Highly sensitive and fast Legionella spp. in situ detection based on a loop mediated isothermal amplification technique combined to an electrochemical transduction system

Evaluation of colorimetric RT-LAMP for screening of SARS-CoV-2 in untreated wastewater

This study compared reverse transcription-loop-mediated isothermal amplification (RT-LAMP) and three reverse transcription-quantitative polymerase chain reaction (RT-qPCR) assays targeting the N and E genes of the SARS-CoV-2 genome for detecting RNA in untreated wastewater samples. RT-qPCR assays exhibited consistent amplification down to 2 × 102 GC/reaction, with greater analytical sensitivity at 2 × 101 GC/reaction by US CDC N1 and US CDC N2 assays. In contrast, RT-LAMP exhibited lower sensitivity, detecting SARS-CoV-2 only at or above 2 × 103 GC/reaction. For SARS-CoV-2 seeded wastewater samples, the US CDC N1 assay exhibited greater analytical sensitivity than the US CDC N2, E_Sarbeco, and RT-LAMP assays. Out of 30 wastewater samples, RT-qPCR detected endogenous SARS-CoV-2 RNA in 29 samples, while RT-LAMP identified 27 positive samples, with 20 displaying consistent amplifications in all three RT-LAMP technical replicates. Agreement analysis revealed a strong concordance between RT-LAMP and the US CDC N1 and E_Sarbeco RT-qPCR assays (κ = 0.474) but lower agreement with the US CDC N2 RT-qPCR assay (κ = 0.359). Quantification of SARS-CoV-2 RNA in positive samples revealed a strong correlation between the US CDC N1 and E_Sarbeco assays, while the US CDC N1 and US CDC N2 assays exhibited weak correlation. Logistic regression analysis indicated that RT-LAMP results correlated with RNA quantified by the US CDC N1 and E_Sarbeco assays, with 95 % limits of detection of 3.99 and 3.47 log10 GC/15 mL, respectively. In conclusion, despite lower sensitivity compared to RT-qPCR assays, RT-LAMP may offer advantages for wastewater surveillance, such as rapid results (estimated as twice as fast), and simplicity, making it a valuable tool in the shifting landscape of COVID-19 wastewater surveillance. Furthermore, LAMP positive wastewater samples might be prioritized for SARS-CoV-2 sequencing due to reduced analytical sensitivity. These findings support the use of RT-LAMP as a specific and efficient method for screening wastewater samples for SARS-CoV-2, particularly in resource-limited settings.

Improved biosensing of Legionella by integrating filtration and immunomagnetic separation of the bacteria retained in filters

A novel approach is presented that combines filtration and the direct immunomagnetic separation of the retained bacteria Legionella in filters, for further electrochemical immunosensing. This strategy allows for the separation and preconcentration of the water-borne pathogen from high-volume samples, up to 1000 mL. The limit of detection of the electrochemical immunosensor resulted in 100 CFU mL-1 and improved up to 0.1 CFU mL-1 when the preconcentration strategy was applied in 1 L of sample (103-fold improvement). Remarkably, the immunosensor achieves the limit of detection in less than 2.5 h and simplified the analytical procedure. This represents the lowest concentration reported to date for electrochemical immunosensing of Legionella cells without the need for pre-enrichment or DNA amplification. Furthermore, the study successfully demonstrates the extraction of bacteria retained on different filtering materials using immunomagnetic separation, highlighting the high efficiency of the magnetic particles to pull out the bacteria directly from solid materials. This promising feature expands the applicability of the method beyond water systems for detecting bacteria retained in air filters of air conditioning units by directly performing the immunomagnetic separation in the filters.

Development of an Electrochemical Sensor for SARS-CoV-2 Detection Based on Loop-Mediated Isothermal Amplification

The pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused more than 6 million deaths all over the world, demonstrating the need for a simple, fast and cost-effective point-of-care (POC) test for the detection of the virus. In this work, we developed an electrochemical sensor for SARS-CoV-2 virus detection on clinical samples based on loop-mediated isothermal amplification (LAMP). With the development of this novel sensor, the time of each measurement is significantly reduced by avoiding the DNA extraction step and replacing it with inactivation of the sample by heating it at 95 °C for 10 min. To make the reaction compatible with the sample pre-treatment, an RNase inhibitor was added directly to the premix. The LAMP product was measured in a novel, easy-to-use manufactured sensor containing a custom-made screen-printed carbon electrode. Electrochemical detection was performed with a portable potentiostat, and methylene blue was used as the redox-transducing molecule. The developed sensor achieved a limit of detection of 62 viral copies and was 100% specific for the detection of the SARS-CoV-2 virus. The performance of the electrochemical sensor was validated with nasopharyngeal samples, obtaining a sensibility and specificity of 100% compared to the gold standard RT-PCR method.

Extraction-Free Colorimetric RT-LAMP Detection of SARS-CoV-2 in Saliva

The pandemic situation caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted the need of fast, simple, and cost-effective tests for the diagnosis of emerging pathogens. RT-qPCR has been established as the reference technique for the diagnosis of SARS-CoV-2 infections. This method requires a time-consuming protocol for the extraction of the nucleic acids present in the sample. A colorimetric reverse transcription loop-mediated isothermal amplification using the calcein molecule combined with a simple extraction-free method for saliva samples (calcein RT-LAMP) has been developed. Samples are heated 95 °C for 10 min before amplification at 63 °C for 40 min. The results can be observed by fluorescence or by the naked eye with a color change from orange to green. The method was compared with commercialized available colorimetric and fluorescent RT-LAMP kits. The developed method shows better sensitivity and specificity than the colorimetric commercial RT-LAMP and the same as the fluorescent RT-LAMP, without the need of a fluorescent reader. Moreover, the calcein RT-LAMP has, compared to RT-qPCR, a sensitivity of 90% and a specificity of 100% for saliva samples with a Ct ≤ 34, without the need for expensive RT-qPCR instruments, demonstrating the potential of this method for population screening.

Strategies for the Voltammetric Detection of Loop-Mediated Isothermal Amplification

Loop-mediated isothermal amplification (LAMP) is rapidly developing into an important tool for the point-of-use detection of pathogens for both clinical and environmental samples, largely due to its sensitivity, rapidity, and adaptability to portable devices. Many methods are used to monitor LAMP, but not all are amenable to point-of-use applications. Common methods such as fluorescence often require bulky equipment, whereas colorimetric and turbidimetric methods can lack sensitivity. Electrochemical biosensors are becoming increasingly important for these applications due to their potential for low cost, high sensitivity, and capacity for miniaturization into integrated devices. This review provides an overview of the use of voltammetric sensors for monitoring LAMP, with a specific focus on how electroactive species are used to interface between the biochemical products of the LAMP reaction and the voltammetric sensor. Various strategies for the voltammetric detection of DNA amplicons as well as pyrophosphate and protons released during LAMP are presented, ranging from direct DNA binding by electroactive species to the creative use of pyrophosphate-detecting aptamers and pH-sensitive oligonucleotide structures. Hurdles for adapting these devices to point-of-use applications are also discussed.

Design and 3D printing of an electrochemical sensor for Listeria monocytogenes detection based on loop mediated isothermal amplification

The aim of this work is the design and 3D printing of a new electrochemical sensor for the detection of Listeria monocytogenes based on loop mediated isothermal amplification (LAMP). The food related diseases involve a serious health issue all over the world. Listeria monocytogenes is one of the major problems of contaminated food, this pathogen causes a disease called listeriosis with a high rate of hospitalization and mortality. Having a fast, sensitive and specific detection method for food quality control is a must in the food industry to avoid the presence of this pathogen in the food chain (raw materials, facilities and products). A point-of-care biosensor based in LAMP and electrochemical detection is one of the best options to detect the bacteria on site and in a very short period of time. With the numerical analysis of different geometries and flow rates during sample injection in order to avoid bubbles, an optimized design of the microfluidic biosensor chamber was selected for 3D-printing and experimental analysis. For the electrochemical detection, a novel custom gold concentric-3-electrode consisting in a working electrode, reference electrode and a counter electrode was designed and placed in the bottom of the chamber. The LAMP reaction was optimized specifically for a primers set with a limit of detection of 1.25 pg of genomic DNA per reaction and 100% specific for detecting all 12 Listeria monocytogenes serotypes and no other Listeria species or food-related bacteria. The methylene blue redox-active molecule was tested as the electrochemical transducer and shown to be compatible with the LAMP reaction and very clearly distinguished negative from positive food samples when the reaction is measured at the end-point inside the biosensor.

Principles and Applications of Loop-Mediated Isothermal Amplification to Point-of-Care Tests

For the identification of nucleic acids, which are important biomarkers of pathogen-mediated diseases and viruses, the gold standard for NA-based diagnostic applications is polymerase chain reaction (PCR). However, the requirements of PCR limit its application as a rapid point-of-care diagnostic technique. To address the challenges associated with regular PCR, many isothermal amplification methods have been developed to accurately detect NAs. Isothermal amplification methods enable NA amplification without changes in temperature with simple devices, as well as faster amplification times compared with regular PCR. Of the isothermal amplifications, loop-mediated isothermal amplification (LAMP) is the most studied because it amplifies NAs rapidly and specifically. This review describes the principles of LAMP, the methods used to monitor the process of LAMP, and examples of biosensors that detect the amplicons of LAMP. In addition, current trends in the application of LAMP to smartphones and self-diagnosis systems for point-of-care tests are also discussed.

Electrochemical Detection for Isothermal Loop-Mediated Amplification of Pneumolysin Gene of Streptococcus pneumoniae Based on the Oxidation of Phenol Red Indicator

A highly sensitive electrochemical methodology for end-point detection of loop-mediated isothermal nucleic acid amplification reactions was developed. It is based on the oxidation process of phenol red (PR), commonly used as a visual indicator. The dependence of its redox process on pH, which changes during amplification, allows performing quantitative measurements. Thus, the change in the oxidation potential of PR during the amplification is used, for the first time, as the analytical signal that correlates with the number of initial DNA copies. As a proof-of-concept, the amplification of the pneumolysin gene from Streptococcus pneumoniae, one of the main pathogens causing community-acquired pneumonia, is performed. Combination of isothermal amplification with electrochemical detection, performed on small-size flexible electrodes, allows easy decentralization. Adaptation to the detection of other pathogens causing infectious diseases would be very useful in the prevention of future epidemics.

Evaluation of a Most Probable Number Method for Detection and Quantification of Legionella pneumophila

The detection and enumeration of Legionella pneumophila (L. pneumophila) in water is crucial for water quality management, human health and has been a research hotspot worldwide. Due to the time-consuming and complicated operation of the plate culture method, it is necessary to adopt a fast and effective method for application. The present study aimed to comprehensively evaluate the performance and applicability of the MPN method by comparing its qualitative and quantitative results with the GB/T 18204.5-2013 and ISO methods, respectively. The qualitative results showed that 372 samples (53%) were negative for both methods; 315 samples (45%) were positively determined by the MPN method, compared with 211 samples (30%) using GB/T 18204.5-2013. The difference in the detection rate between the two methods was statistically significant. In addition, the quantitative results showed that the concentration of L. pneumophila by the MPN method was greater than ISO 11731 and the difference was statistically significant. However, the two methods were different but highly correlated (r = 0.965, p < 0.001). The specificity and sensitivity of the MPN method were 89.85% and 95.73%, respectively. Overall, the results demonstrated that the MPN method has higher sensitivity, a simple operation process and good application prospects in the routine monitoring of L. pneumophila from water samples.

Advances in Environmental Detection and Clinical Diagnostic Tests for Legionella Species

Legionella is a fastidious organism that is difficult to culture in the lab but is widely distributed in environmental, domestic, and hospital settings. The clinical manifestations due to Legionella infections range from mild fever to fatal pneumonia and multiorgan pathologies. Legionella outbreaks though prevalent globally are not reported in developing countries due to difficulties in isolating this organism and the lack of simple diagnostic protocols. Here, we review the literature from across countries to present various methods used to detect Legionella from environmental and clinical samples. We compare the sensitivity and the specificity of the conventional culture-based assays with the recent methods and discuss approaches to develop better detection and diagnostic tests. With better cost-effective detection techniques and regular monitoring of the susceptible sites, which may harbor Legionella colonies, most of the Legionella infections can be prevented. As a result, considerable burden, caused by Legionella infections, on the healthcare system, in especially economically weaker countries, can be mitigated.

Case Report: Metagenomic Next-Generation Sequencing in Diagnosis of Legionella pneumophila Pneumonia in a Patient After Umbilical Cord Blood Stem Cell Transplantation

We report a case of hospital-acquired Legionella pneumonia that was detected by metagenomic next-generation sequencing (mNGS) of blood from a 7-year-old girl after umbilical cord blood stem cell transplantation (UCBT) with myelodysplastic syndrome. UCBT is traditionally associated with an increased risk of infection, particularly during the first 3 months after transplantation. Controlling interstitial pneumonia and severe infection is the key to reducing patient mortality from infection. Legionella pneumophila can cause a mild cough to rapidly fatal pneumonia. After mNGS confirmed that the pathogen was L. pneumophila, azithromycin, cefoperazone sulbactam, and posaconazole were used for treatment, and the patient's temperature decreased and remained normal. The details of this case highlight the benefits of the timely use of metagenomic NGS to identify pathogens for the survival of immunocompromised patients.

Legionella and Biofilms-Integrated Surveillance to Bridge Science and Real-Field Demands

Legionella is responsible for the life-threatening pneumonia commonly known as Legionnaires’ disease or legionellosis. Legionellosis is known to be preventable if proper measures are put into practice. Despite the efforts to improve preventive approaches, Legionella control remains one of the most challenging issues in the water treatment industry. Legionellosis incidence is on the rise and is expected to keep increasing as global challenges become a reality. This puts great emphasis on prevention, which must be grounded in strengthened Legionella management practices. Herein, an overview of field-based studies (the system as a test rig) is provided to unravel the common roots of research and the main contributions to Legionella’s understanding. The perpetuation of a water-focused monitoring approach and the importance of protozoa and biofilms will then be discussed as bottom-line questions for reliable Legionella real-field surveillance. Finally, an integrated monitoring model is proposed to study and control Legionella in water systems by combining discrete and continuous information about water and biofilm. Although the successful implementation of such a model requires a broader discussion across the scientific community and practitioners, this might be a starting point to build more consistent Legionella management strategies that can effectively mitigate legionellosis risks by reinforcing a pro-active Legionella prevention philosophy.

Rapid Detection of Legionella pneumophila in Drinking Water, Based on Filter Immunoassay and Chronoamperometric Measurement

Legionella is a pathogenic bacterium, ubiquitous in freshwater environments and able to colonise man-made water systems from which it can be transmitted to humans during outbreaks. The prevention of such outbreaks requires a fast, low cost, automated and often portable detection system. In this work, we present a combination of sample concentration, immunoassay detection, and measurement by chronoamperometry. A nitrocellulose microfiltration membrane is used as support for both the water sample concentration and the Legionella immunodetection. The horseradish peroxidase enzymatic label of the antibodies permits using the redox substrate 3,3′,5,5′-Tetramethylbenzidine to generate current changes proportional to the bacterial concentration present in drinking water. Carbon screen-printed electrodes are employed in the chronoamperometric measurements. Our system reduces the detection time: from the 10 days required by the conventional culture-based methods, to 2–3 h, which could be crucial to avoid outbreaks. Additionally, the system shows a linear response (R² value of 0.99), being able to detect a range of Legionella concentrations between 10¹ and 10⁴ cfu·mL⁻¹ with a detection limit (LoD) of 4 cfu·mL⁻¹.