Rapid detection of the New Delhi metallo-b-lactamase 1 (NDM-1) gene by loop-mediated isothermal amplification (LAMP)

A multi-channel electrochemical biosensor based on polyadenine tetrahedra for the detection of multiple drug resistance genes

Antimicrobial resistance poses a serious threat to human health due to the high morbidity and mortality caused by drug-resistant microbial infections. Therefore, the development of rapid, sensitive and selective identification methods is key to improving the survival rate of patients. In this paper, a sandwich-type electrochemical DNA biosensor based on a polyadenine-DNA tetrahedron probe was constructed. The key experimental conditions were optimized, including the length of polyadenine, the concentration of the polyadenine DNA tetrahedron, the concentration of the signal probe and the hybridization time. At the same time, poly-avidin-HRP80 was used to enhance the electrochemical detection signal. Finally, excellent biosensor performance was achieved, and the detection limit for the synthetic DNA target was as low as 1 fM. In addition, we verified the practicability of the system by analyzing E. coli with the MCR-1 plasmid and realized multi-channel detection of the drug resistance genes MCR-1, blaNDM, blaKPC and blaOXA. With the ideal electrochemical interface, the polyA-based biosensor exhibits excellent stability, which provides powerful technical support for the rapid detection of antibiotic-resistant strains in the field.

Rapid Detection of New Delhi Metallo-β-Lactamase Gene Using Recombinase-Aided Amplification Directly on Clinical Samples From Children

New Delhi metallo-β-lactamase, a metallo-β-lactamase carbapenemase type, mediates resistance to most β-lactam antibiotics including penicillins, cephalosporins, and carbapenems. Therefore, it is important to detect bla_NDM genes in children’s clinical samples as quickly as possible and analyze their characteristics. Here, a recombinase-aided amplification (RAA) assay, which operates in a single one-step reaction tube at 39°C in 5−15 min, was established to target bla_NDM genes in children’s clinical samples. The analytical sensitivity of the RAA assay was 20 copies, and the various bacterial types without bla_NDM genes did not amplify. This method was used to detect bla_NDM genes in 112 children’s stool samples, 10 of which were tested positive by both RAA and standard PCR. To further investigate the characteristics of carbapenem-resistant bacteria carrying bla_NDM in children, 15 carbapenem-resistant bacteria (Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii, Citrobacter freundii, Klebsiella oxytoca, Acinetobacter junii, and Proteus mirabilis) were isolated from the 10 samples. Notably, more than one bacterial type was isolated from three samples. Most of these isolates were resistant to cephalosporins, cefoperazone-sulbactam, piperacillin-tazobactam, ticarcillin-clavulanic acid, aztreonam, co-trimoxazole, and carbapenems. bla_NDM–1 and bla_NDM–5 were the two main types in these samples. These data show that the RAA assay has potential to be a sensitive and rapid bla_NDM gene screening test for clinical samples. The common existence of bla_NDM and multi-drug resistance genes presents major challenges for pediatric treatment.

Rapid and Sensitive Detection of the Colistin Resistance Gene mcr-3 by Loop-Mediated Isothermal Amplification and Visual Inspection

Objective: The distribution of colistin resistance in mcr-carrying bacteria poses a threat to global public health. In particular, the newly identified mcr-3 allele has spread globally, especially in China, second only to mcr-1. In this study, we aimed to develop a loop-mediated isothermal amplification (LAMP) assay for rapid, sensitive, and visual detection of the presence of the mcr-3 gene. Materials and Methods: A total of 13 clinical bacterial strains and 11 negative strains were used in this study. We designed LAMP Primers, optimized reaction conditions, used three different methods to detect LAMP amplification products: (1) agarose gel electrophoresis, (2) LAMP-hydroxy naphthol blue (HNB) detection, (3) LAMP-SYBR Green I (LAMP-SGI) visual inspection, and evaluated its specificity and sensitivity. Results: The amplification reaction was completed in 1 hr at 62°C under isothermal conditions. The final optimized mixtures contained 100 mM KCl, 100 mM (NH₄)₂SO₄, 20 mM MgSO₄, 1% Triton X-100, 1.2 μL HNB, and 0.5 μL SYBR Green I as additives to the initial reaction mixture. LAMP detection, including two visual methods, LAMP-HNB and LAMP-SGI, of mcr-3 possessed the same specificity and a 10-fold higher sensitivity compared with a conventional polymerase chain reaction assay using the same samples. Conclusion: We successfully established an mcr-3 LAMP detection with portability and rapidity of the reaction by the easily distinguishable color changes in the reaction tubes. This visual LAMP assay for mcr-3 detection was simple, time saving, and economical, especially suited to field laboratories.

Phenotypic and Molecular Detection of BlaNDM Gene Among Drug-Resistant Klebsiella Isolates

BACKGROUND

In the past few centuries, a widespread increase in antimicrobial resistance has been observed among Klebsiella species. The antibiotic- resistant strains of the genus Klebsiella are becoming a serious threat in clinical settings due to their involvement in severe invasive and non-invasive infections. The emergence of resistance among these strains is associated with their strong enzymatic activity against several broad-spectrum antibiotics. These enzymes include beta-lactamases, extended-spectrum beta-lactamases (ESBL), AmpC beta-lactamases, and carbapenemases. These resistance enzymes are capable of hydrolyzing various broad-spectrum drugs like extended-spectrum cephalosporin and carbapenems.

OBJECTIVE

The present study was conducted to determine the emerging resistance among Klebsiella strains by identifying the production of carbapenemase enzyme phenotypically and the frequency of the NDM resistance gene by a polymerase chain reaction.

METHODS

In this study, 236 Gram-negative isolates from different clinical laboratories were identified. Out of which, 125 isolates were found as Klebsiella species by using standard microbiological techniques. Minimum inhibitory concentrations (MIC) were determined using eight representative antibiotics by the Macro broth dilution method. Phenotypic detection of carbapenemase producing Klebsiella species was performed by Modified Hodge Test. Phenotypic findings were then checked and compared with genotypic results obtained by using the Polymerase chain reaction (PCR) for the detection of resistance genes responsible for the production of carbapenemase.

RESULTS

In this study, carbapenemase production was found only in 6 (5%) Klebsiella isolates by using the phenotypic method; however, 3 isolates out of 125 were screened positive for the gene NDM-1.

CONCLUSION

Since we are considering carbapenems as the last therapeutic option for treating infections, mainly caused by Gram-negative isolates, the prevailing resistance against this drug is widely disseminating. It is better to evaluate the antibiotic susceptibility, phenotypic screening as well genotypic screening (where possible) for implementing strict antibiotic control policies in health care settings, hospitals, laboratories, etc.

Rapid detection of the New Delhi metallo-β-lactamase (NDM) gene by recombinase polymerase amplification

New Delhi metallo-β-lactamase (NDM) is a series of enzyme conferring resistance to β-lactam antibiotics including the carbapenems. The bla_NDM gene has been reported in a variety of Gram-negative bacilli, especially in the Enterobacteriaceae and Acinetobacter spp., which is deeply disconcerting for public health worldwide. In this study, recombinase polymerase amplification assays using a basic detection (Basic-RPA) and a real-time fluorescent detection (Exo-RPA) were established for detecting bla_NDM gene. The RPA reactions were performed at 39 °C and finished within 20 min. Using different copy numbers of pMD18T-NDM plasmid DNA as templates, we identified the detection limit of Basic-RPA assay (1.85 × 10³ copies/μL), conventional PCR assay (1.85 × 10⁴ copies/μL), Exo-RPA assay (1.85 × 10² copies/μL) and real-time PCR assay (1.85 × 10² copies/μL). Both Basic-RPA and Exo-RPA assays were highly specific for detecting bla_NDM, as there were no cross-reactions with the strains without bla_NDM gene. Examination of 62 clinical samples by RPA assays and PCR assays showed the same results, suggesting that RPA assays are reliable in clinical diagnosis. The amplification time of RPA is much shorter than that of other molecular techniques, it is easy to implement and has the potential for clinical application.

Diagnostic accuracy of LAMP assay for HBV infection

Background

Detection of hepatitis B virus (HBV) is vital for the diagnosis of hepatitis B infection. A novel test loop‐mediated isothermal amplification (LAMP) has been successfully applied to detect various pathogens. However, the accuracy of LAMP in diagnosing HBV remains unclear. Therefore, in the present study, the accuracy of LAMP for HBV detection was evaluated systematically.

Methods

Embase, Cochrane Library, and PubMed databases were searched for studies using LAMP to detect HBV. Then, two researchers extracted data and assessed the quality of literature using the QUADAS‐2 tool independently. I² statistic and chi‐square test were analyzed to investigate the heterogeneity, and Deek's funnel plot assessed the publication bias. The pooled sensitivity (SEN), specificity (SPE), positive LR (PLR), negative LR (NLR), diagnostic odds ratio (DOR), and 95% confidence intervals were displayed in forest plots. We calculated the area under the curve (AUC) to assess the overall efficiency of LAMP for HBV detection.

Results

A total of nine studies with 1298 samples were finally included in this evaluation. The pooled sensitivity and specificity of HBV detection were 0.91 (95% CI: 0.89 ~ 0.92) and 0.97 (95% CI: 0.94 ~ 0.99), respectively. The PLR, NLR, and DOR were 16.93 (95% CI: 6.15 ~ 46.55), 0.08 (95% CI: 0.05 ~ 0.14), and 397.57 (95% CI: 145.41 ~ 1087.07). Besides, the AUC was 0.9872, and Deek's plot suggested that there existed publication bias in the studies.

Conclusion

Compared with PCR, LAMP is a simple, rapid, and effective assay to diagnose HBV. However, additional evidence is essential to confirm that LAMP can replace other methods in diagnosing HBV infection.

Rapid detection of the New Delhi metallo-b-lactamase 1 (NDM-1) gene by loop-mediated isothermal amplification (LAMP)

BACKGROUND

New Delhi Metallo-b-lactamase (NDM-1) is an enzyme emerging around the world conferring resistance to a wide range of β-lactams agents and whose early detection is extremely important. We proposed to standardize the detection of the bla_NDM-1 gene using the LOOP-mediated isothermal amplification technique (LAMP).

METHODS

In all, 14 Gram-negative bacterial strains isolated from patients presenting pneumonia associated with mechanical ventilation were used for the bla_NDM-1 standardization by LAMP. Klebsiella pneumoniae ATCC BAA-2473 and two clinical strains were used as a positive control. All results were compared to the reaction in polymerase chain reaction (PCR), considered gold standard for this detection.

RESULTS

There was an excellent correlation between the two techniques employed, since all measured clinical strains were negative in both employed tests and two clinical, and a reference strains were positive.

CONCLUSIONS

The lamp technique seems to be an excellent option for the rapid detection of bla_NDM-1. The amplification time is much shorter than other molecular techniques, the PCR machine is not necessary, it is easy of implementation and costs is low.