Novel TaqMan® PCR for detection of Leptospira species in urine and blood: Pit-falls of in silico validation

Can Wastewater Surveillance Enhance Genomic Tracking of Climate-Driven Pathogens?

Climate change heightens the threat of infectious diseases in Europe, necessitating innovative surveillance methods. Based on 390 scientific papers, for the first time, this review associates climate-related pathogens, data related to their presence in wastewater, and associated available genomic detection methods. This deep analysis reveals a wide range of pathogens that can be tracked through methods such as quantitative and digital PCR, as well as genomic pathogen enrichment in combination with sequencing and metagenomics. Nevertheless, significant gaps remain in the development of methods, particularly for vector-borne pathogens, and in their general harmonization relating to performance criteria. By offering an overview of recent advancements while identifying critical gaps, we advocate for collaborative research and validation to integrate detection techniques into surveillance frameworks. This will enhance public health resilience against emerging infectious diseases driven by climate change.

Molecular and serological prevalence of Leptospira spp. among slaughtered cattle and associated risk factors in the Bahr El Ghazal region of South Sudan

INTRODUCTION

Leptospirosis is a neglected emerging and zoonotic disease reported worldwide. This study sought to determine the molecular and serological prevalence of Leptospira spp. and the associated risk factors in slaughtered cattle from the Bahr El Ghazal region of South Sudan.

MATERIALS AND METHODS

Between January 16th and February 25th, 2023, blood and urine samples were collected from 402 cattle at the Lokoloko Municipal Slaughterhouse in Western Bahr El-Ghazal State. Serum samples were tested using the microscopic agglutination test (MAT), with a panel of 12 serovars (sv) from 12 serogroups (sg) and 4 species (spp) of Leptospira spp. These serovars had been previously identified in Sudan and the East African region. Simultaneously, 400 corresponding urine samples were screened using qualitative real-time polymerase chain reaction (PCR) to detect the shedding of Leptospira spp. in urine. To identify the associated risk factors, the age, sex, breed and body condition score of each sampled cattle was noted at the time of sampling and subsequently analysed using logistic regression models.

RESULTS

Among the 402 serum samples screened, a substantial 81.8% (329/402, 95% CI 77.9-85.3) displayed seropositivity for Leptospira spp. with a MAT titre ≥ 100. The prevalence of urine shedding determined by PCR was 6% (23/400, 95% CI 3.8-8.4), while probable recent leptospirosis with a MAT ≥ 1:800 was observed in 33.1% (133/402, 95% CI 28.6-37.8) of the cattle. Multiple reactions were detected in 34.8% (140/402, 95% CI 30.6-39.5) serum samples. The seropositivity was against L. borgpetersenii sg. Tarassovi (78.6%; 316/402, 95% CI 74.4-82.3), followed by L. borgpetersenii sg. Ballum at 20.4% (82/402, 95% CI, 16.7-24.4%), L. kirschneri sg. Autumnalis At 8.7% (35/402, 95% CI 5.7-11.7), L. interrogans sg. of Pomona at 7.0% (28/402, 95% CI 4.5-9.5), and L. interrogans sg. Hebdomadis was 5.0% (20/402, 95% CI 2.8-7.2). Several risk factors are associated with seropositivity. Older animals (≥ 2 years) had 2.0 times greater odds (95% CI 1.14-3.5) of being seropositive than younger animals (< 2 years), P-value = 0.016. Female animals demonstrated 2.1 times greater odds (95% CI 1.2-3.6) of seropositivity than males did (P-value = 0.008). Additionally, Felata/Mbororo cattle exhibited 2.4 times greater odds (95% CI 1.3-4.5) of being seropositive than did local Nilotic cattle (P-value = 0.005). The agreement between the MAT and PCR results was poor, as indicated by a kappa statistic value of 0.001 and a P-value of 0.913. But there was a moderate agreement between MAT high titres ≥ 800 and PCR positivity with a kappa statistic value = 0.501 and a P-value < 0.001.

CONCLUSION

In addition to the high seroprevalence, Leptospira spp. were found in the urine of slaughtered cattle, suggesting that leptospirosis is endemic to the study area. This finding underscores the significance of cattle as potential sources of infection for slaughterhouse workers, the general public, and other animal species. To address this issue effectively in the Bahr El Ghazal Region and South Sudan, a comprehensive strategy involving a multidisciplinary approach is essential to minimize disease among animals, hence reducing potential zoonotic risks to humans.

Detection and Identification of Pathogenic Leptospira spp. Serogroups in Europe between 2017 and 2020 Applying a Novel Gene-Based Molecular Approach

Leptospirosis is a neglected but reemerging worldwide zoonotic disease. Due to a rise in global temperature, precipitation, and urbanization, the risk of acquiring an infection with Leptospira (L.) spp. increases in Europe. One species affected by leptospirosis living close to the human is the dog. Even though dogs can shed low numbers of leptospires, their value as sentinel animal aiding in understanding environmental reservoirs might be even more important for human and animal health. Therefore, it is crucial to study the prevalence of pathogenic L. spp. in dogs and tailor coordinated protective measures like vaccination. This study aimed to screen a collection of purified DNA extracted from canine field samples (blood and urine, n = 239) collected in Europe from dogs suspected of leptospirosis and found positive by the lipL32 PCR used for diagnostics. A new simple and effective molecular approach was developed to identify different leptospiral serogroups using first a 16S rRNA PCR and 16S rRNA gene sequencing for genomospecies determination followed by a PCR targeting the rfb gene locus responsible for LPS biosynthesis for serogroup classification. In total, 172 DNA samples were successfully tested. Results show that L. Icterohaemorrhagiae was detected as the most prevalent serogroup in Europe (53%), followed by L. Australis serogroup (13%). At lower percentages, L. Pomona (5%), L. Autumnalis (4%), and L. Sejroe (2%) were identified. This work emphasizes that current L4 vaccines are relevant and should confer a high efficacy profile at least against L. Icterohaemorrhagiae and L. Australis serogroups.

Serological and molecular detection as well as typing of Leptospira spp. in foxes, raccoons, and other wild carnivores in North-Eastern Germany, 2021-2022

Leptospirosis is a worldwide zoonosis caused by pathogenic Leptospira spp. While the latter are reported from various mammal hosts such as humans, dogs, or rodents, less is known about their presence in wild carnivores. We therefore investigated the presence of Leptospira spp. in foxes, raccoons, badgers, raccoon dogs, and martens in North-Eastern Germany. Kidney, urine, and blood specimens obtained from legally hunted or road-killed animals were tested by real-time PCR and by serogroup specific antibody detection for the presence of Leptospira spp. Additionally, kidney and urine specimens were tested by real-time PCR for the presence of Brucella spp. and Francisella tularensis, with all being negative for these two zoonotic pathogens. Leptospira spp. were detected by PCR in 12.6 % (n = 21/166) and serologically in 26.2 % (n = 53/202) of tissue and serum samples, respectively. Antibodies to 15 different serogroups were identified with Javanica (n = 25) and Bataviae (n = 12) being predominant. A high sero-prevalence of 34.0 % and 18.6 % in foxes and raccoons, respectively, and the presence of ST17 associated with human and animal leptospirosis indicates a reservoir and the zoonotic potential of these wild animals.

TaqMan real-time PCR for detection of pathogenic Leptospira spp. in canine clinical samples

Introduction

Canine leptospirosis has always been a differential diagnosis in dogs presenting with clinical signs and blood profiles associated with kidney and/or liver disease. The conventional polymerase chain reaction (PCR) provides diagnoses, but real-time PCR-based tests provide earlier confirmation and determine the severity of infection, especially in the acute stage, allowing early detection for immediate treatment decisions. To our knowledge, real-time PCR has not been routinely adopted for clinical investigation in Malaysia. This study evaluated TaqMan real-time PCR (qPCR) assays diagnosing leptospirosis and compared their applicability to clinical samples from dogs with kidney and/or liver disease against a conventional PCR reference.

Material and Methods

The qPCR assays were validated using existing leptospiral isolates. Whole blood and urine samples were analysed using a conventional PCR, LipL32(1) and LipL32(2) qPCRs and a microscopic agglutination test. The sensitivity and specificity of the qPCRs were determined.

Results

The LipL32(1) qPCR assay had more diagnostic value than the LipL32(2) qPCR assay. Further evaluation of this assay revealed that it could detect as low as five DNA copies per reaction with high specificity for the tested leptospiral strains. No cross-amplification was observed with other organisms. Analysing the clinical samples, the LipL32(1) qPCR assay had 100.0% sensitivity and >75.0% specificity.

Conclusion

The LipL32(1) qPCR assay is sensitive, specific and has the potential to be applied in future studies.

Diagnostic accuracy of an immunomagnetic separation-PCR assay to detect pathogenic Leptospira spp. in urine from dairy cattle, using a Bayesian latent class model

Leptospirosis is a zoonotic disease that has spread worldwide and causes significant economic losses in the dairy industry. The causal agents of this infectious disease are members of the genus Leptospira, known as pathogenic Leptospira spp. Specific clinical signs of the infection are difficult to detect. Therefore, the disease is normally under-diagnosed, mostly due to the lack of a cost-effective technique for diagnosing animals with a low bacterial load in their urine. The aim of this study was to assess the diagnostic accuracy of a qPCR coupled with a previous Immunomagnetic separation (IMS) step (IMS-qPCR) against a qPCR without using IMS, using a Bayesian latent class model (2 tests, 3 populations) to determine the leptospirosis infectious status in naturally infected dairy cattle. The results revealed that IMS qPCR had a sensitivity (Se) of 95.7% (95% Probability Interval (PI) = 85.0; 99.4%) and a specificity (Sp) of 98% (95% PI = 96.1; 99.4%), indicating that it is more sensitive than conventional qPCR (Se = 69.7% (95% PI = 59.2; 79.0%); median difference = 25.2% (Monte Carlo Error = 10.2%); and the Sp = 98.8% (95% PI = 97.6; 99.5%), median difference = 0.8% (Monte Carlo Error = 2.1%). Therefore, results shows that IMS-qPCR is a more useful diagnostic tool in terms of accuracy for detecting infectious animals with pathogenic Leptospira in their urine.

Trends in human leptospirosis in Denmark, 2012-2021

Leptospirosis is a zoonotic bacterial infection that can cause influenza-like symptoms and severe disease. In Denmark, leptospirosis is rare, non-endemic, and most commonly transferred to humans from mice and rats. Cases of human leptospirosis in Denmark are by law notifiable to Statens Serum Institut. This study aimed to describe trends in incidence of leptospirosis in Denmark from 2012 to 2021. Descriptive analyses were used to calculate the incidence, geographical distribution and possible routes of infection, as well as testing capacity and serological trends. The overall incidence rate was 0.23 per 100,000 inhabitants, with the highest annual incidence of 24 cases in 2017. Men between 40-49 years old were the demographic group most commonly diagnosed with leptospirosis. August and September were the months with highest incidence over the entire study period. The most common serovar observed was Icterohaemorrhagiae, although over a third of cases were diagnosed via polymerase chain reaction alone. The most common sources of exposure reported were travel abroad, farming, and recreational contact with fresh water, the latter being a new exposure compared to previous studies. Overall, a One Health approach would ensure better detection of outbreaks and milder disease. Additionally, preventative measures should be expanded to include recreational water sports.

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.

Survey of rodent-borne pathogens in Singapore reveals the circulation of Leptospira spp., Seoul hantavirus, and Rickettsia typhi

Rodents living alongside humans increases the probability of encounter and also the transmission of rodent-borne diseases. Singapore’s cosmopolitan urban landscape provides a perfect setting to study the prevalence of four rodent-borne pathogens: Seoul hantavirus (SEOV), Leptospira species, Rickettsia typhi and Yersinia pestis, and identify the potential risk factors which may influence rodent density and transmission of rodent-borne diseases. A total of 1143 rodents were trapped from 10 unique landscape structures throughout Singapore. Real-time quantitative Polymerase Chain Reactions were used to detect pathogenic and intermediate Leptospira spp. and Yersinia pestis, whereas the seroprevalence of SEOV and R. typhi were analysed by Enzyme-Linked Immunosorbent Assay and Immunofluorescence Assay respectively. Multivariable logistic regression analysis was used to evaluate the association between prevalence of infection in rodent reservoirs and risk factors. Most of the rodents were caught in public residential developments (62.2%). Among the tested rodents, 42.4% were infected with Leptospira spp., while 35.5% and 32.2% were seropositive for SEOV and R. typhi respectively, whereas Yersinia pestis was not detected. Furthermore, risk factors including habitat, species, gender, and weight of rodents, influenced prevalence of infection to a varying extent. This study highlights the presence of Leptospira spp., SEOV and R. typhi in Singapore’s rodent population, suggesting the need for effective rodent management and sanitation strategies to prevent further circulation and transmission to humans.

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.

Bovine Abortions Revisited-Enhancing Abortion Diagnostics by 16S rDNA Amplicon Sequencing and Fluorescence in situ Hybridization

Abortion in cattle causes significant economic losses for cattle farmers worldwide. The diversity of abortifacients makes abortion diagnostics a complex and challenging discipline that additionally is restrained by time and economy. Microbial culture has traditionally been an important method for the identification of bacterial and mycotic abortifacients. However, it comes with the inherent bias of favoring the easy-to-culture species, e.g., those that do not require cell culture, pre-enrichment, a variety of selective growth media, or different oxygen levels for in vitro growth. Molecular methods such as polymerase chain reaction (PCR) and next-generation sequencing have been established as alternatives to traditional microbial culturing methods in several diagnostic fields including abortion diagnostics. Fluorescence in situ hybridization (FISH), a bridging microscopy technique that combines molecular accuracy with culture independence, and spatial resolution of the pathogen-lesion relation, is also gaining influence in several diagnostic fields. In this study, real-time quantitative PCR (qPCR), 16S rDNA amplicon sequencing, and FISH were applied separately and in combination in order to (i) identify potentially abortifacient bacteria without the bias of culturability, (ii) increase the diagnostic rate using combined molecular methods, (iii) investigate the presence of the difficult-to-culture zoonotic agents Coxiella burnetii, Chlamydia spp., and Leptospira spp. in bovine abortions in Denmark. Tissues from 162 aborted or stillborn bovine fetuses and placentas submitted for routine diagnostics were screened for pathogenic bacteria using 16S rDNA amplicon sequencing. Lesion association of fungal elements, as well as of selection of bacterial abortifacients, was assessed using specific FISH assays. The presence of Chlamydia spp. and chlamydia-like organisms was assessed using qPCR. The study focused on bacterial and fungal abortifacients, because Danish cattle is free from most viral abortifacients. The 16S rDNA amplicon sequencing-guided FISH approach was suitable for enhancing abortion diagnostics, i.e., the diagnostic rate for cases with tissue lesions (n = 115) was increased from 46 to 53% when compared to routine diagnostic methods. Identification of Bacillus licheniformis, Escherichia coli, and Trueperella pyogenes accounted for the majority of additional cases with an established etiology. No evidence for emerging or epizootic bacterial pathogens was found. The difficult-to-culture abortifacients were either not detected or not identified as abortifacients.

Evaluation of TaqMan based real-time PCR assay targeting LipL32 gene for leptospirosis in serologically positive human urine samples from north India

PURPOSE

Rapid diagnosis of leptospirosis, through culture and/or serology, can be difficult without proper expertise and is often delayed because of the length of time required to obtain results. In India, especially in north India; leptospirosis is a grossly underreported disease, probably due to the lack of diagnostic modalities and lack of awareness of the disease among physicians. In this study, we aimed to identify leptospires in urine samples from serologically positive patients of leptospirosis through TaqMan based Real-time PCR using the LipL32 gene. Although environmental conditions are suitable in north India nowadays, very few studies were there and none by real-time PCR.

METHOD

A total of 50 urine and blood samples (40 seropositive and 10 seronegative by IgM ELISA) were recruited in the study. Urine samples were tested by real-time PCR to detect Leptospira DNA and blood samples were used for microscopic agglutination test (MAT) evaluation.

RESULT

We were able to detect leptospires in 20% (10/50) cases using our real-time PCR assay. In all 10 PCR positive urine samples, the LipL32 gene was detected and the lower limit of detection in L. interrogans DNA was found to be 20 GE/μL with a 95% cutoff value.

CONCLUSION

We conclude that this real-time PCR assay with high specificity and sensitivity less prone to contamination may prove to be a promising approach for diagnosing acute leptospires in urine samples in the second week of acute febrile illness due to leptospiruria starts approximately in the second week of illness.

Molecular Detection of Microorganisms Associated with Small Mammals and Their Ectoparasites in Mali

Small mammals are the natural reservoirs for many zoonotic pathogens. Using molecular tools, we assessed the prevalence of bacteria and protozoans in small mammals and their ectoparasites in Faladjè, Bougouni, and Bamoko, Mali. A total of 130 small mammals belonging to 10 different species were captured, of which 74 (56.9%) were infested by ectoparasites, including Laelaps echidnina, Xenopsylla cheopis, Amblyomma variegatum, Rhipicephalus sanguineus sensu lato, and Haemaphysalis spp. nymphs. DNA of Bartonella was found in 14/75 (18.7%), 6/48 (12.5%), and 3/7 (42.8%) small mammals from Faladjè, Bougouni, and Bamako, respectively. In Faladjè, Bartonella DNA was detected in 31/68 (45.6%) of L. echidnina and 14/22 (63.6%) of X. cheopis. In Bougouni, it was found in 2/26 (7.7%) of L. echidnina and 10/42 (23.8%) of X. cheopis. The sequences of Bartonella obtained from small mammals were close to those of Bartonella mastomydis, Bartonella elizabethae, and uncultured Bartonella spp. In Faladjè, Coxiella burnetii DNA was detected in 64.4% (29/45) of Haemaphysalis spp. ticks, 4.5% (2/44) of Mastomys erythroleucus, 12.5% (1/8) of Praomys daltoni, and 1.5% (1/68) of L. echidnina. We found DNA of Wolbachia in X. cheopis from Faladjè and DNA of Rickettsia africae and Ehrlichia ruminantium in Am. variegatum from Bougouni. The results of our study show that several small mammal species harbor and may serve as potential reservoirs of Bartonella spp., likely to play a major role in the maintenance, circulation, and potential transmission of bacteria in Mali. The pathogenicity of these bacteria for humans or animals remains to be demonstrated.

Seven Years Leptospirosis Follow-Up in a Critical Care Unit of a French Metropolitan Hospital; Role of Real Time PCR for a Quick and Acute Diagnosis

(1) Background: Leptospirosis infection can lead to multiple organ failure, requiring hospitalization in an intensive care unit for supportive care, along with initiation of an adapted antibiotic therapy. Achieving a quick diagnosis is decisive in the management of these patients. (2) Methods: We present here a review of leptospirosis cases diagnosed in the intensive care unit of our hospital over seven years. Clinical and biological data were gathered, and we compared the differences in terms of diagnostic method. (3) Results: Molecular biology method by Polymerase Chain Reaction (PCR) allowed quick and reliable diagnosis when performed in the first days after the symptoms began. Moreover, we identified that sampling blood and urine for PCR was more efficient than performing PCR on only one type of biological sample. (4) Conclusions: Our results confirm the efficiency of PCR for the quick diagnosis of leptospirosis and suggest that testing both blood and urine early in the disease might improve diagnosis.

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.

A Validated Multiplex Real-Time PCR Assay for the Diagnosis of Infectious Leptospira spp.: A Novel Assay for the Detection and Differentiation of Strains From Both Pathogenic Groups I and II

Leptospirosis is recognized as the most globally widespread reemerging zoonosis and represents a serious threat for both human and animal health. Indeed, leptospirosis is linked to more than 60,000 human deaths per year and to incalculable economic burden as consequence of medical treatment costs and livestock loss. The increasing number of reports from species of pathogenic Leptospira spp. group II causing disease in both humans and animals constitutes an additional concern to the complex epidemiology of this zoonotic agent. Diagnostic methods based on qPCR have improved the diagnosis of Leptospira spp. in terms of cost, time, and reliability, but most of the validated assays fail to detect species from the pathogenic group II. Hence, the current study was aimed to develop and validate a novel multiplex qPCR to enable the specific and selective detection of the whole group of infectious Leptospira spp., including both pathogenic groups I and II and moreover, selectively discriminate between them. To fit the "fitness of purpose" for the specific detection of infectious Leptospira spp. and further discrimination between both pathogenic groups three target regions on the 16S RNA gene were selected. These targets facilitated a broad and selective spectrum for the detection of all infectious Leptospira spp. with the exclusion of all saprophytic groups and the novel clade of environmental Leptospira spp. The analytical sensitivity (ASe) showed by the new assay also enables a wide window of detection for the agent at different stages of infection since the assay was able to efficiently detect at 95% of confidence ∼5 leptospires/reaction. From the evaluation of the analytical specificity (ASp) by in silico and in vitro approaches, it was congruently revealed that the primers and probes selected only recognized the specific targets for which the assay was intended. Bayesian latent class analysis of performance of the new assay on 684 clinical samples showed values of diagnostic sensitivity of 99.8% and diagnostic specificity of 100%. Thus, from the evaluation of the analytical and diagnostic parameters, the new multiplex qPCR assay is a reliable method for the diagnosis of Leptospira spp.

Evaluation of real-time PCR targeting the lipL32 gene for diagnosis of Leptospira infection

BACKGROUND

Different diagnostic methods have been used for the laboratory confirmation of leptospirosis. Molecular diagnostic techniques are not only faster and more sensitive than culture analysis, but can also detect a Leptospira infection before the appearance of antibodies. The aim of the present study was to analyze and compare two different PCR approaches applied to blood and urine specimens obtained from patients with clinical manifestations that were suggestive of leptospirosis. Furthermore, the results of these different PCR approaches were compared with the results of culture and serology analyses.

RESULTS

A total of 400 samples (234 blood or 58.5% and 166 urine of 41.5%) from 310 Slovenian patients with clinical manifestations suggestive of leptospirosis were tested using conventional PCR assays targeting the rrs gene and RT-PCR targeting the lipL32 gene. Additionally, culture, serology and sequence analysis were performed for the majority of these samples. The PCR and RT-PCR results were concordant in 376 out of 400 of these samples (94.0%). Conventional PCR was positive for 27 out of 400 samples (6.8%) and RT-PCR was positive for 47 out of 400 samples (11.8%). Culture and microscopic agglutination tests supported these diagnoses.

CONCLUSIONS

A comparison of the two PCR methods indicated that the RT-PCR targeting of the lipL32 gene was faster, more sensitive and more specific for the determination of Leptospira DNA in these clinical samples.

Leptospirosis in an asplenic patient -case report

Background

The presentation of clinical leptospirosis has been historically associated with animal workers, slaughterhouse workers and medical veterinarians. This association has shifted to be related to flooding events and outdoor activities; few cases are related to high-risk factors found in immunosuppressed patients. Scarcely a handful of cases have serological evidence of immune response against Leptospira serovar Bratislava representing serogroup Australis, a serovar associated with poor reproductive performance in swine and horses, and recently with cats.

Case presentation

Herein, we describe a rare clinical presentation of disseminated Leptospira infection in an immunosuppressed 65-year-old woman. She was admitted to the emergency room with fever, bacteraemia, bilateral uveitis and pulmonary involvement. The patient denied outdoor activities; she only had wide exposure to faeces and urine from cats living in her home. Her medical history included idiopathic thrombocytopenic purpura (ITP) diagnosed at the age of 18. She did not respond to medical treatment, and a splenectomy was performed. At age 60, she was diagnosed with Chronic Myeloid Leukemia (CML), and was treated with a tyrosine kinase inhibitor (TKI) –Imatinib. The patient voluntarily discontinued the treatment for the last 6 months. After extensive workup, no microorganisms were identified by the commonly used stains in microbiology. The diagnosis was performed through dark-field microscopy, microagglutination test (MAT), Leptospira genus-specific PCR, the IS1500 PCR for identification of pathogenic species, and 16S based sequencing for the genus identification.

Conclusion

Immunosuppressed patients may acquire uncommon infections from ubiquitous microorganisms. In this case, serology evidence of exposure to Leptospira serovar Bratislava by MAT and the presence of the Leptospira genus were identified. It should be on mind for the diagnosis in otherwise healthy patients, and thoroughly search on splenectomised patients exposed to animals. Additionally, this report highlights the usefulness of PCR for diagnosis of this potentially life-threatening illness.

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.

Leptospirosis manifested with severe pulmonary haemorrhagic syndrome successfully treated with venovenous extracorporeal membrane oxygenation

Leptospirosis, one of the most important of neglected tropical diseases, is a common zoonosis in the tropics. Recent reports have demonstrated that pulmonary haemorrhage is one of the fatal complications of severe leptospirosis. In this report, we present a case of leptospirosis manifested with severe pulmonary haemorrhagic syndrome successfully treated with venovenous extracorporeal membrane oxygenation (VV-ECMO). A 39-year-old man who lives in Bangkok presented with fever, severe myalgia and haemoptysis. With rapid progression of acute respiratory failure in 6 hours, he was intubated and a litre of fresh blood was suctioned. Chest x-ray showed diffuse alveolar infiltrates compatible with ARDS, then mechanical ventilator with lung protective strategy was used. Diagnosis of leptospirosis with diffuse alveolar haemorrhage was made. Refractory hypoxaemia was not responsive to positive end-expiratory pressure (PEEP); thus, VV-ECMO was initiated on the first day. Other treatments included plasmapheresis, intravenous pulse methylprednisolone and intravenous antibiotics. The outcome of treatment was successful, and this patient was discharged to home on day 14 after admission.

Investigation and response to an outbreak of leptospirosis among raspberry workers in Australia, 2018

BACKGROUND

In 2018, an outbreak of leptospirosis was identified among raspberry workers from a mixed-berry farm in New South Wales, Australia. Initial testing had not revealed a cause, but eventually leptospirosis was detected via polymerase chain reaction (PCR). Further serological testing detected Leptospira borgpetersenii serovar Arborea, of which rodents are the predominant reservoir. Leptospirosis is rare in Australia, with outbreaks usually related to flooding. We conducted an investigation to identify risk factors for infection, to inform control measures.

METHODS

Cases were detected through laboratory notifications, hospital-based syndromic surveillance, awareness-raising among farm employees and clinician alerts. Confirmed cases had a four-fold rise in antibody titre or single titre ≥400 on microscopic agglutination test, and a positive IgM. Probable cases had a positive Leptospira PCR or IgM, and possible cases had a clinically compatible illness. We conducted a case-control study among raspberry workers on the farm and compared reported exposures between cases and seronegative controls. We assessed environmental risks on-site and tested rodents for leptospirosis.

RESULTS

We identified 84 cases over a 5-month period (50 confirmed, 19 probable and 15 possible). Compared with controls, cases were less likely to wear gloves and more recently employed. Cases also more commonly reported always having scratched hands, likely from the thorns on raspberry plants. We observed evidence of rodent activity around raspberry plants and three of thirteen trapped mice tested positive for Leptospira Arborea. Control measures included enhanced glove use, doxycycline prophylaxis and rodent control.

CONCLUSIONS

This is the largest known outbreak of leptospirosis in Australia. Workers were likely exposed through scratches inflicted during harvesting, which became contaminated with environmental leptospires from mice. Leptospirosis should be considered an occupational risk for raspberry workers, requiring protective measures. Chemoprophylaxis may assist in controlling outbreaks. PCR assists in the early diagnosis and detection of leptospirosis and should be included in surveillance case definitions.

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.

Duplex TaqMan Hydrolysis Probe-Based Molecular Assay for Simultaneous Detection and Differentiation of Burkholderia pseudomallei and Leptospira spp. DNA

Melioidosis and leptospirosis, caused by two different bacteria, Burkholderia pseudomallei and Leptospira spp., are potentially fatal infections that share a very similar spectrum of clinical features and cause significant mortality and morbidity in humans and livestock. Early detection is important for better clinical consequences. To our knowledge, there is no diagnostic tool available to simultaneously detect and differentiate melioidosis and leptospirosis in humans and animals. In this study, we described a duplex TaqMan probe-based qPCR for the detection of B. pseudomallei and Leptospira spp. DNA. The performance of the assay was evaluated on 20 B. pseudomallei isolates, 23 Leptospira strains, and 39 other microorganisms, as well as two sets of serially diluted reference strains. The duplex qPCR assay was able to detect 0.02 pg (~ 4 copies) Leptospira spp. DNA and 0.2 pg (~ 25.6 copies) B. pseudomallei DNA. No undesired amplification was observed in other microorganisms. In conclusion, the duplex qPCR assay was sensitive and specific for the detection of B. pseudomallei & Leptospira spp. DNA and is suitable for further analytical and clinical evaluation.

Bovine leptospirosis in abattoirs in Uganda: Molecular detection and risk of exposure among workers

Leptospirosis is a zoonotic bacterial disease reported worldwide. In Uganda, seropositivity has been reported in both humans and domesticated animals, including cattle. However, it remains unknown whether cattle are shedding leptospires and thus acting as potential source for human leptospirosis. We conducted this cross-sectional study in two cattle abattoirs in Kampala, Uganda between June and July 2017. Kidney and urine samples from 500 cattle sourced from across the country were analysed by real-time PCR to establish the prevalence of Leptospira-positive cattle and risk of exposure to abattoir workers. The species of infecting Leptospira was determined by amplification of secY gene and compared to reference sequences published in GenBank. Of 500 cattle tested, 36 (7.2%) had Leptospira DNA in their kidneys (carriers), 29 (5.8%) in their urine (shedders); with an overall prevalence (kidney and/or urine) of 8.8%. Leptospira borgpetersenii was confirmed as the infecting species in three cattle and Leptospira kirschneri in one animal. Male versus female cattle (OR = 3, p-value 0.003), exotic versus local breeds (OR = 21.3, p-value 0.002) or cattle from Western Uganda (OR = 4.4, p-value 0.001) and from regions across the border (OR = 3.3, p-value 0.032) versus from the central region were more likely to be Leptospira-positive. The daily risk of exposure of abattoir workers to ≥1 (kidney and/or urine) positive carcass ranged from 27% (95% credibility interval 18.6-52.3) to 100% (95% CI 91.0-100.0), with halal butchers and pluck inspectors being at highest risk. In conclusion, cattle slaughtered at abattoirs in Uganda carry and shed pathogenic Leptospira species; and this may pose occupation-related risk of exposure among workers in these abattoirs, with workers who handle larger numbers of animals being at higher risk.

Diagnosis of Human Leptospirosis in a Clinical Setting: Real-Time PCR High Resolution Melting Analysis for Detection of Leptospira at the Onset of Disease

Currently, direct detection of Leptospira can be done in clinical laboratories by conventional and by real-time PCR (qRT-PCR). We tested a biobank of paired samples of serum and urine from the same patient (202 patients) presenting at the hospital in an area endemic for leptospirosis using qRT-PCR followed by high resolution melting (HRM) analysis. The results were compared with those obtained by conventional nested PCR and with the serologic gold standard microscopic agglutination test (MAT). Differences were resolved by sequencing. qRT-PCR-HRM was positive for 46 of the 202 patients (22.7%, accuracy 100%) which is consistent with known prevalence of leptospirosis in the Azores. MAT results were positive for 3 of the 46 patients (6.5%). Analysis of paired samples allowed us to identify the illness point at which patients presented at the hospital: onset, dissemination or excretion. The melting curve analysis of Leptospira species revealed that 60.9% (28/46) of patients were infected with L. interrogans and 39.1% (18/46) were infected with L. borgpetersenii, both endemic to the Azores. We validated the use of qRT-PCR-HRM for diagnosis of leptospirosis and for identification of the Leptospira species at the earliest onset of infection in a clinical setting, in less than 2 hours.

Urinary shedding of pathogenic Leptospira in stray dogs and cats, Algiers: A prospective study

Background

Leptospirosis is an important worldwide zoonosis. This disease is caused by pathogenic species of the genus Leptospira which are maintained in the environment via chronic renal infection of carrier animals which can be asymptomatic excretors of the organisms in their urines and become a source of infection for humans and other hosts. The prevalence of animal leptospirosis in Algiers, Algeria, is unknown.

Methodology/principal findings

Real-time PCR and standard PCR and sequencing were used to detect pathogenic Leptospira organisms in the urines of stray dogs and cats in Algiers. In the presence of appropriate controls, none of the 107 cat urine samples were positive while 5/104 (4.8%) canine urine samples (asymptomatic mixed-breed dogs, three females and two males) were positive in two real-time PCR assays targeting the rrs and hsp genes. The positivity of these samples was confirmed by partial PCR-sequencing of the rpoB gene which yielded 100% sequence similarity with Leptospira interrogans reference sequence. In this study, L. interrogans prevalence was significantly higher in dogs aged < one year (16.46% - 29.41%) than in adults (0%) (P value = 0.0001) and then in the overall dog population (2.68% - 4.8%) (P = 0.0007).

Conclusions/significance

These results suggest that dogs are maintenance hosts for zoonotic leptospirosis in Algiers, Algeria. To face this situation, effective canine vaccination strategies and raising public health awareness are mandatory. Further investigations incorporating a larger sample in more localities will be undertaken to document the epidemiology of urban animal leptospirosis in Algeria at large.

Development and validation of a modified TaqMan based real-time PCR assay targeting the lipl32 gene for detection of pathogenic Leptospira in canine urine samples

A modified TaqMan real-time polymerase chain reaction targeting a 138bp fragment within the lipl32 gene was developed to identify exclusively pathogenic Leptospira spp. in dog urine samples. Thirty-five samples from dogs with suspected clinical leptospirosis and 116 samples from apparently healthy dogs were tested for presence of leptospiral DNA using the TaqMan-based assay. The results were compared with those from a well-established conventional PCR targeting the 16S RNA encoding gene associated with nucleotide sequencing analysis. The overall agreement between the assays was 94.8% (confidence interval [CI] 95% 88-100%). The newly developed assay presented 91.6% (CI 95% 71.5-98.5%) relative sensitivity (22[+] lipl32 PCR/24[+] 16S RNA and sequencing), 100% (CI 95% 96.3-100%) relative specificity and 98.7% accuracy (CI 95% 94.8-100%). The lipl32 assay was able to detect and quantify at least 10 genome equivalents/reaction. DNA extracted from 17 pathogenic Leptospira spp., 8 intermediate/saprophytic strains and 21 different pathogenic microorganisms were also tested using the lipl32 assay, resulting in amplification exclusively for pathogenic leptospiral strains. The results also demonstrated high intra and inter-assay reproducibility (coefficient of variation 1.50 and 1.12, respectively), thereby qualifying the newly developed assay as a highly sensitive, specific and reliable diagnostic tool for leptospiral infection in dogs using urine specimens.

Neglected zoonotic agents in cattle abortion: tackling the difficult to grow bacteria

BACKGROUND

Coxiella burnetii, Chlamydia abortus and Leptospira spp. are difficult to grow bacteria that play a role in bovine abortion, but their diagnosis is hampered by their obligate intracellular lifestyle (C. burnetii, C. abortus) or their lability (Leptospira spp.). Their importance is based on the contagious spread in food-producing animals, but also as zoonotic agents. In Switzerland, first-line routine bacteriological diagnostics in cattle abortions is regulated by national law and includes only basic screening by staining for C. burnetii due to the high costs associated with extended spectrum analysis. The aim of this study was to assess the true occurrence of these zoonotic pathogens in 249 cases of bovine abortion in Switzerland by serology (ELISA for anti-C. burnetii and C. abortus antibodies and microscopic agglutination test for anti-Leptospira spp. antibodies), molecular methods (real-time PCR and sequencing of PCR products of Chlamydiales-positive cases), Stamp's modification of the Ziehl-Neelsen (mod-ZN) stain and, upon availability of material, by histology and immunohistochemistry (IHC).

RESULTS

After seroanalysis the prevalence was 15.9% for C. burnetii, 38.5% for C. abortus and 21.4% for Leptospira spp. By real-time PCR 12.1% and 16.9% of the cases were positive for C. burnetii and Chlamydiales, respectively, but only 2.4% were positive for C. burnetii or Chlamydiales by mod-ZN stain. Sequencing of PCR products of Chlamydiales-positive cases revealed C. abortus in 10% of cases and the presence of a mix of Chlamydiales-related bacteria in 5.2% of cases. Pathogenic Leptospira spp. were detected in 5.6% of cases. Inflammatory lesions were present histologically in all available samples which were real-time PCR-positive for Chlamydiales and Leptospira spp. One of 12 real-time PCR-positive cases for C. burnetii was devoid of histological lesions. None of the pathogens could be detected by IHC.

CONCLUSION

Molecular detection by real-time PCR complemented by histopathological analysis is recommended to improve definitive diagnosis of bovine abortion cases and determine a more accurate prevalence of these zoonotic pathogens.

Use of Multiplex Real-Time PCR To Diagnose Scrub Typhus

Scrub typhus, caused by Orientia tsutsugamushi, is a common cause of acute undifferentiated febrile illness in the Asia-Pacific region. However, its nonspecific clinical manifestation often prevents early diagnosis. We propose the use of PCR and serologic tests as diagnostic tools. Here, we developed a multiplex real-time PCR assay using hydrolysis (TaqMan) probes targeting O. tsutsugamushi 47-kDa, groEL, and human interferon beta (IFN-β gene) genes to improve early diagnosis of scrub typhus. The amplification efficiency was higher than 94%, and the lower detection limit was 10 copies per reaction. We used a human gene as an internal DNA quality and quantity control. To determine the sensitivity of this PCR assay, we selected patients with confirmed scrub typhus who exhibited a clear 4-fold increase in the level of IgG and/or IgM. The PCR assay result was positive in 45 of 52 patients, indicating a sensitivity of 86.5% (95% confidence interval [CI]: 74.2 to 94.4). The PCR assessment was negative for all 136 non-scrub typhus patients, indicating a specificity of 100% (95% CI: 97.3 to 100). In addition, this test helped diagnose patients with inconclusive immunofluorescence assay (IFA) results and using single blood samples. In conclusion, the real-time PCR assay proposed here is sensitive and specific in diagnosing scrub typhus. Combining PCR and serologic tests will improve the diagnosis of scrub typhus among patients presenting with acute febrile illness.

Meta-analysis to estimate the load of Leptospira excreted in urine: beyond rats as important sources of transmission in low-income rural communities

BACKGROUND

Leptospirosis is a major zoonotic disease with widespread distribution and a large impact on human health. Carrier animals excrete pathogenic Leptospira primarily in their urine. Infection occurs when the pathogen enters a host through mucosa or small skin abrasions. Humans and other animals are exposed to the pathogen by direct contact with urine, contaminated soil or water. While many factors influence environmental cycling and the transmission of Leptospira to humans, the load of pathogenic Leptospira in the environment is likely to play a major role. Peridomestic rats are often implicated as a potential source of human disease; however exposure to other animals is a risk factor as well. The aim of this report is to highlight the importance of various carrier animals in terms of the quantity of Leptospira shed into the environment. For this, we performed a systematic literature review and a meta-analysis of the amount of pathogen that various animal species shed in their urine.

RESULTS

The quantity of pathogen has been reported for cows, deer, dogs, humans, mice, and rats, in a total of 14 research articles. We estimated the average Leptospira per unit volume shed by each animal species, and the daily environmental contribution by considering the total volume of urine excreted by each carrier animal. Rats excrete the highest quantity of Leptospira per millilitre of urine (median = 5.7 × 10⁶ cells), but large mammals excrete much more urine and thus shed significantly more Leptospira per day (5.1 × 10⁸ to 1.3 × 10⁹ cells).

CONCLUSIONS

Here we illustrate how, in a low-income rural Ecuadorian community, host population demographics, and prevalence of Leptospira infection can be integrated with estimates of shed Leptospira to suggest that peridomestic cattle may be more important than rats in environmental cycling and ultimately, transmission to humans.

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.

An Extended Multilocus Sequence Typing (MLST) Scheme for Rapid Direct Typing of Leptospira from Clinical Samples

Background

Rapid typing of Leptospira is currently impaired by requiring time consuming culture of leptospires. The objective of this study was to develop an assay that provides multilocus sequence typing (MLST) data direct from patient specimens while minimising costs for subsequent sequencing.

Methodology and Findings

An existing PCR based MLST scheme was modified by designing nested primers including anchors for facilitated subsequent sequencing. The assay was applied to various specimen types from patients diagnosed with leptospirosis between 2014 and 2015 in the United Kingdom (UK) and the Lao Peoples Democratic Republic (Lao PDR). Of 44 clinical samples (23 serum, 6 whole blood, 3 buffy coat, 12 urine) PCR positive for pathogenic Leptospira spp. at least one allele was amplified in 22 samples (50%) and used for phylogenetic inference. Full allelic profiles were obtained from ten specimens, representing all sample types (23%). No nonspecific amplicons were observed in any of the samples. Of twelve PCR positive urine specimens three gave full allelic profiles (25%) and two a partial profile. Phylogenetic analysis allowed for species assignment. The predominant species detected was L. interrogans (10/14 and 7/8 from UK and Lao PDR, respectively). All other species were detected in samples from only one country (Lao PDR: L. borgpetersenii [1/8]; UK: L. kirschneri [1/14], L. santarosai [1/14], L. weilii [2/14]).

Conclusion

Typing information of pathogenic Leptospira spp. was obtained directly from a variety of clinical samples using a modified MLST assay. This assay negates the need for time-consuming culture of Leptospira prior to typing and will be of use both in surveillance, as single alleles enable species determination, and outbreaks for the rapid identification of clusters.

Leptospirosis is a zoonotic disease with more than 1 million cases per year globally and epidemics are increasingly reported. In this setting rapid typing is essential to identify potential clusters and transmission pathways. Typing of bacteria commonly requires bacterial isolates but culturing Leptospira is difficult and time consuming and requires invasive samples, such as blood or cerebrospinal fluid. We modified an existing typing scheme to lower the limit of detection and were able to amplify and sequence alleles directly from clinical specimens. Samples included blood (whole blood, serum, or buffy coat) and urine from patients diagnosed by PCR with leptospirosis between 2014 and 2015 in the United Kingdom and the Lao Peoples Democratic Republic. Using the sequences in phylogenetic analysis we identified the predominant Leptospira species in both countries as L. interrogans. With its increased sensitivity the modified assay allows for typing and species determination of Leptospira directly from blood or urine. It will be of use during epidemics and outbreaks for rapid identification of clusters and can support surveillance without the need to culture fastidious isolates.

The Utility of Blood Culture Fluid for the Molecular Diagnosis of Leptospira: A Prospective Evaluation

Leptospirosis is an important zoonosis worldwide, with infections occurring after exposure to contaminated water. Despite being a global problem, laboratory diagnosis remains difficult with culture results taking up to 3 months, serology being retrospective by nature, and polymerase chain reaction showing limited sensitivity. Leptospira have been shown to survive and multiply in blood culture media, and we hypothesized that extracting DNA from incubated blood culture fluid (BCF), followed by quantitative real-time polymerase chain reaction (qPCR) could improve the accuracy and speed of leptospira diagnosis. We assessed this retrospectively, using preincubated BCF of Leptospira spp. positive (N= 109) and negative (N= 63) febrile patients in Vientiane, Lao PDR. The final method showed promising sensitivities of 66% (95% confidence interval [CI]: 55-76) and 59% (95% CI: 49-68) compared with direct or direct and indirect testing combined, as the respective reference standards (specificities > 95%). Despite these promising diagnostic parameters, a subsequent prospective evaluation in a Lao hospital population (N= 352) showed that the sensitivity was very low (∼30%) compared with qPCR on venous blood samples. The disappointingly low sensitivity does suggest that venous blood samples are preferable for the clinical microbiology laboratory, although BCF might be an alternative if leptospirosis is only suspected postadmission after antibiotics have been used.

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.

A comparison of two real-time polymerase chain reaction assays using hybridization probes targeting either 16S ribosomal RNA or a subsurface lipoprotein gene for detecting leptospires in canine urine

Leptospires are excreted in the urine of infected animals, and the prompt detection of leptospiral DNA using polymerase chain reaction (PCR) is increasingly being used. However, contradictory data has emerged concerning the diagnostic accuracy of the most popular PCR assays that target either the 16S ribosomal RNA ( rrs) or the subsurface lipoprotein ( LipL32) genes. In order to clarify the effect of the gene target, a novel hydrolysis probe–based, quantitative real-time PCR (qPCR) assay targeting the LipL32 gene was developed, validated, and then compared directly to the previously described rrs hydrolysis probe–based qPCR using a convenience collection of canine urine samples. The novel LipL32 qPCR assay was linear from 5.9 × 106 to 59 genome equivalents per reaction. Both the LipL32 and the rrs qPCR assays showed a limit of detection of 10 target copies per reaction indicating an approximately equivalent analytical sensitivity. Both assays amplified all 20 pathogenic leptospiral strains tested but did not amplify a representative collection of bacteria commonly found in voided canine urine. When the field samples were assayed, 1 and 5 out of 184 samples yielded an amplification signal in the LipL32 and rrs assays, respectively. Nevertheless, when the limit of detection was considered as the cutoff for interpreting findings, the 4 discordant cases were judged as negative. In conclusion, our study confirmed that both LipL32 and rrs are suitable targets for qPCR for the detection of leptospiral DNA in canine urine. However, the rrs target requires the mandatory use of a cutoff value in order to correctly interpret spurious amplifications.

Direct detection and differentiation of pathogenic Leptospira species using a multi-gene targeted real time PCR approach

Leptospirosis is a growing public and veterinary health concern caused by pathogenic species of Leptospira. Rapid and reliable laboratory tests for the direct detection of leptospiral infections in animals are in high demand not only to improve diagnosis but also for understanding the epidemiology of the disease. In this work we describe a novel and simple TaqMan-based multi-gene targeted real-time PCR approach able to detect and differentiate Leptospira interrogans, L. kirschneri, L. borgpeteresenii and L. noguchii, which constitute the veterinary most relevant pathogenic species of Leptospira. The method uses sets of species-specific probes, and respective flanking primers, designed from ompL1 and secY gene sequences. To monitor the presence of inhibitors, a duplex amplification assay targeting both the mammal β-actin and the leptospiral lipL32 genes was implemented. The analytical sensitivity of all primer and probe sets was estimated to be <10 genome equivalents (GE) in the reaction mixture. Application of the amplification reactions on genomic DNA from a variety of pathogenic and non-pathogenic Leptospira strains and other non-related bacteria revealed a 100% analytical specificity. Additionally, pathogenic leptospires were successfully detected in five out of 29 tissue samples from animals (Mus spp., Rattus spp., Dolichotis patagonum and Sus domesticus). Two samples were infected with L. borgpetersenii, two with L. interrogans and one with L. kirschneri. The possibility to detect and identify these pathogenic agents to the species level in domestic and wildlife animals reinforces the diagnostic information and will enhance our understanding of the epidemiology of leptopirosis.

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.

Leptospirosis: current situation and trends of specific laboratory tests

Leptospirosis is re-emerging as a worldwide zoonosis and is caused by bacteria of the genus Leptospira. Human leptospirosis is associated with high temperature and humidity. Laboratory tests are indispensible for the early diagnosis and proper disease management. The demand for suitable leptospirosis point-of-care diagnostic tests grows with the awareness and number of incidences. Confirmation is achieved by the microscopic agglutination test, bacterial cultivation, PCR or histopathologic methods. However, high costs, poor standardization and/or elaborate sample preparation prevent routine use at the point of care. Cost-efficient, but insensitive serological methods dominate the diagnostic landscape and, likewise, urgently need improvement toward greater compliance with some of the point-of-care criteria. Combined application of antigen and antibody detection methods increases accuracy, but also new development or transfer of diagnostic technologies should be considered useful. Nano- and microparticle technology may play a key role in improving future antigen detection methods.

Leptospirosis-persistence of a dilemma: an overview with particular emphasis on trends and recent advances in vaccines and vaccination strategies

Leptospirosis, caused by pathogenic spirochetes of the genus Leptospira, affects both humans and animals and is among the most common but neglected direct zoonotic disease in the world, particularly in untreated or undiagnosed animals as well as humans. Now, it has been considered as a re-emerging disease causing global health problem due to its increasing incidences in developing as well as developed nations. It is a multisystemic disease leading to death. Diagnostic tests of importance are Latex Agglutination Test (LAT), lateral flow and immunoglobulin M (IgM) based ELISA, PCR based assays, Multiple-microscopic Agglutination Test (MAT), Loop-mediated Isothermal Amplification (LAMP) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Molecular tools like PCR-RFLP, real-time PCR, multiplex PCR, qPCR and immunocapture PCR have all been found useful for rapid and confirmatory detection and differentiation of pathogenic and non-pathogenic leptospires. Inactivated/killed and attenuated vaccines are always attempted, since the beginning of vaccine and vaccination story, against all emerging pathogens with mixed success stories. The advanced tools and techniques like recombinant DNA technology, reverse genetics, DNA vaccination, molecular genetics and proteomics approaches are being explored for search of novel antigens, proteins and genes as potential candidates to discover safer, efficient and better vaccines for leptospirosis. The present review highlights the leptospirosis, susceptible population, disease transmission and epidemiology, treatment, trends and advances in diagnosis, vaccines and vaccination strategies in humans and animals with a view to combat this organism having public health significance.