Accuracy of loop-mediated isothermal amplification for diagnosis of human leptospirosis in Thailand

Detection of pathogenic Leptospira with rapid extraction followed by recombinase polymerase amplification (RPA) and quantitative polymerase chain reaction (qPCR) assay-A comprehensive study from Sri Lanka

Leptospirosis is the most widespread zoonosis in the world. The disease is more prevalent in tropical regions where the majority of developing countries are located. Leptospirosis is considered a protean manifestation zoonosis with severity of the disease ranging from a mild febrile illness to a severe and life-threatening illness. Clinical symptoms of leptospirosis overlap with other tropical febrile illnesses. Early, rapid, and definitive diagnosis is important for effective patient management. Since Polymerase Chain Reaction (PCR)-based assays are not readily available in most clinical settings, there is a need for an affordable, simple, and rapid diagnostic test. Quantitative PCR (qPCR) and Recombinase Polymerase Amplification (RPA) were implemented at the Faculty of Medicine, University of Kelaniya, and a prospective study to evaluate RPA for diagnosis of acute phase of leptospirosis was conducted. Results indicate that RPA and qPCR were positive in 81% (98/121) of the total positive and acute clinical samples. Of the 81 positive MAT confirmed patients 60 (74%) and 53 (65%) were positive with qPCR and RPA respectively. Retrospective evaluation revealed a high diagnostic accuracy (sensitivity-70% and specificity-87%) of RPA compared to MAT as the reference gold standard. Results further suggest that there is no significant difference between the two assays, qPCR and RPA-SwiftX (P = 0.40). Laboratory procedures for the extraction and detection by qPCR in the laboratory have been optimized to obtain results within 6 hours. However, the RPA-SwiftX method under field conditions took 35 minutes. The RPA-SwiftX method could replace the qPCR which shows similar sensitivity and specificity. Therefore, RPA established under the current study presents a powerful tool for the early and rapid diagnosis of leptospirosis at point-of-care.

Optimization and comparative analysis of LAMP and PCR techniques for the detection of leptospiral DNA in Golden Syrian hamsters

Leptospirosis is a zoonotic disease with significant public health and economic impact worldwide. Rapid and accurate diagnosis is essential for effective prevention and treatment. This study optimized a loop-mediated isothermal amplification (LAMP) assay using BFo isothermal DNA polymerase with different colorimetric indicators. LAMP was able to detect DNA from pathogenic and intermediate leptospires, while non-pathogenic leptospires and other non-leptospiral microorganisms were negative. LAMP assay combined with calcein showed a tenfold higher limit of detection (1 ng of leptospiral DNA per reaction) than LAMP combined with hydroxynaphthol blue or end-point PCR lipL32 (10 ng of DNA per reaction). Animal samples were collected from infected and non-infected Golden Syrian hamsters (Mesocricetus auratus) to evaluate and compare the performance of LAMP and PCR. These techniques showed a substantial agreement according to Cohen's kappa statistic, being both useful techniques for detecting leptospiral DNA in clinical samples. Overall, this study demonstrates that the LAMP assay is a sensitive, specific, rapid, and simple tool for the detection of leptospiral DNA. It has the potential to facilitate the diagnosis of leptospirosis, particularly in low-income regions with limited diagnosis resources.

Molecular Diagnosis as an Alternative for Public Health Surveillance of Leptospirosis in Colombia

Leptospirosis represents a public health problem in Colombia. However, the underreporting of the disease is an unfortunate reality, with a clear trend towards a decrease in cases since 2019, when the guidelines for its confirmatory diagnosis changed with the requirement of two paired samples. The purpose of this review is to highlight the importance of leptospirosis. While the access to rapid diagnosis is available at practically all levels of care for dengue and malaria, leptospirosis-a doubly neglected disease-deserves recognition as a serious public health problem in Colombia. In this manner, it is proposed that molecular tests are a viable diagnostic alternative that can improve the targeted treatment of the patient and the timeliness of data and case reporting to SIVIGILA, and reduce the underreporting of the disease. Taking advantage of the strengthened technological infrastructure derived from the SARS-CoV-2 pandemic for molecular diagnosis in Colombia, with a network of 227 laboratories distributed throughout the national territory, with an installed capacity for PCR testing, it is proposed that molecular diagnosis can be used as an alternative for early diagnosis. This would allow case confirmation through the public health network in Colombia, and, together with the microagglutination (MAT) technique, the epidemiological surveillance of this disease in this country would be strengthened.

Molecular Diagnostic Methods For The Detection of Leptospirosis

Leptospirosis is a widespread infectious disease caused by the spirochete Leptospira. The clinical features of leptospirosis are fever, headache, vomiting, jaundice, and the acute form of the disease is commonly called Weil’s disease. The microscopic agglutination test (MAT) is a gold standard method used to detect leptospirosis. However, it requires 14 days of time and skilled personnel to detect leptospirosis. Various molecular methods were developed for the rapid detection process, including polymerase chain reaction (PCR), multiplex PCR, nested PCR, real-time PCR, and Loop-mediated isothermal amplification (LAMP). Other immuno-based biosensor kits are readily available for the diagnosis of leptospirosis. Though these methods claim to be highly sensitive and specific, each method has its drawbacks. This review discusses the different molecular diagnostic techniques applied for the diagnosis of leptospirosis; elaborating on each method’s sensitivity, specificity, and detection time and the different samples of water, blood, and urine used.

Role of Diagnostics in Epidemiology, Management, Surveillance, and Control of Leptospirosis

A One Health approach to the epidemiology, management, surveillance, and control of leptospirosis relies on accessible and accurate diagnostics that can be applied to humans and companion animals and livestock. Diagnosis should be multifaceted and take into account exposure risk, clinical presentation, and multiple direct and/or indirect diagnostic approaches. Methods of direct detection of Leptospira spp. include culture, histopathology and immunostaining of tissues or clinical specimens, and nucleic acid amplification tests (NAATs). Indirect serologic methods to detect leptospiral antibodies include the microscopic agglutination test (MAT), the enzyme-linked immunosorbent assay (ELISA), and lateral flow methods. Rapid diagnostics that can be applied at the point-of-care; NAAT and lateral flow serologic tests are essential for management of acute infection and control of outbreaks. Culture is essential to an understanding of regional knowledge of circulating strains, and we discuss recent improvements in methods for cultivation, genomic sequencing, and serotyping. We review the limitations of NAATs, MAT, and other diagnostic approaches in the context of our expanding understanding of the diversity of pathogenic Leptospira spp. Novel approaches are needed, such as loop mediated isothermal amplification (LAMP) and clustered regularly interspaced short palindromic repeats (CRISPR)-based approaches to leptospiral nucleic acid detection.

A versatile isothermal amplification assay for the detection of leptospires from various sample types

Background

Leptospirosis is a zoonotic disease caused by bacteria of the genus Leptospira that affects both humans and animals worldwide. Early detection of the pathogen in humans is crucial for early intervention and control of the progression of the disease to a severe state. It is also vitally important to be able to detect the presence of the pathogen in carrier animals to control the spread of the disease from the environment. Here we developed a simple and rapid loop-mediated isothermal amplification (LAMP) assay targeting the leptospiral secY gene.

Results

Several reaction conditions of the LAMP reaction were optimized to ensure efficient amplification of the target DNA. The sensitivity of the developed LAMP assay obtained using a pure Leptospira culture was 2 × 104 copies of genomic DNA per reaction (equivalent to 0.1 ng) for a 40-minute reaction time. No cross-reactions were observed in the LAMP reaction against a series of non-leptospiral bacteria, indicating a specific reaction. The applicability of the LAMP assay was demonstrated on human blood and urine specimens collected from suspected leptospirosis patients and rat kidney specimens collected from suspected leptospirosis outbreak areas and high-risk areas. The developed LAMP assay demonstrated a higher detection rate for leptospiral DNA compared with the polymerase chain reaction (PCR) assay, possibly due to the presence of inhibitory substances, especially in rat kidney specimens, to which the PCR method is more susceptible. The present findings also highlight the importance of urine sample collection from patients for routine monitoring of the disease.

Conclusions

In short, the developed LAMP assay can serve as a feasible alternative tool for the diagnosis of leptospirosis and be used for epidemiological and environmental surveillance of the disease, considering its robustness, rapidity, sensitivity, and specificity, as demonstrated in this study.

Polymerase chain reaction and loop-mediated isothermal amplification targeting lic13162, lic20239, and lipL32 genes for leptospirosis diagnosis

Leptospirosis is a zoonotic disease caused by pathogenic species of Leptospira. Due to the similarity with clinical signs of other febrile diseases, early diagnosis remains challenging. Real-time PCR has been used for direct detection of Leptospira, but it requires thermocyclers and highly trained personnel. Loop-mediated isothermal amplification (LAMP) is a simple and rapid DNA-based assay. Therefore, here we have developed PCR and LAMP assays targeting two novel genes, lic13162 and lic20239, and also lipL32 gene to detect pathogenic Leptospira. Analytical and diagnostic performances were compared with bacterial isolates (including different Leptospira species and serovars) and clinical samples. The results demonstrated that PCR assays targeting lic13162 and lic20239 were successful to amplify Leptospira, but LAMP not. However, both PCR and LAMP targeting lipL32 could detect pathogenic Leptospira. LAMP lipL32 could be performed in 30 min with a detection limit of 156 cells/mL. Diagnostic performance of lipL32-LAMP presented 84.2% sensitivity and 93.2% specificity. In conclusion, lipL32 PCR and LAMP are effective methods to detect pathogenic Leptospira directly from clinical samples.

Rapid and sensitive point-of-care detection of Leptospira by RPA-CRISPR/Cas12a targeting lipL32

Background

One of the key barriers preventing rapid diagnosis of leptospirosis is the lack of available sensitive point-of-care testing. This study aimed to develop and validate a clustered regularly-interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 12a (CRISPR/Cas12a) platform combined with isothermal amplification to detect leptospires from extracted patient DNA samples.

Methodology/Principal findings

A Recombinase Polymerase Amplification (RPA)-CRISPR/Cas12a-fluorescence assay was designed to detect the lipL32 gene of pathogenic Leptospira spp. The assays demonstrated a limit of detection (LOD) of 100 cells/mL, with no cross-reactivity against several other acute febrile illnesses. The clinical performance of the assay was validated with DNA extracted from 110 clinical specimens and then compared to results from qPCR detection of Leptospira spp. The RPA-CRISPR/Cas12a assay showed 85.2% sensitivity, 100% specificity, and 92.7% accuracy. The sensitivity increased on days 4–6 after the fever onset and decreased after day 7. The specificity was consistent for several days after the onset of fever. The overall performance of the RPA-CRISPR/Cas12a platform was better than the commercial rapid diagnostic test (RDT). We also developed a lateral flow detection assay (LFDA) combined with RPA-CRISPR/Cas12a to make the test more accessible and easier to interpret. The combined LFDA showed a similar LOD of 100 cells/mL and could correctly distinguish between known positive and negative clinical samples in a pilot study.

Conclusions/Significance

The RPA-CRISPR/Cas12 targeting the lipL32 gene demonstrated acceptable sensitivity and excellent specificity for detection of leptospires. This assay might be an appropriate test for acute leptospirosis screening in limited-resource settings.

Clinical signs and symptoms of leptospirosis are similar to those of other infectious diseases such as dengue, sepsis, and malaria, making it difficult to diagnose. In this study, we developed an RPA-CRISPR/Cas12a -based detection platform to identify the lipL32 gene of pathogenic Leptospira spp. The results showed that the limit of detection (LOD) was approximately 10² cells/mL without cross-reactivity against other infectious diseases. The platform was validated using 110 patients from 15 hospitals in Sisaket province, Thailand. The sensitivity, specificity, and accuracy was found to be 85.2%, 100% and 92.7%, respectively, for the diagnosis of leptospirosis. Assay sensitivity increased at 4–6 d post-onset of fever, with a consistent specificity every day after the onset of fever. We also developed a lateral flow detection assay combined with RPA-CRISPR/Cas12a, which also had a LOD of 10² cells/mL and could correctly distinguish known positive and negative clinical samples in a pilot study. Findings from this study demonstrate the potential effectiveness of the RPA-CRISPR/Cas12a platform in improving speed and accuracy of leptospirosis diagnosis especially in limited-resource settings.

Evaluation of diagnostic accuracy of loop-mediated isothermal amplification method (LAMP) compared with polymerase chain reaction (PCR) for Leptospira spp. in clinical samples: a systematic review and meta-analysis

Loop-mediated isothermal amplification (LAMP) test is widely used in molecular diagnostics as a point-of-care technique alternative to traditional PCR especially in resource-limited countries. LAMP has been recently used to diagnose leptospirosis. Therefore, we undertook a systematic review and meta-analysis to compare the accuracy of LAMP with PCR in the diagnosis of leptospirosis. Sixty-one studies were extracted from three international databases and analyzed throughout using the PRISMA guideline. The pooled sensitivity of LAMP and PCR technique was 0.80 (95% CI: 0.58-0.90) and 0.54 (95% CI: 0.35-0.67) respectively indicating that LAMP is more sensitive than PCR. The Q* value of LAMP and PCR-based technique is 274.61 and 397.95, respectively. Among the analyzed studies, significant heterogeneity was observed where I² is 90.90% for LAMP-based and 86.18% for PCR-based. Our study suggests that LAMP has better diagnostic accuracy than PCR. However, future work should be carried out to reduce heterogeneity as well as to improve and develop effective intervention strategies.

Laboratory Diagnosis of Leptospirosis

The diagnosis of leptospirosis depends on specific laboratory tests because nonspecific and diverse clinical manifestations make clinical diagnosis difficult and it is easily confused with other infectious diseases in the tropics. Suitable laboratory diagnostic tests vary depending on the stage of the disease, requiring the combination of diagnostic tests using appropriate specimens at each disease stage.

Update on molecular diagnosis of human leptospirosis

Background

Leptospirosis, caused by pathogenic Leptospira spp., is a widespread zoonotic disease worldwide. Early diagnosis is required for proper patient management and reducing leptospirosis morbidity and mortality.

Objective

To summarize current literature regarding commonly used and new promising molecular approaches to Leptospira detection and diagnostic tests of human leptospirosis.

Method

The relevant articles in Leptospira and leptospirosis were retrieved from MEDLINE (PubMed) and Scopus.

Results

Several molecular techniques have been developed for diagnosis of human leptospirosis. Polymerase chain reaction-based techniques targeting on either lipL32 or 16S rRNA (rrs) gene are most commonly used to detect leptospiral DNA in various clinical specimens. Whole blood and urine are recommended specimens for suspected cases in the first (acute) and the second (immune) phases, respectively. Isothermal amplification with less expensive instrument is an alternative DNA detection technique that may be suitable for resource-limited laboratories.

Conclusion

Detection of leptospiral DNA in clinical specimens using molecular techniques enhances sensitivity for diagnosis of leptospirosis. The efficient and robust molecular detection especially in the early leptospiremic phase may prompt early and appropriate treatment leading to reduced morbidity and mortality of patients with leptospirosis.

Diagnostic accuracy of genetic markers and nucleic acid techniques for the detection of Leptospira in clinical samples: A meta-analysis

BACKGROUND

Leptospirosis is often difficult to diagnose because of its nonspecific symptoms. The drawbacks of direct isolation and serological tests have led to the increased development of nucleic acid-based assays, which are more rapid and accurate. A meta-analysis was performed to evaluate the diagnostic accuracy of genetic markers for the detection of Leptospira in clinical samples.

METHODOLOGY AND PRINCIPLE FINDINGS

A literature search was performed in Scopus, PubMed, MEDLINE and non-indexed citations (via Ovid) by using suitable keyword combinations. Studies evaluating the performance of nucleic acid assays targeting leptospire genes in human or animal clinical samples against a reference test were included. Of the 1645 articles identified, 42 eligible studies involving 7414 samples were included in the analysis. The diagnostic performance of nucleic acid assays targeting the rrs, lipL32, secY and flaB genes was pooled and analyzed. Among the genetic markers analyzed, the secY gene showed the highest diagnostic accuracy measures, with a pooled sensitivity of 0.56 (95% CI: 0.50-0.63), a specificity of 0.98 (95% CI: 0.97-0.98), a diagnostic odds ratio of 46.16 (95% CI: 6.20-343.49), and an area under the curve of summary receiver operating characteristics curves of 0.94. Nevertheless, a high degree of heterogeneity was observed in this meta-analysis. Therefore, the present findings here should be interpreted with caution.

CONCLUSION

The diagnostic accuracies of the studies examined for each genetic marker showed a significant heterogeneity. The secY gene exhibited higher diagnostic accuracy measures compared with other genetic markers, such as lipL32, flaB, and rrs, but the difference was not significant. Thus, these genetic markers had no significant difference in diagnostic accuracy for leptospirosis. Further research into these genetic markers is warranted.

Nucleic acid and antigen detection tests for leptospirosis

BACKGROUND

Early diagnosis of leptospirosis may contribute to the effectiveness of antimicrobial therapy and early outbreak recognition. Nucleic acid and antigen detection tests have the potential for early diagnosis of leptospirosis. With this systematic review, we assessed the sensitivity and specificity of nucleic acid and antigen detection tests.

OBJECTIVES

To determine the diagnostic test accuracy of nucleic acid and antigen detection tests for the diagnosis of human symptomatic leptospirosis.

SEARCH METHODS

We searched electronic databases including MEDLINE, Embase, the Cochrane Library, and regional databases from inception to 6 July 2018. We did not apply restrictions to language or time of publication.

SELECTION CRITERIA

We included diagnostic cross-sectional studies and case-control studies of tests that made use of nucleic acid and antigen detection methods in people suspected of systemic leptospirosis. As reference standards, we considered the microscopic agglutination test alone (which detects antibodies against leptospirosis) or in a composite reference standard with culturing or other serological tests. Studies were excluded when the controls were healthy individuals or when there were insufficient data to calculate sensitivity and specificity.

DATA COLLECTION AND ANALYSIS

At least two review authors independently extracted data from each study. We used the revised Quality Assessment of Diagnostic Accuracy Studies tool (QUADAS-2) to assess risk of bias. We calculated study-specific values for sensitivity and specificity with 95% confidence intervals (CI) and pooled the results in a meta-analysis when appropriate. We used the bivariate model for index tests with one positivity threshold, and we used the hierarchical summary receiver operating characteristic model for index tests with multiple positivity thresholds. As possible sources of heterogeneity, we explored: timing of index test, disease prevalence, blood sample type, primers or target genes, and the real-time polymerase chain reaction (PCR) visualisation method. These were added as covariates to the meta-regression models.

MAIN RESULTS

We included 41 studies evaluating nine index tests (conventional PCR (in short: PCR), real-time PCR, nested PCR, PCR performed twice, loop-mediated isothermal amplification, enzyme-linked immunosorbent assay (ELISA), dot-ELISA, immunochromatography-based lateral flow assay, and dipstick assay) with 5981 participants (1834 with and 4147 without leptospirosis). Methodological quality criteria were often not reported, and the risk of bias of the reference standard was generally considered high. The applicability of findings was limited by the frequent use of frozen samples. We conducted meta-analyses for the PCR and the real-time PCR on blood products.The pooled sensitivity of the PCR was 70% (95% CI 37% to 90%) and the pooled specificity was 95% (95% CI 75% to 99%). When studies with a high risk of bias in the reference standard domain were excluded, the pooled sensitivity was 87% (95% CI 44% to 98%) and the pooled specificity was 97% (95% CI 60% to 100%). For the real-time PCR, we estimated a summary receiver operating characteristic curve. To illustrate, a point on the curve with 85% specificity had a sensitivity of 49% (95% CI 30% to 68%). Likewise, at 90% specificity, sensitivity was 40% (95% CI 24% to 59%) and at 95% specificity, sensitivity was 29% (95% CI 15% to 49%). The median specificity of real-time PCR on blood products was 92%. We did not formally compare the diagnostic test accuracy of PCR and real-time PCR, as direct comparison studies were lacking. Three of 15 studies analysing PCR on blood products reported the timing of sample collection in the studies included in the meta-analyses (range 1 to 7 days postonset of symptoms), and nine out of 16 studies analysing real-time PCR on blood products (range 1 to 19 days postonset of symptoms). In PCR studies, specificity was lower in settings with high leptospirosis prevalence. Other investigations of heterogeneity did not identify statistically significant associations. Two studies suggested that PCR and real-time PCR may be more sensitive on blood samples collected early in the disease stage. Results of other index tests were described narratively.

AUTHORS' CONCLUSIONS

The validity of review findings are limited and should be interpreted with caution. There is a substantial between-study variability in the accuracy of PCR and real-time PCR, as well as a substantial variability in the prevalence of leptospirosis. Consequently, the position of PCR and real-time PCR in the clinical pathway depends on regional considerations such as disease prevalence, factors that are likely to influence accuracy, and downstream consequences of test results. There is insufficient evidence to conclude which of the nucleic acid and antigen detection tests is the most accurate. There is preliminary evidence that PCR and real-time PCR are more sensitive on blood samples collected early in the disease stage, but this needs to be confirmed in future studies.

Whole cell matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for identification of Leptospira spp. in Thailand and Lao PDR

Leptospirosis is a zoonosis with a worldwide distribution, caused by pathogenic spirochetes of the genus Leptospira. The classification and identification of leptospires can be conducted by both genotyping and serotyping which are time-consuming and established in few reference laboratories. This study used matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) as rapid and accurate tool for the identification of leptospires. The whole cell protein spectra of 116 Leptospira isolates including 15 references Leptospira spp. (pathogenic, n = 8; intermediate, n = 2; non-pathogenic, n = 5) and 101 Leptospira spp. clinical isolates was created as an in-house MALDI-TOF MS database. Ninety-seven clinical isolates from Thailand and Laos was validated with these protein spectra and revealed 98.9% correct identification when compared with 16S rRNA gene sequences method. Moreover, MALDI-TOF MS could identify spiked leptospires whole cell in urine. Biomarkers for differentiation of leptospires phylogeny and specific protein spectra for most found Leptospira spp. in this area (L. interrogans, L. kirschneri, L. borgpetersenii) based on MALDI-MS algorithm were demonstrated.

Visual and Rapid Detection of Leptospira interrogans Using Multiple Cross-Displacement Amplification Coupled with Nanoparticle-Based Lateral Flow Biosensor

Leptospirosis is a worldwide zoonosis caused by spirochetes from the genus Leptospira. In the present study, a visual and rapid method for detecting Leptospira interrogans was developed based on multiple cross-displacement amplification (MCDA) and nanoparticle-based lateral flow biosensor (LFB). A set of 10 primers was specifically designed to recognize 10 regions of the lipL 41 gene of L. interrogans. The MCDA reaction was optimized at 64°C for only 40 min, and the amplification products were directly applied to the biosensor. The entire process, including DNA extraction (25 min), MCDA reaction (40 min), and result interpretation (∼2 min), could be completed within 70 min. Amplification products were detectable from as few as 10 genomic equivalents per reaction of pure L. interrogans DNA. No cross-reaction with nonpathogenic Leptospira or other bacteria was observed. The MCDA-LFB method established in the current report is suitable for the rapid screening of L. interrogans in clinical, animal, and environmental samples.

Evaluation of LAMP for detection and/or screening of Leptospira spp. infection among domestic animals in the Philippines

Objective:

This study assessed the applicability of loop-mediated isothermal amplification (LAMP) for the detection of leptospirosis among domesticated animals and sewage rats. Specifically, it evaluated the ability of LAMP to amplify Leptospira spp. targeting the 16s rRNA gene in boiled urine samples.

Materials and methods:

A total of 140 samples from different domestic animals were tested for the presence of the antigen. A nested-polymerase chain reaction (nPCR) protocol was used to compare and determine the sensitivity of LAMP in detecting Leptospira spp. The LAMP was also evaluated by comparing its amplification result using agarose gel electrophoresis and color change using dye.

Results:

Positivity rate of Leptospira spp. antigen was 29.0% (40/140) for LAMP and 9.3% (13/140) for nPCR. Also, LAMP results for gel electrophoresis and dye color change varied in some samples that may be due to the interpretation of the result in dye color change.

Conclusion:

Overall, LAMP is a rapid, sensitive, and cost-effective diagnostic method compared with nPCR. Also, LAMP has a potential application as pen-side screening, surveillance, and clinical diagnostic kits of infectious diseases without requiring advance equipment and skilled personnel.

Sensitive Leptospira DNA detection using tapered optical fiber sensor

This paper presents the development of tapered optical fiber sensor to detect a specific Leptospira bacteria DNA. The bacteria causes Leptospirosis, a deadly disease but with common early flu-like symptoms. Optical single mode fiber (SMF) of 125 μm diameter is tapered to produce 12 μm waist diameter and 15 cm length. The novel DNA-based optical fiber sensor is functionalized by incubating the tapered region with sodium hydroxide (NaOH), (3-Aminopropyl) triethoxysilane and glutaraldehyde. Probe DNA is immobilized onto the tapered region and subsequently hybridized by its complementary DNA (cDNA). The transmission spectra of the DNA-based optical fiber sensor are measured in the 1500 to 1600 nm wavelength range. It is discovered that the shift of the wavelength in the SMF sensor is linearly proportional with the increase in the cDNA concentrations from 0.1 to 1.0 nM. The sensitivity of the sensor toward DNA is measured to be 1.2862 nm/nM and able to detect as low as 0.1 fM. The sensor indicates high specificity when only minimal shift is detected for non-cDNA testing. The developed sensor is able to distinguish between actual DNA of Leptospira serovars (Canicola and Copenhageni) against Clostridium difficile (control sample) at very low (femtomolar) target concentrations.

Molecular diagnostics for human leptospirosis

PURPOSE OF REVIEW

The definitive diagnosis of leptospirosis, which results from infection with spirochetes of the genus Leptospira, currently relies on the use of culture, serological testing (microscopic agglutination testing), and molecular detection. The purpose of this review is to describe new molecular diagnostics for Leptospira and discuss advancements in the use of available methods.

RECENT FINDINGS

Efforts have been focused on improving the clinical sensitivity of Leptospira detection using molecular methods. In this review, we describe a reoptimized pathogenic species-specific real-time PCR (targeting lipL32) that has demonstrated improved sensitivity, findings by two groups that real-time reverse-transcription PCR assays targeting the 16S rrs gene can improve detection, and two new loop-mediated amplification techniques. Quantitation of leptospiremia, detection in different specimen types, and the complementary roles played by molecular detection and microscopic agglutination testing will be discussed. Finally, a protocol for Leptospira strain subtyping using variable number tandem repeat targets and high-resolution melting will be described.

SUMMARY

Molecular diagnostics have an established role for the diagnosis of leptospirosis and provide an actionable diagnosis in the acute setting. The use of real-time reverse-transcription PCR for testing serum/plasma and cerebrospinal fluid, when available, may improve the detection of Leptospira without decreasing clinical specificity.

The use of loop-mediated isothermal DNA amplification for the detection and identification of the anthrax pathogen

The results of detection and identification of Bacillus anthracis strains in loop-mediated isothermal DNA amplification (LAMP) reaction performed under optimized conditions with original primers and thermostable DNA polymerase are presented. Reproducible LAMP-based detection of chromosomal and plasmid DNA targets specific for B. anthracis strains has been demonstrated. No cross reactions with DNA from bacterial strains of other species of the B. cereus group were detected. The development of tests for anthrax-pathogen detection based on the optimized reaction of loop isothermal DNA amplification is planned. These tests will be convenient for clinical studies and field diagnostics due to the absence of requirements for sophisticated equipment.

Utility of Loop-mediated Isothermal Amplification Assay, Polymerase Chain Reaction, and ELISA for Diagnosis of Leptospirosis in South Indian Patients

BACKGROUND

Leptospirosis is a zoonotic disease which requires laboratory diagnosis for confirmation.

MATERIALS AND METHODS

In this study serum samples from adults with acute undifferentiated fever (duration ≤15 days) were tested for IgM antibodies to Leptospira by ELISA, PCR for rrs gene and loop-mediated isothermal amplification (LAMP) assay for LipL32 and LipL41.

RESULTS

Among the 150 sera tested, three were positive by PCR, LAMP and IgM ELISA/modified Faines' criteria, two by only PCR; seven only by LAMP assay and forty fulfilled modified Faine's criteria (illness clinically compatible and IgM ELISA positive for leptospirosis). Clinical correlation revealed renal compromise, low platelet count and severe jaundice were significantly related to leptospirosis (P < 0.05).

CONCLUSION

This study suggests that LAMP assay could be useful for diagnosis of leptospirosis during the 1^st week of illness whereas IgM ELISA forms the mainstay of diagnosis from the 2^nd week onward. Further studies especially community based, comparing ELISA, PCR, LAMP, culture and microscopic agglutination test are required to evaluate the veracity of these findings.

A comparison of the reliability of two gene targets in loop-mediated isothermal amplification assays for detecting leptospiral DNA in canine urine

We compared 2 novel loop-mediated isothermal amplification (LAMP) assays that target either the 16S ribosomal RNA ( rrs) gene or the gene encoding a 32-kDa leptospiral lipoprotein ( lipL32) in order to assess the effect of the target on the accuracy of the LAMP assays. The most sensitive assay was the rrs assay with a limit of detection (LOD) of 1.2 × 10¹ genome equivalents per reaction. The novel lipL32 assay showed an LOD of 1.2 × 10² genome equivalents per reaction. Both assays showed adequate specificity when tested against a collection of bacteria commonly found in voided canine urine. However, when field samples were assayed, the rrs assays gave many false-positive results and a poor positive predictive value of 8.33%. In conclusion, even if the LAMP assay is used in low prevalence areas, the lipL32 assay would be preferable. Conversely, the higher analytical sensitivity of the rrs assay could be effectively used as a screening test in endemic areas with high disease prevalence, followed by confirmation of the positive results using the lipL32 assay.

Leptospirosis: risk factors and management challenges in developing countries

Leptospirosis is a widespread bacterial zoonosis with highest burden in low-income populations living in tropical and subtropical regions, both in urban and in rural environments. Rodents are known as the main reservoir animals, but other mammals may also significantly contribute to human infections in some settings. Clinical presentation of leptospirosis is nonspecific and variable, and most of the early signs and symptoms point to the so-called “acute fever of unknown origin”, a major diagnostic challenge in tropical and subtropical areas. However, leptospirosis can rapidly evolve to life-threatening complications, especially if left untreated. There is a need for good awareness of leptospirosis and rapid antibiotic treatment based on clinical and epidemiological suspicion. Severe leptospirosis cases include renal and/or respiratory failure and shock, necessitating intensive care, also seldom available or with limited capacity. Confirmation of leptospirosis relies on biological diagnosis, which unfortunately uses tricky methods seldom available. This biological confirmation, however, is essential for surveillance and public health purpose. A good knowledge of leptospirosis epidemiology (eg, the reservoir animals involved, the Leptospira strains circulating, the seasonal and geographical patterns, and specific populations at risk) can be achieved through adequate surveillance and diagnosis. This can pave the way to prevention and intervention strategies and in turn alleviate the toll leptospirosis takes on affected populations. Over the past few years, leptospirosis has been increasingly recognized, as the need for multidisciplinary approaches in a One-Health perspective has been acknowledged, raising hope to successfully tackle the challenges of this zoonosis.

Combined antibody and DNA detection for early diagnosis of leptospirosis after a disaster

Early diagnosis based on laboratory confirmation is essential for managing leptospirosis. This study investigated the effectiveness of a novel method of detecting leptospirosis that combines measurement of anti-Leptospira antibodies by the microscopic agglutination test (MAT), enzyme-linked immunosorbent assay (ELISA), and immunochromatographic test (ICT) and leptospiral DNA by loop-mediated isothermal amplification (LAMP) and real-time PCR in plasma and 2 types of urine pellets. Of 113 suspected cases, 68.1%, 76.1%, and 60.2% were positive by MAT, ELISA, and ICT, respectively. Real-time PCR using DNA purified from urine pellets collected by low-speed centrifugation yielded positive signals for patients in late acute as well as early phase who were positive by LAMP using plasma DNA or urine pellets. Among antibody-negative patients, 9.5% were positive by DNA detection. These findings indicate that the leptospirosis detection rate is increased by combining antibody and DNA detection, providing a new tool for timely diagnosis of infection.

Efficient Detection of Pathogenic Leptospires Using 16S Ribosomal RNA

Pathogenic Leptospira species cause a prevalent yet neglected zoonotic disease with mild to life-threatening complications in a variety of susceptible animals and humans. Diagnosis of leptospirosis, which primarily relies on antiquated serotyping methods, is particularly challenging due to presentation of non-specific symptoms shared by other febrile illnesses, often leading to misdiagnosis. Initiation of antimicrobial therapy during early infection to prevent more serious complications of disseminated infection is often not performed because of a lack of efficient diagnostic tests. Here we report that specific regions of leptospiral 16S ribosomal RNA molecules constitute a novel and efficient diagnostic target for PCR-based detection of pathogenic Leptospira serovars. Our diagnostic test using spiked human blood was at least 100-fold more sensitive than corresponding leptospiral DNA-based quantitative PCR assays, targeting the same 16S nucleotide sequence in the RNA and DNA molecules. The sensitivity and specificity of our RNA assay against laboratory-confirmed human leptospirosis clinical samples were 64% and 100%, respectively, which was superior then an established parallel DNA detection assay. Remarkably, we discovered that 16S transcripts remain appreciably stable ex vivo, including untreated and stored human blood samples, further highlighting their use for clinical detection of L. interrogans. Together, these studies underscore a novel utility of RNA targets, specifically 16S rRNA, for development of PCR-based modalities for diagnosis of human leptospirosis, and also may serve as paradigm for detection of additional bacterial pathogens for which early diagnosis is warranted.

Highly Sensitive Loop-Mediated Isothermal Amplification for the Detection of Leptospira

Leptospirosis is a worldwide zoonosis caused by an infection with the pathogenic species of Leptospira. We have developed a loop-mediated isothermal amplification (LAMP) assay to detect the DNA of Leptospira spp. Six sets of primers targeting the gene of the subsurface protein, lipL32, were evaluated for their detection sensitivity. The best primer set detected less than 25 copies of lipL32 per reaction of both plasmid DNA template and purified leptospiral genomic DNA. By combining primers targeting lipL32 with the previously published primer set targeting lipL41, the sensitivity of the assay was improved to 12 copies of L. interrogans. The specificity of the LAMP assay was evaluated by using the genomic DNA from other clinically encountered bacterial species such as different strains of Orientia tsutsugamushi, Rickettsia typhi, Rickettsia conorii, Rickettsia rickettsii, Coxiella burnetii, and Bartonella bacilliformis. These genomic DNA samples were all negative in our LAMP assay. The sensitivity of the LAMP assay was very similar to that of quantitative real time PCR. Several detection methods for the amplified product of LAMP assay were performed to demonstrate the simplicity of the assay. In summary, our results have suggested that this assay is rapid, robust, and easy to perform and has the potential to be used in endemic locations.

Diagnostic Accuracy of Recombinant Immunoglobulin-like Protein A-Based IgM ELISA for the Early Diagnosis of Leptospirosis in the Philippines

BACKGROUND

Leptospirosis is an important but largely under-recognized public health problem in the tropics. Establishment of highly sensitive and specific laboratory diagnosis is essential to reveal the magnitude of problem and to improve treatment. This study aimed to evaluate the diagnostic accuracy of a recombinant LigA protein based IgM ELISA during outbreaks in the clinical-setting of a highly endemic country.

METHODOLOGY/PRINCIPAL FINDINGS

A prospective study was conducted from October 2011 to September 2013 at a national referral hospital for infectious diseases in Manila, Philippines. Patients who were hospitalized with clinically suspected leptospirosis were enrolled. Plasma and urine were collected on admission and/or at discharge and tested using the LigA-IgM ELISA and a whole cell-based IgM ELISA. Sensitivity and specificity of these tests were evaluated with cases diagnosed by microscopic agglutination test (MAT), culture and LAMP as the composite reference standard and blood bank donors as healthy controls: the mean+3 standard deviation optical density value of healthy controls was used as the cut-off limit (0.062 for the LigA-IgM ELISA and 0.691 for the whole cell-based IgM ELISA). Of 304 patients enrolled in the study, 270 (89.1%) were male and the median age was 30.5 years; 167 (54.9%) were laboratory confirmed. The sensitivity and ROC curve AUC for the LigA-IgM ELISA was significantly greater than the whole cell-based IgM ELISA (69.5% vs. 54.3%, p<0.01; 0.90 vs. 0.82, p<0.01) on admission, but not at discharge. The specificity of LigA-IgM ELISA and whole cell-based IgM ELISA were not significantly different (98% vs. 97%). Among 158 MAT negative patients, 53 and 28 were positive by LigA- and whole cell-based IgM ELISA, respectively; if the laboratory confirmation was re-defined by LigA-IgM ELISA and LAMP, the clinical findings were more characteristic of leptospirosis than the diagnosis based on MAT/culture/LAMP.

CONCLUSIONS/SIGNIFICANCE

The newly developed LigA-IgM ELISA is more sensitive than the whole cell-based IgM based ELISA. Although the final diagnosis must be validated by more specific tests, LigA-IgM ELISA could be a useful diagnostic test in a real clinical-setting, where diagnosis is needed in the early phase of infection.

Sensitive real-time PCR detection of pathogenic Leptospira spp. and a comparison of nucleic acid amplification methods for the diagnosis of leptospirosis

Background

Bacteria of the genus Leptospira, the causative agents of leptospirosis, are categorized into pathogenic and non-pathogenic species. However, the benefit of using a clinical diagnostic that is specific for pathogenic species remains unclear. In this study, we present the development of a real-time PCR (rtPCR) for the detection of pathogenic Leptospira (the pathogenic rtPCR), and we perform a comparison of the pathogenic rtPCR with a published assay that detects all Leptospira species [the undifferentiated febrile illness (UFI) assay] and a reference 16S Leptospira rtPCR, which was originally designed to detect pathogenic species.

Methodology/Principal Findings

For the pathogenic rtPCR, a new hydrolysis probe was designed for use with primers from the UFI assay, which targets the 16S gene. The pathogenic rtPCR detected Leptospira DNA in 37/37 cultured isolates from 5 pathogenic and one intermediate species. Two strains of the non-pathogenic L. biflexa produced no signal. Clinical samples from 65 patients with suspected leptospirosis were then tested using the pathogenic rtPCR and a reference Leptospira 16S rtPCR. All 65 samples had tested positive for Leptospira using the UFI assay; 62 (95.4%) samples tested positive using the pathogenic rtPCR (p = 0.24). Only 24 (36.9%) samples tested positive in the reference 16S rtPCR (p<0.0001 for comparison with the pathogenic rtPCR and UFI assays). Amplicon sequencing confirmed the detection of pathogenic Leptospira species in 49/50 cases, including 3 cases that were only detected using the UFI assay.

Conclusions/Significance

The pathogenic rtPCR displayed similar sensitivity to the UFI assay when testing clinical specimens with no difference in specificity. Both assays proved significantly more sensitive than a real-time molecular test used for comparison. Future studies are needed to investigate the clinical and epidemiologic significance of more sensitive Leptospira detection using these tests.

Loop-mediated isothermal amplification of DNA (LAMP): a new diagnostic tool lights the world of diagnosis of animal and human pathogens: a review

Diagnosis is an important part in case of animal husbandry as treatment of a disease depends on it. Advancement in molecular biology has generated various sophisticated tools like Polymerase Chain Reaction (PCR), its versions along with pen-side diagnostic techniques. Every diagnostic test however has both advantages and disadvantages; PCR is not an exception to this statement. To ease the odds faced by PCR several non-PCR techniques which can amplify DNA at a constant temperature has become the need of hour, thus generating a variety of isothermal amplification techniques including Nucleic Acid Sequence-Based Amplification (NASBA) along with Self-Sustained Sequence Replication (3SR) and Strand Displacement Amplification (SDA) and Loop mediated isothermal amplification (LAMP) test. LAMP stands out to be a good and effective diagnostic test for empowering in developing countries as it does not require sophisticated equipments and skilled personnel and proves to be cost-effective. Performance of LAMP mainly relies on crafting of six primers (including 2 loop primers) ultimately accelerating the reaction. LAMP amplifies DNA in the process pyrophosphates are formed causing turbidity that facilitates visualisation in a more effective way than PCR. The Bst and Bsm polymerase are the required enzymes for LAMP that does not possess 5'-3' exonuclease activity. Results can be visualized by adding DNA binding dye, SYBR green. LAMP is more stable than PCR and real-time PCR. Non-involvement of template DNA preparation and ability to generate 10(9) copies of DNA are added benefits that make it more effective than NASBA or 3SR and SDA. Thus, it fetches researcher's interest in developing various versions of LAMP viz., its combination with lateral flow assay or micro LAMP and more recently lyophilized and electric (e) LAMP. Availability of ready to use LAMP kits has helped diagnosis of almost all pathogens. LAMP associated technologies however needs to be developed as a part of LAMP platform rather than developing them as separate entities. This review deals with all these salient features of this newly developed tool that has enlightened the world of diagnosis.

Development of a recombinase polymerase amplification assay for the detection of pathogenic Leptospira

Detection of leptospires based on DNA amplification techniques is essential for the early diagnosis of leptospirosis when anti-Leptospira antibodies are below the detection limit of most serological tests. In middle and low income countries where leptospirosis is endemic, routine implementation of real-time PCR is financially and technically challenging due to the requirement of expensive thermocycler equipment. In this study we report the development and evaluation of a novel isothermal recombinase polymerase amplification assay (RPA) for detection of pathogenic Leptospira based on TwistAmp chemistry. RPA enabled the detection of less than two genome copies per reaction. Retrospective evaluation revealed a high diagnostic accuracy (sensitivity and specificity of 94.7% and 97.7%, respectively) compared to culturing as the reference standard. RPA presents a powerful tool for the early diagnosis of leptospirosis in humans and in animals. Furthermore, it enables the detection of the causative agent in reservoirs and environment, and as such is a valuable adjunct to current tools for surveillance and early outbreak warning.

Rapid tests for diagnosis of leptospirosis: current tools and emerging technologies

Leptospirosis is an emerging zoonosis with a worldwide distribution but is more commonly found in impoverished populations in developing countries and tropical regions with frequent flooding. The rapid detection of leptospirosis is a critical step to effectively manage the disease and to control outbreaks in both human and animal populations. Therefore, there is a need for accurate and rapid diagnostic tests and appropriate surveillance and alert systems to identify outbreaks. This review describes current in-house methods and commercialized tests for the rapid diagnosis of acute leptospirosis. It focuses on diagnostic tests that can be performed with minimal training and limited equipment in less-developed and newly industrialized countries, particularly in resource-limited settings and with results in minutes to less than 4 hours. We also describe recent technological advances in the field of diagnostic tests that could allow for the development of innovative rapid tests in the near future.

Loop-mediated isothermal amplification assay for the rapid detection of Staphylococcus aureus

Staphylococcus aureus, including methicillin-resistant S. aureus (MRSA), is an important human pathogen that produces a variety of toxins and causes a wide range of infections, including soft-tissue infections, bacteremia, and staphylococcal food poisoning. A loop-mediated isothermal amplification (LAMP) assay targeting the arcC gene of S. aureus was developed and evaluated with 119 S. aureus and 25 non-S. aureus strains. The usefulness of the assay was compared with the PCR method that targets spa and arcC genes. The optimal temperature for the LAMP assay was 58.5°C with a detection limit of 2.5 ng/μL and 10(2) CFU/mL when compared to 12.5 ng/μL and 10(3) CFU/mL for PCR (spa and arcC). Both LAMP and PCR assays were 100% specific, 100% sensitive, 100% positive predictive value (PPV), and 100% negative predictive value (NPV). When tested on 30 spiked blood specimens (21 MRSA, eight non-S. aureus and one negative control), the performance of LAMP and PCR was comparable: 100% specific, 100% sensitive, 100% PPV, and 100% NPV. In conclusion, the LAMP assay was equally specific with a shorter detection time when compared to PCR in the identification of S. aureus. The LAMP assay is a promising alternative method for the rapid identification of S. aureus and could be used in resource-limited laboratories and fields.

A new loop-mediated isothermal amplification method for rapid, simple, and sensitive detection of Leptospira spp. in urine

We developed a new loop-mediated isothermal amplification (LAMP) method to detect rrs, a 16S rRNA gene of pathogenic Leptospira spp. in urine. The method enables detection of two leptospiral cells per reaction mixture following boiling of urine specimens. The sensitivity of this method is higher than that of culture or of flaB nested PCR.