Rapid detection ofmecAandspaby the loop-mediated isothermal amplification (LAMP) method

Rapid Visual Detection of Methicillin-Resistant Staphylococcus aureus in Human Clinical Samples via Closed LAMP Assay Targeting mecA and spa Genes

The emergence of antimicrobial resistance (AMR), particularly methicillin-resistant Staphylococcus aureus (MRSA), poses a significant global health threat as these bacteria increasingly become resistant to the most available therapeutic options. Thus, developing an efficient approach to rapidly screen MRSA directly from clinical specimens has become vital. In this study, we establish a closed-tube loop-mediated isothermal amplification (LAMP) method incorporating hydroxy-naphthol blue (HNB) colorimetric dye assay to directly detect MRSA from clinical samples based on the presence of mecA and spa genes. In total, 125 preidentified S. aureus isolates and 93 clinical samples containing S. aureus were sourced from the microbiology laboratory at Hamad General Hospital (HGH). The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were computed based on conventional PCR. The assay demonstrated 100% specificity, 91.23% sensitivity, 0.90 Cohen Kappa (CK), 100% PPV, and 87.8% NPV for the clinical samples, while clinical isolates exhibited 100% specificity, 97% sensitivity, 0.926 CK, 100% PPV, and 88.89% NPV. Compared to cefoxitin disk diffusion, LAMP provided 100% specificity and sensitivity, 1.00 CK, and 100% for PPV and NPV. The study revealed that the closed-tube LAMP incorporating (HNB) dye is a rapid technique with a turnaround time of less than 1 h and high specificity and sensitivity.

A signal-off Cas14a1-based platform for highly specific detection of methicillin-resistant Staphylococcus aureus

Antibiotic usage has become very widespread in aquaculture, and the abuse or overuse of antibiotics has led to the evolution of antibiotic-resistance bacteria, which has adverse effects on aquatic products and ecosystems. Moreover, this evolution can potentially cause harm to human health. Thus, there is an urgent need for diagnostic tools for antibiotic-resistant microorganisms. Herein, we proposed a signal-off Cas14a1-based platform (SOCP) for the detection of methicillin-resistant Staphylococcus aureus (MRSA). In this SOCP, we have designed single-stranded DNA (ssDNA) that not only can activate the trans-cleavage ability of dual Cas14a1-sgRNA complex but also can be used as the primers for the amplified methicilin-resistant gene (mecA). When MRSA is present, the primers can be transformed into products with amplification, leading to the signal decrease of trans-cleavage activity of Cas14a1. The SOCP showed high specificity and fair sensitivity for mecA gene and MRSA. In the detection of real samples, this platform also showed consistent results compared with qPCR. The SOCP could provide an alternative tool for the diagnosis of antibiotic-resistant bacteria in aquaculture, food industry and other fields.

Sensitive colorimetric detection of antibiotic resistant Staphylococcus aureus on dairy farms using LAMP with pH-responsive polydiacetylene

Rapidly and accurately detecting antibiotic-resistant pathogens in agriculture and husbandry is important since these represent a major threat to public health. While much attention has been dedicated to detecting now-common resistant bacteria, such as methicillin-resistant Staphylococcus aureus, fewer methods have been developed to assess resistance against macrolides in Staphylococcus aureus (SA). Here, we report a visual on-site detection system for macrolide resistant SA in dairy products. First, metagenomic sequencing in raw milk, cow manure, water and aerosol deposit collected from dairy farms around Tianjin was used to identify the most abundant macrolide resistance gene, which was found to be the macB gene. In parallel, SA housekeeping genes were screened to allow selective identification of SA, which resulted in the selection of the SAOUHSC_01275 gene. Next, LAMP assays targeting the above-mentioned genes were developed and interpreted by agarose gel electrophoresis. For on-site application, different pH-sensitive colorimetric LAMP indicators were compared, which resulted in selection of polydiacetylene (PDA) as the most sensitive candidate. Additionally, a semi-quantitative detection could be realized by analyzing the RGB information via smartphone with a LOD of 1.344 × 10-7 ng/μL of genomic DNA from a milk sample. Finally, the proposed method was successfully carried out at a real farm within 1 h from sample to result by using freeze-dried reagents and portable devices. This is the first instance in which PDA is used to detect LAMP products, and this generic read-out system can be expanded to other antibiotic resistant genes and bacteria.

Rapid and visual detection of Staphylococcus aureus in milk using a recombinase polymerase amplification-lateral flow assay combined with immunomagnetic separation

AIMS

The aim of this study was to develop a novel approach using lateral flow recombinase polymerase amplification (RPA-LF) combined with immunomagnetic separation (IMS) for the rapid detection of Staphylococcus aureus in milk.

METHODS AND RESULTS

Under optimum conditions, the average capture efficiency values (CEs) for S. aureus strains (10⁴ CFU ml^-1 ) was above 95.0% in PBST and ~80% in milk within 45 min with 0.7 mg immunomagnetic beads. The RPA-LF assay, which comprised DNA amplification via RPA at 39°C for 10 min and visualization of the amplicons through LF strips for 5 min, detected S. aureus within 15 min. The method only detected S. aureus and did not show cross-reaction with other bacteria, exhibiting a high level of specificity. Sensitivity experiments confirmed a detection limit of RPA-LF assay as low as 600 fg reaction^-1 for the S. aureus genome (corresponding to approximately 36 CFU of S. aureus), which was about 16.7-fold more sensitive than that of the conventional PCR method. When RPA-LF was used in combination with IMS to detect S. aureus inoculated into artificially contaminated milk, it exhibited a detection limit of approximately 40 CFU reaction^-1 .

CONCLUSIONS

The newly developed IMS-RPA-LF method enabled detection of S. aureus at levels as low as 40 CFU reaction^-1 in milk samples without culture enrichment for an overall testing time of only 70 min.

SIGNIFICANCE AND IMPACT OF THE STUDY

The newly developed IMS-RPA-LF assay effectively combines sample preparation, amplification, and detection into a single platform. Because of its high sensitivity, specificity, and speed, the IMS-RPA-LF assay will have important implications for the rapid detection of S. aureus in contaminated food.

Loop-mediated isothermal amplification (LAMP): a sensitive molecular tool for detection of Staphylococcus aureus in meat and dairy product

Staphylococcus aureus-mediated food poisoning is a primary concern worldwide. The presence of the organism in food is an indicative of poor sanitation during production, and it is essential to have efficient methods for detecting this pathogen. A novel molecular diagnostic technique called loop-mediated isothermal amplification (LAMP) serves as a rapid and sensitive detection method, which amplifies nucleic acids at isothermal conditions. In this study, a LAMP-based diagnostic assay was developed to detect Staphylococcus aureus (S. aureus) using two target genes femA and arcC. The optimum reaction temperature was found to be 65 °C and at 60 °C for femA and arcC genes, respectively. The developed assay specifically amplified DNA from S. aureus, not from other related bacterial species and compared to PCR, and a 100-fold higher sensitivity was observed. Furthermore, the LAMP assay could detect the pathogen from food samples mainly meat and dairy samples when analyzed in both intact and enriched conditions. Thirteen samples were found positive for S. aureus with LAMP showing a greater number of positive samples in comparison to PCR. This study established a highly sensitive and a rapid diagnostic procedure for the detection and surveillance of this major foodborne pathogen.

The application of the loop-mediated isothermal amplification method for rapid detection of methicillin-resistant Staphylococcus aureus

Methicillin-resistant Staphylococcus aureus (MRSA) is an important problem associated with significant mortality and morbidity and well known as a predominant bacterial pathogen. The aim of this study was to identify MRSA strains. In this study (June 2018 to June 2019) isolates of S. aureus were obtained from patients referred to teaching hospitals of Ahvaz, Iran. All isolates were confirmed by conventional microbiological methods. In following, antimicrobial susceptibility testing (AST), MRSA screening, PCR detection of MRSA and LAMP assay were performed. Out of a total of 156 staphylococcal isolates, 126 isolates were identified as MRSA. Seventy-two (57.1%) MRSA isolates were recovered from wound. All MRSA isolates were sensitive to vancomycin, linezolid, teicoplanin, quinupristin-dalfopristin, and tigecycline. The results of LAMP showed 100% agreement with PCR. Sensitivity and specificity of the LAMP assays for the mecA genes were 100% and 100%, respectively. The LAMP assay is a rapid and simple method for the identifications of MRSA. Because of its performance without the need for specific instrumentation, this method can be easily employed in medical centers for the detection of mecA.

Diagnostic Values of Multiplex Loop-Mediated Isothermal Amplification and Multiplex Polymerase Chain Reaction for Detection of Methicillin-Resistant Staphylococcus aureus

Background: Methicillin-resistant Staphylococcus aureus (MRSA) has emerged as a significant pathogen in community and hospital environments and is associated with high mortality and morbidity. Both polymerase chain reaction (PCR) and loop-mediated isothermal amplification (LAMP) methods are sensitive and acceptable molecular methods for the diagnosis of infectious diseases. Objectives: This study aimed to develop detection assays for Staphylococcal mecA and spa using multiplex PCR and LAMP. Methods: Both methods were standardized, and detection limits were determined using serial dilutions of S. aureus DNA samples. Fifty-three clinical isolates of S. aureus were confirmed to the species level using biochemical tests and multiplex PCR and multiplex LAMP for the spa gene, while disk diffusion, minimum inhibitory concentration, and detection of mecA genes were used for the assessment of methicillin resistance. Results: The PCR could detect the mecA and spa genes at 1 fg/mL and 10 fg/mL of bacterial DNA, which were equal to 35 and 350 gene copy numbers, respectively. Similarly, multiplex LAMP detected the spa and mecA genes at 0.1 fg/mL and 1 fg/mL of bacterial DNA, which were equal to 3.5 and 35 genome copy numbers, respectively. According to MIC and disk diffusion methods, four (7.54%) cases were oxacillin-sensitive methicillin-resistant S. aureus, 16 isolates were methicillin-sensitive, and 37 isolates were methicillin-resistant. According to multiplex PCR, 47.75% of the isolates were mecA-positive while in multiplex LAMP, 41 (35.77%) isolates were mecA-positive. Conclusions: The sensitivity and specificity of the multiplex LAMP were higher than those of multiplex PCR and biochemical methods. Thus, we can apply the LAMP for the routine detection of MRSA.

Platinum ions mediate the interactions between DNA and carbon quantum dots: diagnosis of MRSA infections

In this study, we have developed a rapid and cost-effective method employing platinum ion (Pt4+)-capped fluorescent carbon quantum dots (CQDs) coupled with loop-mediated isothermal amplification (LAMP) to detect dual MRSA genes. We synthesized nitrogen- and chlorine-co-doped fluorescent CQDs (CQDSPDs) from spermidine trihydrochloride via a simple one-step pyrolysis. The CQDSPDs capped with Pt4+ ions through the cooperative coordination of the amine and chlorine groups on the surface of CQDs facilitated the double-stranded DNA (dsDNA)-induced fluorescence quenching of CQDs, and enabled the construction of the CQDSPDs/Pt4+ probe for the detection of as few as 10 copies of the MRSA gene (mecA and femA). The sensitivity and specificity of the CQDSPDs/Pt4+ probe for MRSA detection in clinical specimens (n = 24) were 94% and 86%, respectively. Our results reveal that the CQDSPDs/Pt4+ probe has great potential for the diagnosis of antibiotic-resistant superbugs with high sensitivity, specificity, and agreement.

Molecular Tools To Study Preharvest Food Safety Challenges

Preharvest food safety research and activities have advanced over time with the recognition of the importance and complicated nature of the preharvest phase of food production. In developed nations, implementation of preharvest food safety procedures along with strict monitoring and containment at various postharvest stages such as slaughter, processing, storage, and distribution have remarkably reduced the burden of foodborne pathogens in humans. Early detection and adequate surveillance of pathogens at the preharvest stage is of the utmost importance to ensure a safe meat supply. There is an urgent need to develop rapid, cost-effective, and point-of-care diagnostics which could be used at the preharvest stage and would complement postmortem and other quality checks performed at the postharvest stage. With newer methods and technologies, more efforts need to be directed toward developing rapid, sensitive, and specific methods for detection or screening of foodborne pathogens at the preharvest stage. In this review, we will discuss the molecular methods available for detection and molecular typing of bacterial foodborne pathogens at the farm. Such methods include conventional techniques such as endpoint PCR, real-time PCR, DNA microarray, and more advanced techniques such as matrix-assisted layer desorption ionization-time of flight mass spectrometry and whole-genome sequencing.

Hemoculture and Direct Sputum Detection of mecA-Mediated Methicillin-Resistant Staphylococcus aureus by Loop-Mediated Isothermal Amplification in Combination With a Lateral-Flow Dipstick

This study reports loop-mediated isothermal amplification (LAMP) for rapid detection of methicillin-resistant Staphylococcus aureus from direct clinical specimens. Four primers including outer and inner primers were specifically designed on the two target sequences-femB to identify S. aureus and mecA to identify antibiotic-resistant gene. Reference strains including various species of gram-positive/gram-negative isolates were used to evaluate and optimize LAMP assays. The optimum LAMP condition was found at 63°C within 70 min assay time (include hybridization with FITC probe for 5 min and further 5 min for reading the results on the lateral flow dipstick). The detection limits of LAMP for mecA was 10 pg of total DNA or 100 CFU/ml. The LAMP assays were applied to a total of 155 samples of direct DNA extraction from sputum and hemoculture bottles. The sensitivity of LAMP for mecA detection in sputum and hemoculture bottles was 93.3% (28/30) and 100% (52/52), respectively. In conclusion, LAMP assay is an alternative technique for rapid detection of MRSA infection with a technical simplicity and cost-effective method in a routine diagnostic laboratory.

Rapid detection of Staphylococcus aureus by loop-mediated isothermal amplification

Staphylococcus aureus, including methicillin-resistant S. aureus (MRSA), is a major bacterial pathogen associated with nosocomial and community-acquired S. aureus infections all over the world. A rapid detection assay for staphylococcal gene of nuc and mecA is needed. In this study, a rapid identification assay based on the loop-mediated isothermal amplification (LAMP) method was established. PCR and LAMP assays were used to detect Staphylococcus aureus and other related species for nuc and mecA. With optimization of the primers and reaction temperature, the LAMP successfully amplified the genes under isothermal conditions at 62 °C within 60 min, of which the results were identical with those of the conventional PCR methods. The detection limits of the LAMP for nuc and mecA were 1.47 and 14.7 pg/μl DNA per tube, respectively, by naked eye inspections, while the detection limits of the PCR for nuc and mecA were 14.7 pg/μl and 147 pg/μl DNA, respectively. Finally, The LAMP method was then applied to clinical blood plaque samples. The LAMP and PCR demonstrated identical results for the plaque samples with the culture assay. Together, the LAMP offers an alternative detection assay for nuc and mecA with a great advantage of the sensitivity and rapidity.

Isothermal nucleic acid amplification technologies for point-of-care diagnostics: a critical review

Nucleic Acid Testing (NAT) promises rapid, sensitive and specific diagnosis of infectious, inherited and genetic disease. The next generation of diagnostic devices will interrogate the genetic determinants of such conditions at the point-of-care, affording clinicians prompt reliable diagnosis from which to guide more effective treatment. The complex biochemical nature of clinical samples, the low abundance of nucleic acid targets in the majority of clinical samples and existing biosensor technology indicate that some form of nucleic acid amplification will be required to obtain clinically relevant sensitivities from the small samples used in point-of-care testing (POCT). This publication provides an overview and thorough review of existing technologies for nucleic acid amplification. The different methods are compared and their suitability for POCT adaptation are discussed. Current commercial products employing isothermal amplification strategies are also investigated. In conclusion we identify the factors impeding the integration of the methods discussed in fully automated, sample-to-answer POCT devices.

Rapid detection of live methicillin-resistant Staphylococcus aureus by using an integrated microfluidic system capable of ethidium monoazide pre-treatment and molecular diagnosis

Methicillin-resistant Staphylococcus aureus (MRSA) is a bacterium resistant to all existing penicillin and lactam-based antimicrobial drugs and, therefore, has become one of the most prevalent antibiotic-resistant pathogens found in hospitals. The multi-drug resistant characteristics of MRSA make it challenging to clinically treat infected patients. Therefore, early diagnosis of MRSA has become a public-health priority worldwide. Conventionally, cell-culture based methodology and microscopic identification are commonly used for MRSA detection. However, they are relatively time-consuming and labor-intensive. Recently, molecular diagnosis based on nucleic acid amplification techniques, such as polymerase chain reaction (PCR), has been widely investigated for the rapid detection of MRSA. However, genomic DNA of both live and dead pathogens can be distinguished by conventional PCR. These results thus could not provide sufficient confirmation of an active infection for clinicians. In this study, live MRSA was rapidly detected by using a new integrated microfluidic system. The microfluidic system has been demonstrated to have 100% specificity to detect live MRSA with S. aureus and other pathogens commonly found in hospitals. The experimental results showed that the limit of detection for live MRSA from biosamples was approximately 10(2) CFU/μl. In addition, the entire diagnostic protocol, from sample pre-treatment to fluorescence observation, can be automatically completed within 2.5 h. Consequently, this microfluidic system may be a powerful tool for the rapid molecular diagnosis of live MRSA.

A magnetic bead-based assay for the rapid detection of methicillin-resistant Staphylococcus aureus by using a microfluidic system with integrated loop-mediated isothermal amplification

This study reports a new diagnostic assay for the rapid detection of methicillin-resistant Staphylococcus aureus (MRSA) by combing nucleic acid extraction and isothermal amplification of target nucleic acids in a magnetic bead-based microfluidic system. By using specific probe-conjugated magnetic beads, the target deoxyribonucleic acid (DNA) of the MRSA can be specifically recognized and hybridized onto the surface of the magnetic beads which are then mixed with clinical sample lysates. This is followed by purifying and concentrating the target DNA from the clinical sample lysates by applying a magnetic field. Nucleic acid amplification of the target genes can then be performed by the use of a loop-mediated isothermal amplification (LAMP) process via the incorporation of a built-in micro temperature control module, followed by analyzing the optical density (OD) of the LAMP amplicons using a spectrophotometer. Significantly, experimental results show that the limit of detection (LOD) for MRSA in the clinical samples is approximately 10 fg μL(-1) by performing this diagnostic assay in the magnetic bead-based microfluidic system. In addition, the entire diagnostic protocol, from bio-sample pre-treatment to optical detection, can be automatically completed within 60 min. Consequently, this miniature diagnostic assay may become a powerful tool for the rapid purification and detection of MRSA and a potential point-of-care platform for detection of other types of infections.