life-threatening infections with limited treatment options. Rigor and rapid detection of CPGN-associated infections is usually associated with proper treatment and better disease prognosis. Accordingly, this study aimed at evaluating the phenotypic methods versus genotypic methods used for the detection of such pathogens and determining their sensitivity/specificity values.

Methods:

A total of 71 CPGN bacilli (30 Enterobacterales and 41 non-glucose-fermenting bacilli) were tested for the carbapenemase production by the major phenotypic approaches including, the modified Hodge test (MHT), modified carbapenem inactivation method (mCIM), combined disk test by EDTA (CDT) and blue-carba test (BCT). The obtained results were statistically analyzed and correlated to the obtained resistant genotypes that were determined by using polymerase chain reactions (PCR) for the detection of the major carbapenemase-encoding genes covering the three classes (Class A, B, and D) of carbapenemases.

Results:

In comparison to PCR, the overall sensitivity/specificity values for detection of carbapenemase-producing organism were 65.62%/100% for MHT, 68.65%/100% for mCIM, 55.22%/100% for CDT and 89.55%/75% for BCT. The sensitivity/specificity values for carbapenemase-producing Enterobacterales were, 74%100% for MHT, 51.72%/ 100% for mCIM, 62.07%/100% for CDT and 82.75%/100% for BCT. The sensitivity/specificity values for carbapenemase-producing non-glucose fermenting bacilli were, 62.16%/100% for MHT, 81.57%/100% for mCIM, 50/100% for CDT and 94.74%/66.66% for BCT. Considering these findings, BCT possess a relatively high performance for the efficient and rapid detection of carbapenemase producing isolates. Statistical analysis showed significant association (p < 0.05) between bla_NDM and/or bla_VIM genotypes with MHT/CDT; bla_KPC/bla_GIM genotypes with CDT and bla_GIM genotype with BCT.

Conclusion:

The current study provides an update on the performance of the phenotypic tests which are varied depending on the tested bacterial genera and the type of the carbapenemase. The overall sensitivity/specificity values for detection of CPO were 65.62%/100% for MHT, 68.65%/100% for mCIM, 55.22%/100% for CDT and 89.55%/75% for BCT. Based on its respective diagnostic efficiency and rapid turnaround time, BCT is more likely to be recommended in a resource-limited settings particularly, when molecular tests are not available.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02660-5.