Rapid Leptospira identification by direct sequencing of the diagnostic PCR products in New Caledonia

Leptospira borgptersenii and Leptospira interrogans identified in wild mammals in Rio Grande do Sul, Brazil

Leptospira spp. are bacteria responsible for leptospirosis, a zoonotic disease with considerable impacts on the economy, animal health, and public health. This disease has a global distribution and is particularly prevalent in Brazil. Both rural and urban environments are habitats for Leptospira spp., which are primarily transmitted through contact with the urine of infected animals. Consequently, domestic and wild species can harbor these prokaryotes and serve as infection sources for other hosts. In the context of wild animals, there is a dearth of molecular studies elucidating the roles of various animal and bacterial species in the epidemiology of leptospirosis. Therefore, this study aimed to evaluate the presence of Leptospira spp. DNA in different species of free-living and captive wild animals and to assess the phylogenetic relationships of the identified microorganisms in Rio Grande do Sul, Brazil. The samples were evaluated for the presence of the gene lipL32 by polymerase chain reaction (PCR) and sequencing of the amplified fragment after which phylogenetic analyzes were carried out. DNA from Leptospira spp. was extracted from kidney tissue from wild animals (Mammalia class). Pathogenic Leptospira spp. DNA was detected in 9.6% (11/114) of the samples, originating from nine species of wild animals, including the white-eared opossum (Didelphis albiventris), skunk (Conepatus chinga), geoffroy's cat (Leopardus geoffroyi), margay (Leopardus wiedii), pampas fox (Lycalopex gymnocercus), capybara (Hydrochoerus hydrochaeris), common marmoset (Callithrix jacchus), neotropical river otter (Lontra longicaudis), and european hare (Lepus europaeus). Phylogenetic analysis revealed the presence of Leptospira borgpetersenii and Leptospira interrogans in these animals. This research is the first study contributing to the epidemiology of leptospirosis by identifying L. borgpetersenii and L. interrogans in free-living and captive wild animals in Rio Grande do Sul, Brazil, potentially acting as bacterial reservoirs. Additionally, our findings can inform sanitary measures for controlling and preventing the disease, thereby safeguarding public health.

First isolation and genotyping of pathogenic Leptospira spp. from Austria

Leptospirosis is a globally distributed zoonotic disease. The standard serological test, known as Microscopic Agglutination Test (MAT), requires the use of live Leptospira strains. To enhance its sensitivity and specificity, the usage of locally circulating strains is recommended. However, to date, no local strain is available from Austria. This study aimed to isolate circulating Leptospira strains from cattle in Austria to enhance the performances of the routine serological test for both humans and animals. We used a statistical approach combined with a comprehensive literature search to profile cattle with greater risk of leptospirosis infection and implemented a targeted sampling between November 2021 and October 2022. Urine and/or kidney tissue were sampled from 410 cattle considered at higher risk of infection. Samples were inoculated into EMJH-STAFF culture media within 2-6 h and a real-time PCR targeting the lipL32 gene was used to confirm the presence/absence of pathogenic Leptospira in each sample. Isolates were further characterised by core genome multilocus sequence typing (cgMLST). Nine out of 429 samples tested positive by PCR, from which three isolates were successfully cultured and identified as Leptospira borgpetersenii serogroup Sejroe serovar Hardjobovis, cgMLST cluster 40. This is the first report on the isolation and genotyping of local zoonotic Leptospira in Austria, which holds the potential for a significant improvement in diagnostic performance in the country. Although the local strain was identified as a cattle-adapted serovar, it possesses significant zoonotic implications. Furthermore, this study contributes to a better understanding of the epidemiology of leptospirosis in Europe.

Rainfall-driven resuspension of pathogenic Leptospira in a leptospirosis hotspot

Leptospirosis is a zoonosis caused by Leptospira bacteria present in the urine of mammals. Leptospira is able to survive in soils and can be resuspended during rain events. Here, we analyzed the pathogenic Leptospira concentration as a function of hydrological variables in a leptospirosis hot spot. A total of 226 samples were collected at the outlet of a 3 km2 watershed degraded by ungulate mammals (deer and feral pigs) and rats which are reservoirs for leptospirosis. Water samples collected at the beginning of a rain event following a dry period contained high concentrations of pathogenic Leptospira. The concentration was generally correlated with the water level and the suspended matter concentration (SMC) during the main flood event. A secondary peak of pathogenic Leptospira was sometimes detected after the main flood and in slightly turbid waters. Lastly, the pathogenic Leptospira concentration was extremely high at the end of a wet season. The pathogenic Leptospira concentrations could not be explained by a linear combination of hydrological variables (e.g. the rainfall, water level, SMC and soil moisture). However, nonlinear machine learning models of rainfall data only provided a fair fit to the observations and explained 75 % of the variance in the log10-transformed pathogenic Leptospira concentration. A comparison of identical machine learning models for the water level, SMC and pathogenic Leptospira concentration showed that the residual error in the Leptospira concentration was due to not only the small dataset but also the intrinsic characteristics of the signal. Our results support the hypothesis whereby pathogenic Leptospira survive at different depths in soils and superficial river sediments (depending on their water saturation) and are transferred to surface water during erosion. These results might help to refine leptospirosis warnings given to the local population. Future research should be focused on larger watersheds in more densely populated areas.

Genetic diversity of Leptospira strains circulating in humans and dogs in France in 2019-2021

Leptospirosis is a bacterial zoonotic disease. Humans and dogs are susceptible hosts, with similar clinical manifestations ranging from a febrile phase to multiple organ dysfunction. The incidence of leptospirosis in mainland France is relatively high, at about 1 case per 100,000 inhabitants, but our knowledge of the strains circulating in humans and dogs remains limited. We studied the polymorphism of the lfb1 gene sequences in an exhaustive database, to facilitate the identification of Leptospira strains. We identified 46 species-groups (SG) encompassing the eight pathogenic species of Leptospira. We sequenced the lfb1 gene amplification products from 170 biological samples collected from 2019 to 2021: 110 from humans and 60 from dogs. Epidemiological data, including vaccination status in dogs, were also collected. Three Leptospira species displaying considerable diversity were identified: L. interrogans, with eight lfb1 species-groups (including five new lfb1 species-groups) in humans and dogs; L. kirschneri, with two lfb1 species-groups in humans and dogs; and L. borgpetersenii, with one lfb1 species-group in humans only. The lfb1 species-group L. interrogans SG1, corresponding to serovar Icterohaemorrhagiae or Copenhageni, was frequently retrieved from both humans and dogs (n=67/110; 60.9% and n=59/60; 98.3% respectively). A high proportion of the affected dogs developed the disease despite vaccination (n=30/60; 50%). Genotyping with the polymorphic lfb1 gene is both robust and simple. This approach provided the first global picture of the Leptospira strains responsible for acute infections in mainland France, based on biological samples but without the need for culture. Identification of the Leptospira strains circulating and their changes over time will facilitate more precise epidemiological monitoring of susceptible and reservoir species. It should also facilitate the monitoring of environmental contamination, making it possible to implement preventive measures and to reduce the burden of this disease.

Molecular Characterization of Leptospira Species Detected in the Kidneys of Slaughtered Livestock in Abattoirs in Gauteng Province, South Africa

Leptospira was investigated in kidneys (n = 305) from slaughtered livestock in the Gauteng Province abattoirs, South Africa, using a culture medium to isolate Leptospira, followed by the LipL32 qPCR to detect Leptospira DNA. The SecY gene region was amplified, sequenced, and analyzed for LipL32 qPCR-positive samples or Leptospira isolates. The overall frequency of isolation of Leptospira spp. was 3.9% (12/305), comprising 4.8% (9/186), 4.1% (3/74), and 0% (0/45) from cattle, pigs, and sheep, respectively (p > 0.05). However, with LipL32 qPCR, the overall frequency of Leptospira DNA was 27.5%, consisting of 26.9%, 20.3%, and 42.2% for cattle, pigs, and sheep, respectively (p = 0.03). Based on 22 SecY sequences, the phylogenetic tree identified the L. interrogans cluster with serovar Icterohaemorrhagiae and the L. borgpetersenii cluster with serovar Hardjo bovis strain Lely 607. This study is the first molecular characterization of Leptospira spp. from livestock in South Africa. The reference laboratory uses an eight-serovar microscopic agglutination test panel for leptospirosis diagnosis, of which L. borgpetersenii serovar Hardjo bovis is not part. Our data show that pathogenic L. interrogans and L. borgpetersenii are circulating in the livestock population. Diagnostic use of molecular methods will eliminate or reduce the under-reporting of leptospirosis in livestock, particularly sheep, in South Africa.

Core genome sequencing and genotyping of Leptospira interrogans in clinical samples by target capture sequencing

BACKGROUND

The life-threatening pathogen Leptospira interrogans is the most common agent of leptospirosis, an emerging zoonotic disease. However, little is known about the strains that are currently circulating worldwide due to the fastidious nature of the bacteria and the difficulty to isolate cultures. In addition, the paucity of bacteria in blood and other clinical samples has proven to be a considerable challenge for directly genotyping the agent of leptospirosis directly from patient material. Our understanding of the genetic diversity of strains during human infection is therefore limited.

METHODS

Here, we carried out hybridization capture followed by Illumina sequencing of the core genome directly from 20 clinical samples that were PCR positive for pathogenic Leptospira to elucidate the genetic diversity of currently circulating Leptospira strains in mainland France.

RESULTS

Capture with RNA probes covering the L. interrogans core genome resulted in a 72 to 13,000-fold increase in pathogen reads relative to standard sequencing without capture. Variant analysis of the genomes sequenced from the biological samples using 273 Leptospira reference genomes was then carried out to determine the genotype of the infecting strain. For samples with sufficient coverage (19/20 samples with coverage > 8×), we could unambiguously identify L. interrogans serovars Icterohaemorrhagiae and Copenhageni (14 samples), L. kirschneri serovar Grippotyphosa (4 samples), and L. interrogans serovar Pyrogenes (1 sample) as the infecting strains.

CONCLUSIONS

We obtained high-quality genomic data with suitable coverage for confident core genome genotyping of the agent of leptospirosis for most of our clinical samples. The recovery of the genome of the serovars Icterohaemorrhagiae and Copenhageni directly from multiple clinical samples revealed low adaptive diversification of the core genes during human infection. The ability to generate culture-free genomic data opens new opportunities for better understanding of the epidemiology of this fastidious pathogen and pathogenesis of this neglected disease.

Utility evaluation of two molecular methods for Leptospira spp. typing in human serum samples

Most of the available genotyping methods were applied and evaluated in Leptospira isolates and only few of them in a relevant sample size of blood specimens but not of sera. The objective of this study was to evaluate the utility of one partial 16S rRNA gene sequencing assay (16S rRNA) and an optimized. Multilocus sequence typing scheme (MLST) for Leptospira typing directly in serum samples. Confirmed leptospirosis patients (n = 228) from Argentina (2005-2016) were randomly included. Septicemic-phase serum samples (n = 228) were studied by two genotyping methods. Available immune-phase serum samples of the included patients (n = 159) were studied by MAT to compare serological and molecular results. In culture-proven cases (n = 8), genotyping results between clinical samples and isolates were compared. Typing success rate (TSR) was 21.9% for 16S rRNA and 11.4% for MLST (full allelic profile) and a positive trend in both TSR during the study period was observed. Two species (L. interrogans and L. borgpertesenii) were identified by both methods and MLST assigned 8 different STs. The probable serogroups identified by MLST were coincident with the presumptive infecting serogroups identified by MAT, but with different frequencies. The three serogroups (Canicola, Sejroe and Icterohaemorrhagiae) most frequently identified by MAT were also genotyped by MLST. Typing results via 16S rRNA and MLST in clinical samples and isolates of culture-proven cases, were consistent except for one case. Performance of partial 16S rRNA gene sequencing assay and the optimized MLST scheme directly in sera may increase and improve the knowledge about species and serogroups causing human leptospirosis, especially in countries with low rates of culture sample collection or Leptospira isolation.

Diversity of Leptospira spp. in bats and rodents from Papua New Guinea

Leptospirosis is the most common bacterial zoonosis globally. The pathogen, Leptospira spp., is primarily associated with rodent reservoirs. However, a wide range of other species has been implicated as reservoirs or dead-end hosts. We conducted a survey for Leptospira spp. in bats and rodents from Papua New Guinea. Kidney samples were collected from 97 pteropodid bats (five species), 37 insectivorous bats from four different families (six species) and 188 rodents (two species). Leptospires were detected in a high proportion of pteropodid bats, including Nyctimene cf. albiventer (35%), Macroglossus minimus (34%) and Rousettus amplexicaudatus (36%). Partial sequencing of the secY gene from rodent and bat leptospires showed host species clustering, with Leptospira interrogans and L. weilii detected in rodents and L. kirschneri and a potential novel species of Leptospira detected in bats. Further research is needed in Papua New Guinea and other locales in the Pacific region to gain a better understanding of the circulation dynamics of leptospires in reservoir species and the risks to public and veterinary health.

Comparison of the Serion IgM ELISA and Microscopic Agglutination Test for diagnosis of Leptospira spp. infections in sera from different geographical origins and estimation of Leptospira seroprevalence in the Wiwa indigenous population from Colombia

Leptospirosis is among the most important zoonotic diseases in (sub-)tropical countries. The research objective was to evaluate the accuracy of the Serion IgM ELISA EST125M against the Microscopic Agglutination Test (MAT = imperfect reference test); to assess its ability to diagnose acute leptospirosis infections and to detect previous exposure to leptospires in an endemic setting. In addition, to estimate the overall Leptospira spp. seroprevalence in the Wiwa indigenous population in North-East Colombia. We analysed serum samples from confirmed leptospirosis patients from the Netherlands (N = 14), blood donor sera from Switzerland (N = 20), and sera from a cross-sectional study in Colombia (N = 321). All leptospirosis ELISA-positive, and a random of negative samples from Colombia were tested by the MAT for confirmation. The ELISA performed with a sensitivity of 100% (95% CI 77% - 100%) and a specificity of 100% (95% CI 83% - 100%) based on MAT confirmed Leptospira spp. positive and negative samples. In the cross-sectional study in Colombia, the ELISA performed with a sensitivity of 100% (95% CI 2–100%) and a specificity of 21% (95% CI 15–28%). Assuming a 5% Leptospira spp. seroprevalence in this population, the positive predictive value was 6% and the negative predictive value 100%. The Leptospira spp. seroprevalence in the Wiwas tested by the ELISA was 39%; however, by MAT only 0.3%. The ELISA is suitable to diagnose leptospirosis in acutely ill patients in Europe several days after onset of disease. For cross-sectional studies it is not recommended due to its low specificity. Despite the evidence of a high leptospirosis prevalence in other study areas and populations in Colombia, the Wiwa do not seem to be highly exposed to Leptospira spp.. Nevertheless, leptospirosis should be considered and tested in patients presenting with febrile illness.

Leptospirosis is among the most important zoonotic diseases in (sub-)tropical countries. The correct diagnosis of leptospirosis is very important to take a medical or public health decision. Therefore, we tested a serological test (ELISA) for its ability to correctly diagnose a negative sample as truly negative and a positive sample as truly positive. We tested the ELISA with European acute leptospirosis confirmed positive and negative samples and compared results with another serological test (microscopic agglutination test), which is the recognized reference test. Further, the ELISA was assessed for its ability to detect previous exposure to leptospires in serum samples from the indigenous Wiwa population from Colombia, where leptospirosis is expected to be endemic.

The ELISA performed very well with sera from patients with acute leptospirosis, however had difficulties to diagnose negative samples as truly negative in the Colombian field samples; hence unexposed persons were falsely diagnosed to be positive. Therefore, we recommend using the ELISA to detect acute leptospirosis several days after onset of illness in a non-endemic environment, but are not convinced of its usefulness to screen a population for previous Leptospira spp. exposure.

Detection of Leptospira interrogans in Wild Sambar Deer (Rusa unicolor), Brazil

Leptospirosis is an emerging zoonotic disease caused by bacteria of the genus Leptospira. Wild animals may present acute disease or become chronic hosts. The present study aimed to identify Leptospira spp. infection and determine circulating serogroups in free-ranging sambar deer (Rusa unicolor) in a fragment of peri-urban tropical forest in northeastern Brazil. Blood samples were collected and subjected to microscopic agglutination testing (MAT) and PCR analysis (genes lipL32 and secY). Anti-Leptospira antibodies were detected in 60% of the animals tested, with serogroups Cynopteri (33.4%), Hebdomadis (22.2%) and Grippotyphosa (22.2%) identified as most prevalent. DNA corresponding to the pathogenic species Leptospira interrogans was detected in 2/15 (13.3%) of the samples tested. Sambar deer experience a high level of exposure to Leptospira spp. in our epidemiological setting. It is important to emphasize the implementation of effective measures (i.e., maintaining habitats and reducing human contact) for the conservation of endangered species.

Fatal Rodentborne Leptospirosis in Prison Inmates, South Africa, 2015

Leptospirosis is a neglected zoonotic disease. In 2015, leptospirosis was diagnosed in 2 prison inmates in South Africa. Using real-time PCR and DNA sequencing, we identified Leptospira interrogans serogroup Icterohaemorrhagiae in rodents and water samples within the prison. Leptospirosis might be frequently underdiagnosed in South Africa.

Next-Generation Sequencing Analysis of Pathogenic Leptospira: A Way Forward for Understanding Infectious Disease Dynamics in Low/Middle-Income, Disease-Endemic Settings

In the current genomic era, knowledge of diversity of Leptospira, the spirochetal agents of leptospirosis, is changing rapidly. Next-generation sequencing has decreased in price and increased in scale, with the potential to democratize large-scale analysis of pathogens in resource-limited, low/middle-income (LMIC) regions. Consequently, the molecular classification of Leptospira, a pathogen disproportionately affecting LMIC countries, has changed dramatically over the last decade. Leptospira classification and molecular understandings of pathogen diversity have rapidly evolved, now most precisely based on core genome analysis supplemented by new insights provided by culture-independent methods directly using body fluids such as blood and urine. In places where leptospirosis disease burden is highest, genomic technologies have not been available, and serology-based methods remain the mainstay of leptospiral classification. Understanding the epidemiology, pathogenesis, and ultimately new approaches to treating and preventing leptospirosis requires detailed knowledge of regionally circulating Leptospira in highly endemic settings. Next-generation sequencing-based, culture-independent typing overcomes the limitation of culture isolation of Leptospira from clinical samples, with promise of providing public health-actionable information applicable to leptospirosis-endemic LMIC settings.

Development of a Multiplex PCR Assay for Detection and Discrimination of Pathogenic and Saprophytic Leptospira in Water

Leptospirosis is a zoonosis prevalent in tropical countries and affects animals and humans alike. Leptospira interrogans, the causative organism for this waterborne infection, spreads through the urine of infected animals. There is a direct link between contaminated water and Leptospira outbreaks. This study reports a rapid assay to detect and differentiate pathogenic Leptospira from non-pathogenic in environmental water using multiplex PCR. The assay uses primers targeting the Lipl32 and Lipl21 gene. The multiplex PCR has been standardized using 11 pathogenic and one saprophytic serovar of Leptospira. The analytical sensitivity of the developed method was evaluated with different concentrations of template DNA. This method was used to screen water samples collected from 20 different sources from Chengalpattu town in Kancheepuram District, Tamil Nadu, India. Of the 20 water samples screened, 13 samples tested positive for pathogenic Leptospira, and seven samples tested negative. Four water samples were found to carry both pathogenic and saprophytic species. The developed multiplex PCR assay is highly useful for detecting and distinguishing pathogenic and saprophytic leptospires in water.

Identification of Leptospira spp. in the animal-environment interface (swine-water) in pig production cycle

INTRODUCTION

Leptospirosis, caused by Leptospira spp., is a zoonosis with multiple hosts and reservoirs. Thus, the "One Health" approach must be addressed in order to guide prevention and control measures regarding this microorganism. There are few studies involving all stages of the pig production cycle and potential sources of infection such as water sources, which could represent a risk for local rural communities.

OBJECTIVE

To identify Leptospira spp. in the animal-environment interface (swine-water) in the pig production cycle.

MATERIALS AND METHODS

The study was conducted in a swine farm in Puerto López in the department of Meta, Colombia. Swine blood samples (n = 65) were collected for microscopic agglutination test (MAT), while urine and water samples (n = 80) were tested for Leptospira using bacterial isolation, serotyping of the isolates, and polymerase chain reaction (PCR).

RESULTS

A total of 58 (89.2%) porcine sera were positive for at least one Leptospira serogroup, with Grippotyphosa as the most frequent serogroup. Leptospira spp. were isolated in 25% (20/80) of the urine and water samples. Leptospira-positive cultures were 100% (20/20) identified within the genus Leptospira (rrl gene) and 50% (10/20) corresponded to pathogenic species (lipL32 gene) by PCR, and 45% (9/20) were positive to at least one antiserum. None of the direct urine and water samples was positive by PCR.

CONCLUSION

It is suggested that the bacteria might be transmitted in the animal-environment interface in the pig production cycle.

Evaluation of three qPCR for the detection of pathogenic leptospires in domestic animals in Nicaragua

Introducción.

En Nicaragua es necesario estandarizar pruebas moleculares como la PCR en tiempo real (quantitative Polymerase Chain Reaction, qPCR) que mejoren el diagnóstico de leptospirosis en humanos y animales.

Objetivo.

Evaluar tres qPCR para la detección de leptospiras patógenas en animales domésticos de Nicaragua.

Materiales y métodos.

Se diseñaron cebadores para la amplificación del gen LipL32 en SYBR Green (SYBR Green-A) y TaqMan, y en otros descritos previamente (SYBR Green-B). Las secuencias de 12 cepas obtenidas de la base de datos del National Center for Biotechnology Information (NCBI) se alinearon para la búsqueda de sondas y cebadores. La sensibilidad analítica se determinó calculando el equivalente genómico detectable, se utilizaron 18 cepas de referencia para la sensibilidad diagnóstica y 28 controles negativos para la especificidad. Los métodos se aplicaron en 129 muestras de orina de animales domésticos.

Resultados.

En SYBR Green-A se obtuvo un límite de detección de cuatro equivalentes genómicos; en TaqMan, la sensibilidad fue del 94,4 % (IC_95% 81,1-100,0). Con SYBR Green-A, se obtuvo una sensibilidad del 77,8 % (IC₉₅% 55,8-99,8), en tanto que con SYBR Green-B fue del 61,1 % (IC_95% 35,8-86,4). En las tres pruebas se logró una especificidad del 100 % (IC_95% 98,2-100,0). El 26,4 % de las muestras de animales domésticos fueron positivas con SYBR Green-A y el 6,2 % con SYBR Green-B.

Conclusiones.

El SYBR Green-A presentó un límite de detección bajo, en tanto que las tres técnicas evaluadas mostraron alta especificidad, en tanto que la TaqMan tuvo la mayor sensibilidad.

Age-specific epidemiology of human leptospirosis in New Caledonia, 2006-2016

With over one million cases worldwide annually and a high fatality in symptomatic forms, human leptospirosis is a growing public health concern for the most vulnerable populations, especially in the context of global warming and unplanned urbanization. Although the Asia-Pacific region is particularly affected, accurate epidemiological data are often lacking. We conducted an eleven-year retrospective laboratory-based epidemiological survey of human leptospirosis in New Caledonia. From 2006 to 2016, 904 cases were laboratory-confirmed, including 29 fatalities, corresponding to an average annual incidence of 30.6/100,000 and a case fatality rate of 3.2%. Over the period, there was a major shift from indirect serological diagnosis by MAT to direct diagnosis by real-time PCR, a more specific and sensitive test when performed early in the course of the disease. The systematic implementation of genotyping informed on the variety of the infective strains involved, with a predominance of serogroups Icterohaemorrhagiae and Pyrogenes. The epidemiological pattern showed a marked seasonality with an annual peak in March-April. Interestingly, the seasonal peak in children of school age was significantly earlier and corresponded to school holidays, suggesting that attending school from February on could protect children from environment-borne leptospirosis.

Multi-locus sequence analyses reveal a clonal L. borgpetersenii genotype in a heterogeneous invasive Rattus spp. community across the City of Johannesburg, South Africa

BACKGROUND

Rattus spp. are frequently implicated as key reservoir hosts for leptospirosis, one of the most common, but neglected, bacterial zoonoses in the world. Although leptospirosis is predicted to be a significant public health threat in Africa, studies from the continent are limited.

METHODS

Rattus spp. (n = 171) were sampled (January-May 2016) across the City of Johannesburg, South Africa's largest inland metropole. Rattus spp. genetic diversity was evaluated by full length (1140 bp) cyt b sequencing of 42 samples. For comparison, a further 12 Rattus norvegicus samples collected in Cape Town, South Africa's largest coastal metropole, were also genotyped. Leptospira infections were identified and genotyped using real-time PCR and multi-locus (lfb1, secY and lipL41) DNA sequencing.

RESULTS

Five R. norvegicus haplotypes were identified across Johannesburg, four of which have not previously been detected in South Africa, and one in Cape Town. Across Johannesburg we identified a Leptospira spp. infection prevalence of 44% (75/171) and noted significant differences in the prevalence between administrative regions within the metropole. Multi-locus sequence analyses identified a clonal genotype consistent with L. borgpetersenii serogroup Javanica (serovar Ceylonica).

DISCUSSION

The prevalence of infection identified in this study is amongst the highest detected in Rattus spp. in similar contexts across Africa. Despite the complex invasion history suggested by the heterogeneity in R. norvegicus haplotypes identified in Johannesburg, a single L. borgpetersenii genotype was identified in all infected rodents. The lack of L. interrogans in a rodent community dominated by R. norvegicus is notable, given the widely recognised host-pathogen association between these species and evidence for L. interrogans infection in R. norvegicus in Cape Town. It is likely that environmental conditions (cold, dry winters) in Johannesburg may limit the transmission of L. interrogans. Spatial heterogeneity in prevalence suggest that local factors, such as land use, influence disease risk in the metropole.

CONCLUSIONS

In South Africa, as in other African countries, leptospirosis is likely underdiagnosed. The high prevalence of infection in urban rodents in Johannesburg suggest that further work is urgently needed to understand the potential public health risk posed by this neglected zoonotic pathogen.

Circulating genotypes of Leptospira in French Polynesia : An 9-year molecular epidemiology surveillance follow-up study

Background

Leptospirosis is a widespread zoonosis with global impact, particularly among vulnerable populations in resource-poor settings in tropical countries. Rodents have been considered to be the main reservoir of the disease; however, a wide variety of mammals can act as hosts as well. Here we examine the genetic diversity of Leptospira strains from biological samples of patients and animals in French Polynesia (FP) from 2011 to 2019.

Methodology/Principal findings

From 2011 to 2019, we have collected 444 blood samples from patients diagnosed as having leptospirosis. The limited volume of clinical material and low amount of leptospiral DNA in blood samples led us to develop a nested PCR targeting the secY locus that enabled us to amplify and sequence 244 samples (55%). In addition, 20 Leptospira strains recovered from the blood of patients from 2002 to 2011 were sequenced and fully characterized at the serogroup level and used as reference strains for the association of different phylogenetic branches with respective serogroups. The secY sequences were compared with publicly available sequences from patients and animal reservoirs in FP (n = 79). We identified rats as the main source of infection for L. borgpetersenii serogroup Ballum and L. interrogans serogroup Icterohaemorrhagiae, dogs as the main source of infection for L. interrogans serogroup Australis, and farm pigs as the main source of infection for L. interrogans serogroups Pomona or Canicola. L. interrogans was associated with the most severe infections with 10 and 5 fatal cases due to serogroups Icterohaemorrhagiae and Australis, respectively. Mortality was significantly associated with older age (p-value < 0.001).

Conclusions/Significance

We described the population dynamics of leptospires circulating among patients in FP, including two patients who were reinfected with unrelated Leptospira genotypes, and clarified the local role of the animal reservoirs in the transmission route of leptospirosis to humans. Routine Leptospira genotyping directly on biological samples should allow the epidemiological follow-up of circulating strains and assess the impact of control interventions on disease transmission.

Pathogenic Leptospira are the causative agents for leptospirosis, a neglected zoonosis occurring worldwide with the highest incidence of the disease found in the Pacific region, including French Polynesia (FP). In this study, a nested PCR of blood specimens allowed a high isolation frequency of Leptospira DNA among patients with febrile illness in FP. Infecting Leptospira isolates were characterized by sequencing of the secY gene from 244 clinical samples from 2011 to 2019. The genotypes have been assigned to Leptospira species and serogroups by comparing the secY sequences with the genomes of strains isolated prior to 2011 in FP. This study therefore enables to follow the distribution of genotypes/serogroups over a 18-year time period. Leptospiral sequences from patients were also compared with secY sequences from different animal reservoirs from a previous study in FP showing that not only rats but also dogs and pigs might play an important role in the circulation of pathogenic Leptospira strains in FP. Further progress in our understanding of the epidemiology of Leptospira circulating genotypes should contribute to the implementation of prevention and intervention measures to reduce the risk of leptospirosis transmission in FP.

Laboratory Diagnosis of Bovine Abortions Caused by Non-Maintenance Pathogenic Leptospira spp.: Necropsy, Serology and Molecular Study Out of a Belgian Experience

: Bovine leptospirosis is a bacterial zoonotic disease caused by pathogenic Leptospira spp.. The pathology and epidemiology of this infection are influenced by the numerous existing serovars and their adaptation to specific hosts. Infections by host-maintained serovars such as Hardjo are well documented, unlike those from the incidental ones. In July 2014, an emerging phenomenon of an increased incidence of icteric abortions associated with leptospiral infection occurred in southern Belgium. First-line serological analyses targeting cattle-adapted serovars failed at initial diagnosis. This study provides a comprehensive description of laboratory findings-at the level of necropsy, serology and molecular diagnosis-regarding icteric and non-icteric abortions (n = 116) recorded during this time (years 2014-2015) and associated with incidental infection by serovars such as Grippotyphosa, Australis and Icterohaemorrhagiae. Based on these tests, a diagnostic pathway is proposed for these types of infection in cattle to establish an affordable but accurate diagnosis in the future. These investigations add insights into the understanding of the pathogenesis of bovine leptospirosis associated with serovars classically described as non-maintenance.

Leptospira interrogans and Leptospira kirschneri are the dominant Leptospira species causing human leptospirosis in Central Malaysia

BACKGROUND

Leptospirosis, commonly known as rat-urine disease, is a global but endemic zoonotic disease in the tropics. Despite the historical report of leptospirosis in Malaysia, the information on human-infecting species is limited. Determining the circulating species is important to understand its epidemiology, thereby to strategize appropriate control measures through public health interventions, diagnostics, therapeutics and vaccine development.

METHODOLOGY/PRINCIPLE FINDINGS

We investigated the human-infecting Leptospira species in blood and serum samples collected from clinically suspected leptospirosis patients admitted to three tertiary care hospitals in Malaysia. From a total of 165 patients, 92 (56%) were confirmed cases of leptospirosis through Microscopic Agglutination Test (MAT) (n = 43; 47%), Polymerase Chain Reaction (PCR) (n = 63; 68%) or both MAT and PCR (n = 14; 15%). The infecting Leptospira spp., determined by partial 16S rDNA (rrs) gene sequencing revealed two pathogenic species namely Leptospira interrogans (n = 44, 70%) and Leptospira kirschneri (n = 17, 27%) and one intermediate species Leptospira wolffii (n = 2, 3%). Multilocus sequence typing (MLST) identified an isolate of L. interrogans as a novel sequence type (ST 265), suggesting that this human-infecting strain has a unique genetic profile different from similar species isolated from rodents so far.

CONCLUSIONS/SIGNIFICANCE

Leptospira interrogans and Leptospira kirschneri were identified as the dominant Leptospira species causing human leptospirosis in Central Malaysia. The existence of novel clinically important ST 265 (infecting human), that is different from rodent L. interrogans strains cautions reservoir(s) of these Leptospira lineages are yet to be identified.

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.

Leptospira spp., a genus in the stage of diversity and genomic data expansion

Leptospirosis is a widespread global zoonotic bacterial disease with a noteworthy human-animal-ecosystem interface. The disease presents different clinical manifestations and a high mortality and morbidity rates in humans and animals throughout the world. Characterization and correct classification of Leptospira isolates is essential for a better understanding the epidemiological properties of the disease. In the last ten years, molecular typing tools have been developed and applied to this field. These methods together with the availability of hundreds of new whole genome sequences that belong to known and new described species are shaping the understanding and structure of the entire genus.

A systematic review of Leptospira in water and soil environments

Background

Leptospirosis, caused by pathogenic Leptospira, is a zoonosis of global distribution. This infectious disease is mainly transmitted by indirect exposure to urine of asymptomatic animals via the environment. As human cases generally occur after heavy rain, an emerging hypothesis suggests that rainfall re-suspend leptospires together with soil particles. Bacteria are then carried to surface water, where humans get exposed. It is currently assumed that pathogenic leptospires can survive in the environment but do not multiply. However, little is known on their capacity to survive in a soil and freshwater environment.

Methods

We conducted a systematic review on Leptospira and leptospirosis in the environment in order to collect current knowledge on the lifestyle of Leptospira in soil and water. In total, 86 scientific articles retrieved from online databases or institutional libraries were included in this study.

Principals findings/significance

This work identified evidence of survival of Leptospira in the environment but major gaps remain about the survival of virulent species associated with human and animal diseases. Studies providing quantitative data on Leptospira in soil and water are a very recent trend, but must be interpreted with caution because of the uncertainty in the species identification. Several studies mentioned the presence of Leptospira in soils more frequently than in waters, supporting the hypothesis of the soil habitat and dispersion of Leptospira with re-suspended soil particles during heavy rain. In a near future, the growing use of high throughput sequencing will offer new opportunities to improve our understanding of the habitat of Leptospira in the environment. This better insight into the risk of leptospirosis will allow implementing efficient control measures and prevention for the human and animal populations exposed.

A Large Leptospirosis Outbreak following Successive Severe Floods in Fiji, 2012

Severe flooding has been linked to outbreaks of leptospirosis. Two sequential extreme flood events in Western Fiji caused the largest outbreak of leptospirosis recorded in the South Pacific, with 1,217 total suspected cases, of which 314 were probable and confirmed. Most (83%) cases occurred within 6 weeks of the flood events, displaying a biphasic epidemic curve associated with the floods. Given the temporal proximity of cases to flooding events, most of the transmission appeared to occur during or immediately after the floods; therefore, prevention of exposure to contaminated environments is a priority in the immediate flood and post-flood period. In addition, genotyping studies suggest that multiple animal reservoirs were implicated in the outbreak, reaffirming the importance of integrated human and animal health strategies for leptospirosis control.

Leptospirosis: a diagnostic conundrum

Leptospirosis is a serious public health concern worldwide. It is highly endemic in the Andaman Islands and its prevalence is increasing in other Indian states. Clinical features are non-specific and diagnosis relies on laboratory confirmation. The gold standard is microscopic agglutination testing, but this is not widely available. Real-time polymerase chain reaction testing of LipL32 antigen provides the earliest detection of pathogenic Leptospira in the body. We found it to be 100% specific, but it should be used in the first 10 days of illness for reliable results.

A systematic review of human and animal leptospirosis in the Pacific Islands reveals pathogen and reservoir diversity

Background

The Pacific Islands have environmental conditions highly favourable for transmission of leptospirosis, a neglected zoonosis with highest incidence in the tropics, and Oceania in particular. Recent reports confirm the emergence and outbreaks of leptospirosis in the Pacific Islands, but the epidemiology and drivers of transmission of human and animal leptospirosis are poorly documented, especially in the more isolated and less developed islands.

Methodology/Principal findings

We conducted a systematic review of human and animal leptospirosis within 25 Pacific Islands (PIs) in Polynesia, Melanesia, Micronesia, as well as Easter Island and Hawaii. We performed a literature search using four international databases for articles published between January 1947 and June 2017. We further included grey literature available on the internet. We identified 148 studies describing leptospirosis epidemiology, but the number of studies varied significantly between PIs. No data were available from four PIs. Human leptospirosis has been reported from 13 PIs, with 63% of all studies conducted in Hawaii, French Polynesia and New Caledonia. Animal leptospirosis has been investigated in 19 PIs and from 14 host species, mainly pigs (18% of studies), cattle (16%) and dogs (11%). Only 13 studies provided information on both human and animal leptospirosis from the same location. Serology results were highly diverse in the region, both in humans and animals.

Conclusions/Significance

Our study suggests that, as in other tropical regions, leptospirosis is widespread in the PIs while showing some epidemiological heterogeneity. Data are scarce or absent from many PIs. Rodents, cattle, pigs and dogs are all likely to be important carriers, but the relative importance of each animal species in human infection needs to be clarified. Epidemiological surveys with appropriate sampling design, pathogen typing and data analysis are needed to improve our understanding of transmission patterns and to develop effective intervention strategies.

Leptospirosis is an important bacterial zoonosis that affects people and animals worldwide. It is common in tropical areas, especially in island ecosystems. Because islands are relatively small, isolated, and have limited health and diagnostic facilities, the disease burden is often underestimated. In this systematic review, we aimed to describe the extent of leptospirosis in the Pacific Islands, including the diversity of pathogens and animal reservoirs. We identified 148 studies from 21 Pacific islands that described Leptospira infection in humans or animals. In hospitalized febrile patients, leptospirosis was a common cause of the acute febrile illness, but accurate diagnosis was challenging and often delayed because symptoms overlapped with many other infectious diseases, and access to laboratory diagnosis was limited. A wide variety of animal hosts of Leptospira were identified, with rodents, cattle, pigs and dogs reported as important hosts; however, their relative importance in human infection remains unclear. Our review demonstrates that the epidemiology of leptospirosis varies across the Pacific Islands, but information about risk factors and transmission routes is currently limited. We recommend more integrated studies, using an eco-epidemiological approach that includes human, veterinary and environmental factors, and interactions between factors at different ecological scales.

Biodiversity of Environmental Leptospira: Improving Identification and Revisiting the Diagnosis

Leptospirosis is an important environmental disease and a major threat to human health causing at least 1 million clinical infections annually. There has recently been a growing interest in understanding the environmental lifestyle of Leptospira. However, Leptospira isolation from complex environmental samples is difficult and time-consuming and few tools are available to identify Leptospira isolates at the species level. Here, we propose a polyphasic isolation and identification scheme, which might prove useful to recover and identify environmental isolates and select those to be submitted to whole-genome sequencing. Using this approach, we recently described 12 novel Leptospira species for which we propose names. We also show that MALDI-ToF MS allows rapid and reliable identification and provide an extensive database of Leptospira MALDI-ToF mass spectra, which will be valuable to researchers in the leptospirosis community for species identification. Lastly, we also re-evaluate some of the current techniques for the molecular diagnosis of leptospirosis taking into account the extensive and recently revealed biodiversity of Leptospira in the environment. In conclusion, we describe our method for isolating Leptospira from the environment, confirm the usefulness of mass spectrometry for species identification and propose names for 12 novel species. This also offers the opportunity to refine current molecular diagnostic tools.

Advances and challenges in barcoding pathogenic and environmental Leptospira

Leptospirosis is a zoonotic bacterial disease of global importance. A large spectrum of asymptomatic animal hosts can carry the infection and contribute to the burden of human disease. Environmental sources of human contamination also point to the importance of a hydrotelluric reservoir. Leptospirosis can be caused by as many as 15 different pathogenic or intermediate Leptospira species. However, classification of these bacteria remains complicated through the use of both serological and genetic classification systems that show poor correlation. With the advent of molecular techniques, DNA-based barcoding offers a conceptual framework that can be used for leptospirosis surveillance as well as source tracking. In this review, we summarize some of the current techniques, highlight significant successes and weaknesses and point to the future opportunities and challenges to successfully establish a widely applicable barcoding scheme for Leptospira.

Continuous Excretion of Leptospira borgpetersenii Ballum in Mice Assessed by Viability Quantitative Polymerase Chain Reaction

Rodents are the main reservoir animals of leptospirosis. In this study, we characterized and quantified the urinary excretion dynamics of Leptospira by Mus musculus infected with 2 × 108 virulent Leptospira borgpetersenii serogroup Ballum. Each micturition was collected separately in metabolic cages, at 12 time points from 7 to 117 days post-infection (dpi). We detected Leptospira in all urine samples collected (up to 8 per time point per mouse) proving that Leptospira excretion is continuous with ca. 90% live L. borgpetersenii Ballum, revealed by viability quantitative polymerase chain reaction. Microscopic visualization by Live/Dead fluorescence confirmed this high proportion of live bacteria and demonstrated that L. borgpetersenii Ballum are excreted, at least partly, as bacterial aggregates. We observed two distinct phases in the excretion dynamics, first an increase in Leptospira concentration shed in the urine between 7 and 63 dpi followed by a plateau phase from 63 dpi onward, with up to 3 × 107Leptospira per mL of urine. These two phases seem to correspond to progressive colonization of renal tubules first, then to stable cell survival and maintenance in kidneys. Therefore, chronically infected adult mice are able to contaminate the environment via urine at each micturition event throughout their lifetime. Because Leptospira excretion reached its maximum 2 months after infection, older rodents have a greater risk of contaminating their surrounding environment.

A cross-sectional epidemiological study of domestic animals related to human leptospirosis cases in Nicaragua

Leptospirosis is one of the most extended zoonosis worldwide and humans become infected most commonly through contact with the urine of carrier animals, either directly or via contaminated water or soil. The aim in this study was to analyse the epidemiological behaviour of Leptospira spp., from domestic animals around the sites of human leptospirosis cases in Nicaragua, from 2007 through 2013. We report the results of a cross-sectional epidemiological study with a non-probability sampling of blood (n=3050) and urine (n=299) from Domestic Animals (DA) around the sites of human leptospirosis cases in Nicaragua. We analysed data obtained through Microscopic Agglutination Test (MAT), in-vitro culture, real time PCR and sequencing of lfb1 locus. Frequencies of 30.31% (95% CI: 28.66-31.95) and 15.38% (95% CI: 11.12-19.64) were obtained from serological test and from in-vitro culture, respectively. Although similar frequencies from serology test (P≥0.05) were found in DA species, in-vitro culture frequencies were significantly higher from bovine, equine and sheep (P<0.05) in comparison with swine and canine species. Ten serogroups of pathogenic Leptospira spp. were encountered, with the highest presence of Icterohaemorrhagiae serogroup 34.65% (95% CI: 29.35-39.94). We identified 7 samples homologous to L. interrogans species Pyrogenes serovar and 3 samples as L. noguchii Louisiana or Panama serovars by analysis of lfb1 sequences. We were able to establish a temporal and spatial correlation from DA and cumulative incidence of human cases. Therefore an effective epidemiological surveillance should be implemented with a specific control program toward DA in order to reduce human leptospirosis incidence.

Leptospira diversity in animals and humans in Tahiti, French Polynesia

BACKGROUND

Leptospirosis is a highly endemic bacterial zoonosis in French Polynesia (FP). Nevertheless, data on the epidemiology of leptospirosis in FP are scarce. We conducted molecular studies on Leptospira isolated from humans and the potential main animal reservoirs in order to identify the most likely sources for human infection.

METHODOLOGY/PRINCIPAL FINDINGS

Wild rats (n = 113), farm pigs (n = 181) and domestic dogs (n = 4) were screened for Leptospira infection in Tahiti, the most populated island in FP. Positive samples were genotyped and compared to Leptospira isolated from human cases throughout FP (n = 51), using secY, 16S and LipL32 sequencing, and MLST analysis. Leptospira DNA was detected in 20.4% of rats and 26.5% of pigs. We identified two Leptospira species and three sequence types (STs) in animals and humans: Leptospira interrogans ST140 in pigs only and L. interrogans ST17 and Leptospira borgpetersenii ST149 in humans and rats. Overall, L. interrogans was the dominant species and grouped into four clades: one clade including a human case only, two clades including human cases and dogs, and one clade including human cases and rats. All except one pig sample showed a unique L. interrogans (secY) genotype distinct from those isolated from humans, rats and dogs. Moreover, LipL32 sequencing allowed the detection of an additional Leptospira genotype in pigs, clearly distinct from the previous ones.

CONCLUSIONS/SIGNIFICANCE

Our data confirm rats as a major potential source for human leptospirosis in FP. By contrast to what was expected, farm pigs did not seem to be a major reservoir for the Leptospira genotypes identified in human patients. Thus, further investigations will be required to determine their significance in leptospirosis transmission in FP.

Seeking the environmental source of Leptospirosis reveals durable bacterial viability in river soils

Background

Leptospirosis is an important re-emerging infectious disease that affects humans worldwide. Infection occurs from indirect environment-mediated exposure to pathogenic leptospires through contaminated watered environments. The ability of pathogenic leptospires to persist in the aqueous environment is a key factor in transmission to new hosts. Hence, an effort was made to detect pathogenic leptospires in complex environmental samples, to genotype positive samples and to assess leptospiral viability over time.

Methodology/Principal findings

We focused our study on human leptospirosis cases infected with the New Caledonian Leptospira interrogans serovar Pyrogenes. Epidemiologically related to freshwater contaminations, this strain is responsible for ca. 25% of human cases in New Caledonia. We screened soil and water samples retrieved from suspected environmental infection sites for the pathogen-specific leptospiral gene lipL-32. Soil samples from all suspected infection sites tested showed detectable levels of pathogenic leptospiral DNA. More importantly, we demonstrated by viability qPCR that those pathogenic leptospires were viable and persisted in infection sites for several weeks after the index contamination event. Further, molecular phylogenetic analyses of the leptospiral lfb-1 gene successfully linked the identity of environmental Leptospira to the corresponding human-infecting strain.

Conclusions/Significance

Altogether, this study illustrates the potential of quantitative viability-PCR assay for the rapid detection of viable leptospires in environmental samples, which might open avenues to strategies aimed at assessing environmental risk.

Leptospirosis is an emerging zoonotic disease caused by infection with pathogenic strains of Leptospira. Most human infections arise from environmental exposure to contaminated freshwater environments or watered soils where pathogenic Leptospira are considered as able to survive for prolonged periods. Therefore, a good understanding of Leptospira survival strategy in the environment is a key step to identifying crucial factors amenable to interventions and public health actions to lower leptospirosis burden. In this study, we investigated the environmental presence and survival of pathogenic leptospires in areas where recent human leptospirosis cases had been reported. Although detection of Leptospira from complex environmental samples is difficult, we successfully detected the presence of pathogenic Leptospira in soils of suspected infection sites. In addition, we showed that these pathogenic leptospires were alive and present in soils several weeks after the infecting event. Typing of leptospiral DNA retrieved from the environment revealed identities between environmental pathogenic Leptospira and the causative strains involved in human leptospirosis index cases. Interestingly, we also identified yet unreported genotypes. Altogether, our work illustrates the potential of quantitative molecular assays for the rapid detection and typing of viable leptospires in environmental samples, which could prove useful to assess the risk of environmental exposure.

Isolation of Leptospira from blood culture bottles

With the increasing use of real-time PCR techniques, Leptospira isolation has mostly been abandoned for the diagnosis of human leptospirosis. However, there is a great value of collecting Leptospira isolates to better understand the epidemiology of this complex zoonosis and to provide the researchers with different isolates. In this study, we have successfully isolated different Leptospira strains from BacT/Alert aerobic blood culture bottles and suggest that this privileged biological material offers an opportunity to isolate leptospires.

Rodent management issues in South Pacific islands: a review with case studies from Papua New Guinea and Vanuatu

Rodents are a key pest to agricultural and rural island communities of the South Pacific, but there is limited information of their impact on the crops and livelihoods of small-scale farmers. The rodent pest community is known, but the type and scales of damage to different crops on different islands are unknown. Knowledge about rodent pest management in other geographical regions may not be directly transferable to the Pacific region. Many studies on islands have largely focussed on the eradication of rodents from uninhabited islands for conservation benefits. These broadscale eradication efforts are unlikely to translate to inhabited islands because of complex social and agricultural issues. The livelihoods, culture and customs of poor small-scale farmers in the South Pacific have a large bearing on the current management of rodents. The aim of the present review was to describe the rodent problems, impacts and management of rodents on South Pacific islands, and identify gaps for further research. We compared and contrasted two case studies. The situation in Papua New Guinea is emergent as several introduced rodent species are actively invading new areas with wide-ranging implications for human livelihoods and conservation. In Vanuatu, we show how rodent damage on cocoa plantations can be reduced by good orchard hygiene through pruning and weeding, which also has benefits for the management of black pod disease. We conclude that (1) damage levels are unknown and unreported, (2) the impacts on human health are unknown, (3) the relationships between the pest species and their food sources, breeding and movements are not known, and (4) the situation in Papua New Guinea may represent an emergent crisis that warrants further investigation. In addition, there is a need for greater understanding of the invasive history of pest rodents, so as to integrate biological information with management strategies. Ecologically based rodent management can be achieved on Pacific Islands, but only after significant well funded large-scale projects are established and rodent ecologists are trained. We can learn from experiences from other locations such as Southeast Asia to guide the way.

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.

Distribution and Diversity of Pathogenic Leptospira Species in Peri-domestic Surface Waters from South Central Chile

Background

Leptospirosis is a neglected zoonosis affecting animals and humans caused by infection with Leptospira. The bacteria can survive outside of hosts for long periods of time in soil and water. While identification of Leptospira species from human cases and animal reservoirs are increasingly reported, little is known about the diversity of pathogenic Leptospira species in the environment and how surveillance of the environment might be used for monitoring and controlling disease.

Methods and Findings

Water samples (n = 104) were collected from the peri-domestic environment of 422 households from farms, rural villages, and urban slums participating in a broader study on the eco-epidemiology of leptospirosis in the Los Rios Region, Chile, between October 2010 and April 2012. The secY region of samples, previously detected as pathogenic Leptospira by PCR, was amplified and sequenced. Sequences were aligned using ClustalW in MEGA, and a minimum spanning tree was created in PHYLOViZ using the goeBURST algorithm to assess sequence similarity. Sequences from four clinical isolates, 17 rodents, and 20 reference strains were also included in the analysis. Overall, water samples contained L. interrogans, L. kirschneri, and L. weilii, with descending frequency. All species were found in each community type. The distribution of the species differed by the season in which the water samples were obtained. There was no evidence that community-level prevalence of Leptospira in dogs, rodents, or livestock influenced pathogen diversity in the water samples.

Conclusions

This study reports the presence of pathogenic Leptospira in the peri-domestic environment of households in three community types and the differences in Leptospira diversity at the community level. Systematic environmental surveillance of Leptospira can be used for detecting changes in pathogen diversity and to identify and monitor contaminated areas where an increased risk of human infection exists.

Leptospirosis is a zoonotic disease that is caused by either direct contact with the urine of animals infected with pathogenic forms of Leptospira, or indirectly, through contact with contaminated water or soil. Because many people become infected through the environment, where the bacteria can live for many months if the conditions are suitable, we tested water samples from the peri-domestic area in twelve different communities from Los Rios region, Chile, to examine whether the Leptospira species were different in urban, rural village, and farm areas. We found that all three community types had L. interrogans, L. kirschneri, and L. weilii. No evident associations were seen between animal infection and the frequency or diversity of Leptospira. The proposed surveillance method has potential for systematic monitoring of surface waters that will help us better understand the importance of animal, climate, and environmental factors in the variation of Leptospira species present in a community in order to predict infection risk and inform prevention programs.

Zika virus infection as an unexpected finding in a Leptospirosis patient

Introduction:

Areas where leptospirosis and arboviruses are endemic largely overlap in the tropics. However, the number of arbovirus infections is usually much higher. The initial clinical presentation can be highly confusing; therefore, laboratory confirmation is key to an accurate diagnosis.

Case Presentation:

A 19–year–old man presented to a peripheral health centre with an acute febrile illness. Dengue was initially suspected, but the patient deteriorated to a shock syndrome. Leptospirosis as well as a co-infection with Zika virus were both confirmed in the laboratory, the latter being clinically masked in this dual infection.

Conclusion:

This case highlights the importance of not only considering the differential diagnosis of acute febrile syndromes, but also to consider the possibility of dual infections in the context of global spread of arboviruses. The specific context of travellers returning from endemic areas and pregnant women is also highlighted and discussed.

Human Leptospirosis on Reunion Island, Indian Ocean: Are Rodents the (Only) Ones to Blame?

BACKGROUND

Although leptospirosis is a zoonosis of major concern on tropical islands, the molecular epidemiology of the disease aiming at linking human cases to specific animal reservoirs has been rarely explored within these peculiar ecosystems.

METHODOLOGY/PRINCIPAL FINDINGS

Five species of wild small mammals (n = 995) as well as domestic animals (n = 101) were screened for Leptospira infection on Reunion Island; positive samples were subsequently genotyped and compared to Leptospira from clinical cases diagnosed in 2012-2013 (n = 66), using MLST analysis. We identified two pathogenic species in human cases, namely Leptospira interrogans and Leptospira borgpetersenii. Leptospira interrogans was by far dominant both in clinical samples (96.6%) and in infected animal samples (95.8%), with Rattus spp and dogs being its exclusive carriers. The genetic diversity within L. interrogans was apparently limited to two sequence types (STs): ST02, identified among most clinical samples and in all rats with complete MLST, and ST34, identified in six humans, but not in rats. Noteworthy, L. interrogans detected in two stray dogs partially matched with ST02 and ST34. Leptospira borgpetersenii was identified in two clinical samples only (3.4%), as well as in cows and mice; four haplotypes were identified, of which two seemingly identical in clinical and animal samples. Leptospira borgpetersenii haplotypes detected in human cases were clearly distinct from the lineage detected so far in the endemic bat species Mormopterus francoismoutoui, thus excluding a role for this volant mammal in the local human epidemiology of the disease.

CONCLUSIONS/SIGNIFICANCE

Our data confirm rats as a major reservoir of Leptospira on Reunion Island, but also pinpoint a possible role of dogs, cows and mice in the local epidemiology of human leptospirosis. This study shows that a comprehensive molecular characterization of pathogenic Leptospira in both clinical and animal samples helps to gaining insight into leptospirosis epidemiology within a specific environmental setting.

Malagasy bats shelter a considerable genetic diversity of pathogenic Leptospira suggesting notable host-specificity patterns

Pathogenic Leptospira are the causative agents of leptospirosis, a disease of global concern with major impact in tropical regions. Despite the importance of this zoonosis for human health, the evolutionary and ecological drivers shaping bacterial communities in host reservoirs remain poorly investigated. Here, we describe Leptospira communities hosted by Malagasy bats, composed of mostly endemic species, in order to characterize host-pathogen associations and investigate their evolutionary histories. We screened 947 individual bats (representing 31 species, 18 genera and seven families) for Leptospira infection and subsequently genotyped positive samples using three different bacterial loci. Molecular identification showed that these Leptospira are notably diverse and include several distinct lineages mostly belonging to Leptospira borgpetersenii and L. kirschneri. The exploration of the most probable host-pathogen evolutionary scenarios suggests that bacterial genetic diversity results from a combination of events related to the ecology and the evolutionary history of their hosts. Importantly, based on the data set presented herein, the notable host-specificity we have uncovered, together with a lack of geographical structuration of bacterial genetic diversity, indicates that the Leptospira community at a given site depends on the co-occurring bat species assemblage. The implications of such tight host-specificity on the epidemiology of leptospirosis are discussed.

An Unprecedented High Incidence of Leptospirosis in Futuna, South Pacific, 2004 - 2014, Evidenced by Retrospective Analysis of Surveillance Data

Futuna is a small Polynesian island in the South Pacific with a population of 3,612 in 2013. The first human leptospirosis case was confirmed in 1997. Active surveillance started in 2004. Cases were confirmed by PCR or real time PCR, or by serology using MAT or a combination of IgM-ELISA and MAT. A retrospective analysis of surveillance data shows that the disease was endemic with a mean annual incidence of 844 cases per 100,000 over an 11-year period from 2004 to 2014. An epidemic peak as high as 1,945 cases per 100,000 occurred in 2008. Serogroup Australis was predominant until 2007, Icterohaemorrhagiae was dominant afterwards. Cluster analysis revealed different hot spots over time. Lifestyle habits, such as walking barefoot in irrigated taro fields or pig pens probably contributed to contamination from the swine and rodent reservoirs to humans. Severe forms were rare, and the case fatality rate was 0.5%. The medical community and general population were aware of leptospirosis and rapid treatment with amoxycillin was the main treatment, probably contributing to this low fatality rate.

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.

Recent advances in canine leptospirosis: focus on vaccine development

Leptospirosis is a global infection of humans and animals caused by pathogenic Leptospira spp. Leptospirosis is a major zoonosis, with infection acquired from wild and domestic animals. It is also a significant cause of morbidity, mortality, and economic loss in production and companion animals. Leptospirosis in dogs is prevalent worldwide and as well as a cause of canine disease, it presents a zoonotic risk to human contacts. Canine leptospirosis does not differ greatly from the syndromes seen in other animal species, with hepatic, renal, and pulmonary involvement being the main manifestations. While the pathogenesis of disease is well documented at the whole animal level, the cellular and molecular basis remains obscure. Killed, whole-cell bacterin vaccines are licensed worldwide and have not changed greatly over the past several decades. Vaccine-induced immunity is restricted to serologically related serovars and is generally short-lived, necessitating annual revaccination. The appearance of new serovars as causes of canine leptospirosis requires constant epidemiological surveillance and tailoring of vaccines to cover emerging serovars. At the present time, there is no realistic prospect of alternative, non-bacterin vaccines in the foreseeable future.

Genotyping of Leptospira directly in urine samples of cattle demonstrates a diversity of species and strains in Brazil

The aim of this study was to identify Leptospira in urine samples of cattle by direct sequencing of the secY gene. The validity of this approach was assessed using ten Leptospira strains obtained from cattle in Brazil and 77 DNA samples previously extracted from cattle urine, that were positive by PCR for the genus-specific lipL32 gene of Leptospira. Direct sequencing identified 24 (31·1%) interpretable secY sequences and these were identical to those obtained from direct DNA sequencing of the urine samples from which they were recovered. Phylogenetic analyses identified four species: L. interrogans, L. borgpetersenii, L. noguchii, and L. santarosai with the most prevalent genotypes being associated with L. borgpetersenii. While direct sequencing cannot, as yet, replace culturing of leptospires, it is a valid additional tool for epidemiological studies. An unexpected finding from this study was the genetic diversity of Leptospira infecting Brazilian cattle.

A multilocus variable number tandem repeat analysis assay provides high discrimination for genotyping Leptospira santarosai strains

Considering the prevalence of Leptospira santarosai infections in the Americas and the scarce information about the species, we aimed to apply a multilocus variable number tandem repeat (VNTR) analysis (MLVA) for the molecular typing of L. santarosai isolates from various sources. Amplification of three VNTR loci selected from L. santarosai genome sequences resulted in a wide range of sizes for the amplified products amongst the 21 L. santarosai strains analysed. This suggested a variation in tandem repeat copy numbers in the VNTR loci. secY sequencing also showed a high nucleotide diversity, confirming the MLVA data. In conclusion, this novel MLVA provided a high level of discrimination between L. santarosai isolates, and this new typing tool could be used to investigate leptospirosis in regions where L. santarosai predominates.

Leptospirosis after a stay in Madagascar

We report a case of polymerase chain reaction (PCR)-confirmed leptospirosis in a patient who recently traveled to Madagascar, a country where only two cases have been reported since 1955. Although laboratory and clinical presentations were atypical and despite leptospirosis not being a documented disease in Madagascar, blood and urine tests for leptospirosis enabled retrospective confirmation of the diagnosis.

Leptospirosis in humans

Leptospirosis is a widespread and potentially fatal zoonosis that is endemic in many tropical regions and causes large epidemics after heavy rainfall and flooding. Infection results from direct or indirect exposure to infected reservoir host animals that carry the pathogen in their renal tubules and shed pathogenic leptospires in their urine. Although many wild and domestic animals can serve as reservoir hosts, the brown rat (Rattus norvegicus) is the most important source of human infections. Individuals living in urban slum environments characterized by inadequate sanitation and poor housing are at high risk of rat exposure and leptospirosis. The global burden of leptospirosis is expected to rise with demographic shifts that favor increases in the number of urban poor in tropical regions subject to worsening storms and urban flooding due to climate change. Data emerging from prospective surveillance studies suggest that most human leptospiral infections in endemic areas are mild or asymptomatic. Development of more severe outcomes likely depends on three factors: epidemiological conditions, host susceptibility, and pathogen virulence (Fig. 1). Mortality increases with age, particularly in patients older than 60 years of age. High levels of bacteremia are associated with poor clinical outcomes and, based on animal model and in vitro studies, are related in part to poor recognition of leptospiral LPS by human TLR4. Patients with severe leptospirosis experience a cytokine storm characterized by high levels of IL-6, TNF-alpha, and IL-10. Patients with the HLA DQ6 allele are at higher risk of disease, suggesting a role for lymphocyte stimulation by a leptospiral superantigen. Leptospirosis typically presents as a nonspecific, acute febrile illness characterized by fever, myalgia, and headache and may be confused with other entities such as influenza and dengue fever. Newer diagnostic methods facilitate early diagnosis and antibiotic treatment. Patients progressing to multisystem organ failure have widespread hematogenous dissemination of pathogens. Nonoliguric (high output) renal dysfunction should be supported with fluids and electrolytes. When oliguric renal failure occurs, prompt initiation of dialysis can be life saving. Elevated bilirubin levels are due to hepatocellular damage and disruption of intercellular junctions between hepatocytes, resulting in leaking of bilirubin out of bile caniliculi. Hemorrhagic complications are common and are associated with coagulation abnormalities. Severe pulmonary hemorrhage syndrome due to extensive alveolar hemorrhage has a fatality rate of >50 %. Readers are referred to earlier, excellent summaries related to this subject (Adler and de la Peña-Moctezuma 2010; Bharti et al. 2003; Hartskeerl et al. 2011; Ko et al. 2009; Levett 2001; McBride et al. 2005).

Animal leptospirosis

Leptospirosis is a global disease of animals, which can have a major economic impact on livestock industries and is an important zoonosis. The current knowledge base is heavily biased towards the developed agricultural economies. The disease situation in the developing economies presents a major challenge as humans and animals frequently live in close association. The severity of disease varies with the infecting serovar and the affected species, but there are many common aspects across the species; for example, the acute phase of infection is mostly sub-clinical and the greatest economic losses arise from chronic infection causing reproductive wastage. The principles of, and tests for, diagnosis, treatment, control and surveillance are applicable across the species.