Diversification of an emerging pathogen in a biodiversity hotspot: Leptospira in endemic small mammals of Madagascar

Genetic diversity of P1/pathogenic Leptospira species hosted by bats worldwide

INTRODUCTION

Bats are a diverse group of mammals that have unique features allowing them to act as reservoir hosts for several zoonotic pathogens such as Leptospira. Leptospires have been classified into pathogenic, intermediate, and saprophytic groups and more recently into clades P1, P2, S1, and S2, being all the most important pathogenic species related to leptospirosis included within the P1/pathogenic clade. Leptospira has been detected from bats in several regions worldwide; however, the diversity of leptospires harboured by bats is still unknown.

AIM

The aim of the present study was to determine the genetic diversity of Leptospira spp. harboured by bats worldwide.

METHODS

A systematic review was conducted on four databases to retrieve studies in which Leptospira was detected from bats. All studies were screened to retrieve all available Leptospira spp. 16S rRNA sequences from the GenBank database and data regarding their origin. Sequences obtained were compared with each other and reference sequences of Leptospira species and analysed through phylogenetic analysis.

RESULTS

A total of 418 Leptospira spp. 16S rRNA sequences isolated from 55 bat species from 14 countries were retrieved from 15 selected manuscripts. From these, 417 sequences clustered within the P1/pathogenic group, and only one sequence clustered within the P2/intermediate group. Six major clades of P1/pathogenic Leptospira spp. were identified, three of them composed exclusively of sequences obtained from bats.

CONCLUSION

We identified that bats harbour a great genetic diversity of Leptospira spp. that form part of the P1/pathogenic clade, some of which are closely related to leptospirosis-associated species. This finding contributes to the knowledge of the diversity of leptospires hosted by bats worldwide and reinforces the role of bats as reservoirs of P1/pathogenic Leptospira spp.

Ancestral African Bats Brought Their Cargo of Pathogenic Leptospira to Madagascar under Cover of Colonization Events

Madagascar is home to an extraordinary diversity of endemic mammals hosting several zoonotic pathogens. Although the African origin of Malagasy mammals has been addressed for a number of volant and terrestrial taxa, the origin of their hosted zoonotic pathogens is currently unknown. Using bats and Leptospira infections as a model system, we tested whether Malagasy mammal hosts acquired these infections on the island following colonization events, or alternatively brought these bacteria from continental Africa. We first described the genetic diversity of pathogenic Leptospira infecting bats from Mozambique and then tested through analyses of molecular variance (AMOVA) whether the genetic diversity of Leptospira hosted by bats from Mozambique, Madagascar and Comoros is structured by geography or by their host phylogeny. This study reveals a wide diversity of Leptospira lineages shed by bats from Mozambique. AMOVA strongly supports that the diversity of Leptospira sequences obtained from bats sampled in Mozambique, Madagascar, and Comoros is structured according to bat phylogeny. Presented data show that a number of Leptospira lineages detected in bat congeners from continental Africa and Madagascar are imbedded within monophyletic clades, strongly suggesting that bat colonists have indeed originally crossed the Mozambique Channel while infected with pathogenic Leptospira.

Pathogenic Leptospira Infections in Hubei Province, Central China

Leptospirosis is an important zoonosis that is caused by pathogenic Leptospira, which is considered to be a re-emerging infectious disease in many countries. Rodents are the most important reservoirs for both human and animal infection. An epidemiological survey of pathogenic Leptospira in rodents is important for the prevention and control of leptospirosis. In this study, a total of 964 rodents were captured from six cities in Hubei Province, and two pathogenic Leptospira species (L. interrogans and L. borgpetersenii) were detected using nested PCR with an overall prevalence of 4.8%. L. interrogans was distributed in five sampling sites, which may be the dominant species of pathogenic Leptospira in Hubei Province. In addition, Rattus norvegicus showed a relatively high infection rate, which may play an important role in the transmission and infection of pathogenic Leptospira. This study reveals the prevalence of pathogenic Leptospira in wild rodents in Hubei Province, suggesting that the risk of leptospirosis infection in Hubei Province still exists.

Co-Radiation of Leptospira and Tenrecidae (Afrotheria) on Madagascar

Leptospirosis is a bacterial zoonosis caused by pathogenic Leptospira that are maintained in the kidney lumen of infected animals acting as reservoirs and contaminating the environment via infected urine. The investigation of leptospirosis through a One Health framework has been stimulated by notable genetic diversity of pathogenic Leptospira combined with a high infection prevalence in certain animal reservoirs. Studies of Madagascar’s native mammal fauna have revealed a diversity of Leptospira with high levels of host-specificity. Native rodents, tenrecids, and bats shelter several distinct lineages and species of Leptospira, some of which have also been detected in acute human cases. Specifically, L. mayottensis, first discovered in humans on Mayotte, an island neighboring Madagascar, was subsequently identified in a few species of tenrecids on the latter island, which comprise an endemic family of small mammals. Distinct L. mayottensis lineages were identified in shrew tenrecs (Microgale cowani and Nesogale dobsoni) on Madagascar, and later in an introduced population of spiny tenrecs (Tenrec ecaudatus) on Mayotte. These findings suggest that L. mayottensis (i) has co-radiated with tenrecids on Madagascar, and (ii) has recently emerged in human populations on Mayotte following the introduction of T. ecaudatus from Madagascar. Hitherto, L. mayottensis has not been detected in spiny tenrecs on Madagascar. In the present study, we broaden the investigation of Malagasy tenrecids and test the emergence of L. mayottensis in humans as a result of the introduction of T. ecaudatus on Mayotte. We screened by PCR 55 tenrecid samples from Madagascar, including kidney tissues from 24 individual T. ecaudatus. We describe the presence of L. mayottensis in Malagasy T. ecaudatus in agreement with the aforementioned hypothesis, as well as in M. thomasi, a tenrecid species that has not been explored thus far for Leptospira carriage.

Original Leptospira spp. in island native terrestrial mammals: a case study in Pteropus spp. bats of New Caledonia

Leptospirosis is a bacterial zoonosis that occurs in tropical and subtropical regions worldwide. Chiroptera are known to be a formidable reservoir of zoonotic pathogens, including leptospires. The epidemiology of leptospirosis in bats in the Pacific Islands is poorly known, both in terms of prevalence and in terms of the bacterial strains involved. A strong host specificity between leptospiral strains and their mammalian reservoir is recognized. This phenomenon has notably been studied recently in bat communities, providing strong evidence of coevolution. In New Caledonia, a biodiversity hotspot where leptospirosis is endemic and enzootic, Chiroptera are the only indigenous terrestrial mammals. In this study, we aimed to investigate leptospires associated with three flying fox species in New Caledonia. Kidneys and urine samples of Pteropus spp. from captures and seizures were analyzed. Among 254 flying foxes analyzed, 24 harboured pathogenic leptospires corresponding to an observed prevalence of 9.45% with 15.8% on the Main Island and 4.3% on Loyalty Islands. The analysis of the rrs gene, lfb1, MLST sequences evidenced 4 distinct clusters of undescribed strains, likely corresponding to undescribed species. All four strains belong to the Group I of pathogenic Leptospira spp., which includes Leptospira interrogans, Leptospira noguchii and Leptospira kirschneri. We detected pathogenic leptospires in all 3 Pteropus spp. studied (including 2 endemic species) with no evidence of host specificity in two co-roosting species. For a better understanding of Leptospira-host coevolution, notably to genetically characterize and evaluate the virulence of these original bat-associated leptospires, it is essential to improve isolation techniques. Flying foxes are traditionally hunted and eaten in New Caledonia, a massive cause of bat-human interactions. Our results should encourage vigilance during these contacts to limit the spillover risk of these pathogens to humans. This article is protected by copyright. All rights reserved.

Serological and molecular characteristics of pathogenic Leptospira in rodent populations in Fujian Province, China, 2018-2020

Background

Leptospirosis is a significant emerging infectious disease worldwide. Rodents are considered to be the most critical hosts of Leptospira spp. Fujian Province is a region highly endemic for leptospirosis in China. However, the genetic diversity of leptospires circulating among rodents in Fujian is limited.

Results

The carrier status of rodents for Leptospira spp. was investigated by culture and serological detection in Fujian during 2018–2020. A total of 710 rodents, including 11 species, were trapped, with Rattus losea being the dominant trapped species (50.56%). Fourteen pathogenic Leptospira strains were obtained. Seven L. borgpetersenii serogroup Javanica strains belonging to ST143, 4 L. interrogans serogroup Icterohaemorrhagiae strains belonging to ST1 and ST17, 2 L. interrogans serogroup Bataviae strains belonging to ST96 and ST333, and 1 L. interrogans serogroup Pyrogenes strains belonging to ST332 were identified using 16S rDNA gene sequencing, microscopic agglutination test (MAT) and Multilocus sequence typing (MLST). L. borgpetersenii serogroup Javanica belonging to ST143 was the dominant type (50.00%). A total of 387 rodent serum samples were tested by MAT. Serum were considered positive for seroreactivity at a titer ≥ 1:160 against at least one serovar. A total of 90 (23.26%) serum samples tested positive, and four serogroups were identified, with Javanica being the dominant serogroup (87.78%), which was similar to the dominant serogroup isolated from rodents. This study demonstrates a high prevalence of leptospirosis in rodents and public health education among high-risk workers is highly recommended.

Conclusions

R. losea was the dominant trapped rodent, and L. borgpetersenii serogroup Javanica ST143 was widely distributed among rodents in Fujian from 2018 to 2020. Despite the low number of isolates obtained from rodents, this study suggests that continuous epidemiological surveillance of the aetiological characteristics of pathogenic Leptospira in wild animal reservoirs may help reduce the possible risk of disease transmission.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02566-2.

Gut microbiota of ring-tailed lemurs (Lemur catta) vary across natural and captive populations and correlate with environmental microbiota

BACKGROUND

Inter-population variation in host-associated microbiota reflects differences in the hosts' environments, but this characterization is typically based on studies comparing few populations. The diversity of natural habitats and captivity conditions occupied by any given host species has not been captured in these comparisons. Moreover, intraspecific variation in gut microbiota, generally attributed to diet, may also stem from differential acquisition of environmental microbes-an understudied mechanism by which host microbiomes are directly shaped by environmental microbes. To more comprehensively characterize gut microbiota in an ecologically flexible host, the ring-tailed lemur (Lemur catta; n = 209), while also investigating the role of environmental acquisition, we used 16S rRNA sequencing of lemur gut and soil microbiota sampled from up to 13 settings, eight in the wilderness of Madagascar and five in captivity in Madagascar or the U.S. Based on matched fecal and soil samples, we used microbial source tracking to examine covariation between the two types of consortia.

RESULTS

The diversity of lemur gut microbes varied markedly within and between settings. Microbial diversity was not consistently greater in wild than in captive lemurs, indicating that this metric is not necessarily an indicator of host habitat or environmental condition. Variation in microbial composition was inconsistent both with a single, representative gut community for wild conspecifics and with a universal 'signal of captivity' that homogenizes the gut consortia of captive animals. Despite the similar, commercial diets of captive lemurs on both continents, lemur gut microbiomes within Madagascar were compositionally most similar, suggesting that non-dietary factors govern some of the variability. In particular, soil microbial communities varied across geographic locations, with the few samples from different continents being the most distinct, and there was significant and context-specific covariation between gut and soil microbiota.

CONCLUSIONS

As one of the broadest, single-species investigations of primate microbiota, our study highlights that gut consortia are sensitive to multiple scales of environmental differences. This finding begs a reevaluation of the simple 'captive vs. wild' dichotomy. Beyond the important implications for animal care, health, and conservation, our finding that environmental acquisition may mediate aspects of host-associated consortia further expands the framework for how host-associated and environmental microbes interact across different microbial landscapes.

Molecular detection and characterization of pathogenic Leptospira species in bats (Chiroptera) roosting in human habitats in Nigeria, West Africa

Leptospirosis is a neglected zoonosis with a nearly global distribution. In order to determine the role of bats in the epidemiology of leptospirosis in Nigeria, a total of 231 bats belonging to three families, Pteropodidae (n = 117), Molossidae (n = 107) and Nycteridae (n = 17), roosting in human habitats were screened by PCR and sequencing for the detection of pathogenic Leptospira species. DNA extracted from the kidneys of bats were subjected to conventional PCR targeting the rrs1, rrs2, flaB and secY genes for the detection of pathogenic Leptospira spp. Overall, 27 out of the 231 (11.7%) of the samples screened were positive for Leptospira spp. High prevalence (>80%) of Leptospira spp. DNA was detected in Chaerophon and Nycteris bat species captures in an abandoned well located within a human habitation. Sequences generated in this study were highly identical to Leptospira borgpetersenii and Leptospira interrogans and clustered with sequences of pathogenic species in GenBank. The detection of pathogenic Leptospira spp. was significantly associated (p < .001) with the bat species, feeding habit, roosting site and study location. To the best of our knowledge, this is the first molecular detection and characterization of pathogenic Leptospira spp. in bats from Nigeria. Results show that bats in Nigeria are infected with diverse Leptospira genotypes phylogenetically related to known pathogenic, including zoonotic taxa. Together, these findings reinforce bats' roles as potential reservoirs of Leptospira spp. and should be considered as a starting point for future comparative studies to improve our understanding of the epidemiology of this bacterial pathogen in Nigeria.

Tracking Animal Reservoirs of Pathogenic Leptospira: The Right Test for the Right Claim

Leptospirosis is the most prevalent bacterial zoonosis worldwide and, in this context, has been extensively investigated through the One Health framework. Diagnosis of human leptospirosis includes molecular and serological tools, with the serological Microscopic Agglutination Test (MAT) still being considered as the gold standard. Mammals acting as reservoirs of the pathogen include species or populations that are able to maintain chronic infection and shed the bacteria via their urine into the environment. Animals infected by Leptospira are often identified using the same diagnosis tool as in humans, i.e., serological MAT. However, this tool may lead to misinterpretations as it can signal previous infection but does not provide accurate information regarding the capacity of animals to maintain chronic infection and, hence, participate in the transmission cycle. We employ in this paper previously published data and present original results on introduced and endemic small mammals from Indian Ocean islands to show that MAT should not be used for the identification of Leptospira reservoirs. By contrast, serological data are informative on the level of exposure of animals living in a specific environment. We present a sequential methodology to investigate human leptospirosis in the One Health framework that associates molecular detection in humans and animals, together with MAT of human samples using Leptospira isolates obtained from reservoir animals occurring in the same environment.

Molecular epidemiology of Leptospira spp. among wild mammals and a dog in Amami Oshima Island, Japan

Leptospirosis is a worldwide zoonosis caused by the pathogenic Leptospira spp. Canine and human leptospirosis sometimes occur on Amami Oshima Island, located in the Nansei Archipelago, southwestern Japan; however, information on the causative Leptospira spp. on this island is quite limited. This study aimed to investigate the molecular and serological characteristics of Leptospira spp. isolated from wild animals and a dog in Amami Oshima Island. We obtained seven Leptospira strains by culturing kidney tissues of wild animals, such as black rats (2), wild boars (3), and rabbit (1) as well as blood from a symptomatic dog. Using flaB sequencing and microscopic agglutination test with antisera for 18 serovars, the isolates were identified as Leptospira borgpetersenii serogroups Javanica (black rat), L. interrogans serogroup Australis (black rat and dog), and L. interrogans serogroup Hebdomadis (wild boar and rabbit). The sequence type (ST) of L. borgpetersenii serogroup Javanica was determined to be ST143 via multilocus sequence typing (MLST) using seven housekeeping genes. For L. interrogans, MLST and multiple-locus variable-tandem repeat analysis (MLVA) revealed identical ST and MLVA types in rat and canine isolates, whereas two STs and MLVA types were identified in wild boar isolates. The STs and MLVA types of rabbit and one of the wild boars were identical. Bacterial culture and flaB-nested polymerase chain reaction demonstrated a high rate of Leptospira infection in wild boars (58.3%, 7/12), whereas Leptospira spp. were detected in 4.8% of black rats (2/42). This study revealed diverse Leptospira genotype and serotype maintenance in wild mammals on Amami Oshima Island. MLST and MLVA indicated that black rats were a source of canine infection. Wild boars carry L. interrogans and are considered an important maintenance host because antibodies against serogroup Hebdomadis were detected in human and canine leptospirosis patients on this island.

Diversity, distribution, and drivers of Polychromophilus infection in Malagasy bats

Background

Numerous studies have been undertaken to advance knowledge of apicomplexan parasites infecting vertebrates, including humans. Of these parasites, the genus Plasmodium has been most extensively studied because of the socio-economic and public health impacts of malaria. In non-human vertebrates, studies on malaria or malaria-like parasite groups have been conducted but information is far from complete. In Madagascar, recent studies on bat blood parasites indicate that three chiropteran families (Miniopteridae, Rhinonycteridae, and Vespertilionidae) are infected by the genus Polychromophilus with pronounced host specificity: Miniopterus spp. (Miniopteridae) harbour Polychromophilus melanipherus and Myotis goudoti (Vespertilionidae) is infected by Polychromophilus murinus. However, most of the individuals analysed in previous studies were sampled on the western and central portions of the island. The aims of this study are (1) to add new information on bat blood parasites in eastern Madagascar, and (2) to highlight biotic and abiotic variables driving prevalence across the island.

Methods

Fieldworks were undertaken from 2014 to 2016 in four sites in the eastern portion of Madagascar to capture bats and collect biological samples. Morphological and molecular techniques were used to identify the presence of haemosporidian parasites. Further, a MaxEnt modelling was undertaken using data from Polychromophilus melanipherus to identify variables influencing the presence of this parasite

Results

In total, 222 individual bats belonging to 17 species and seven families were analysed. Polychromophilus infections were identified in two families: Miniopteridae and Vespertilionidae. Molecular data showed that Polychromophilus spp. parasitizing Malagasy bats form a monophyletic group composed of three distinct clades displaying marked host specificity. In addition to P. melanipherus and P. murinus, hosted by Miniopterus spp. and Myotis goudoti, respectively, a novel Polychromophilus lineage was identified from a single individual of Scotophilus robustus. Based on the present study and the literature, different biotic and abiotic factors are shown to influence Polychromophilus infection in bats, which are correlated based on MaxEnt modelling.

Conclusions

The present study improves current knowledge on Polychromophilus blood parasites infecting Malagasy bats and confirms the existence of a novel Polychromophilus lineage in Scotophilus bats. Additional studies are needed to obtain additional material of this novel lineage to resolve its taxonomic relationship with known members of the genus. Further, the transmission mode of Polychromophilus in bats as well as its potential effect on bat populations should be investigated to complement the results provided by MaxEnt modelling and eventually provide a comprehensive picture of the biology of host-parasite interactions.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12936-021-03696-0.

Preserve a Voucher Specimen! The Critical Need for Integrating Natural History Collections in Infectious Disease Studies

Despite being nearly 10 months into the COVID-19 (coronavirus disease 2019) pandemic, the definitive animal host for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the causal agent of COVID-19, remains unknown. Unfortunately, similar problems exist for other betacoronaviruses, and no vouchered specimens exist to corroborate host species identification for most of these pathogens. This most basic information is critical to the full understanding and mitigation of emerging zoonotic diseases. To overcome this hurdle, we recommend that host-pathogen researchers adopt vouchering practices and collaborate with natural history collections to permanently archive microbiological samples and host specimens. Vouchered specimens and associated samples provide both repeatability and extension to host-pathogen studies, and using them mobilizes a large workforce (i.e., biodiversity scientists) to assist in pandemic preparedness. We review several well-known examples that successfully integrate host-pathogen research with natural history collections (e.g., yellow fever, hantaviruses, helminths). However, vouchering remains an underutilized practice in such studies. Using an online survey, we assessed vouchering practices used by microbiologists (e.g., bacteriologists, parasitologists, virologists) in host-pathogen research. A much greater number of respondents permanently archive microbiological samples than archive host specimens, and less than half of respondents voucher host specimens from which microbiological samples were lethally collected. To foster collaborations between microbiologists and natural history collections, we provide recommendations for integrating vouchering techniques and archiving of microbiological samples into host-pathogen studies. This integrative approach exemplifies the premise underlying One Health initiatives, providing critical infrastructure for addressing related issues ranging from public health to global climate change and the biodiversity crisis.

Effects of land use, habitat characteristics, and small mammal community composition on Leptospira prevalence in northeast Madagascar

Human activities can increase or decrease risks of acquiring a zoonotic disease, notably by affecting the composition and abundance of hosts. This study investigated the links between land use and infectious disease risk in northeast Madagascar, where human subsistence activities and population growth are encroaching on native habitats and the associated biota. We collected new data on pathogenic Leptospira, which are bacteria maintained in small mammal reservoirs. Transmission can occur through close contact, but most frequently through indirect contact with water contaminated by the urine of infected hosts. The probability of infection and prevalence was compared across a gradient of natural moist evergreen forest, nearby forest fragments, flooded rice and other types of agricultural fields, and in homes in a rural village. Using these data, we tested specific hypotheses for how land use alters ecological communities and influences disease transmission. The relative abundance and proportion of exotic species was highest in the anthropogenic habitats, while the relative abundance of native species was highest in the forested habitats. Prevalence of Leptospira was significantly higher in introduced compared to endemic species. Lastly, the probability of infection with Leptospira was highest in introduced small mammal species, and lower in forest fragments compared to other habitat types. Our results highlight how human land use affects the small mammal community composition and in turn disease dynamics. Introduced species likely transmit Leptospira to native species where they co-occur, and may displace the Leptospira species naturally occurring in Madagascar. The frequent spatial overlap of people and introduced species likely also has consequences for public health.

Many neglected tropical diseases have reservoirs in wildlife. The effects of human activities on wildlife include changes in species abundance, community composition, and the transmission dynamics of parasites. Introduced species, especially black rats (Rattus rattus) are known to transmit zoonotic diseases among wildlife species and people. Leptospira, a water-borne bacterium that infects wildlife and people, is an important pathogen in the tropics, and in Madagascar, multiple strains and hosts have been identified. We tested how land use gradients in a forest-frontier agricultural system affect the composition of small mammal communities, and in turn the prevalence of Leptospira. We investigated 11 species of small mammals, including native rodents and tenrecs, as well as introduced rodents and shrews, in old growth forest, forest fragments, agricultural fields, and in a village. Leptospira prevalence and infection risk were highest in introduced species compared to native species and lower in forest fragments. The results highlight how the introduction of non-native species affects the variation in disease prevalence in small mammals, with potential consequences for spill-over to people.

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.

Molecular Detection and Typing of Pathogenic Leptospira in Febrile Patients and Phylogenetic Comparison with Leptospira Detected among Animals in Tanzania

Molecular data are required to improve our understanding of the epidemiology of leptospirosis in Africa and to identify sources of human infection. We applied molecular methods to identify the infecting Leptospira species and genotypes among patients hospitalized with fever in Tanzania and compared these with Leptospira genotypes detected among animals in Tanzania to infer potential sources of human infection. We performed lipL32 real-time PCR to detect the presence of pathogenic Leptospira in acute-phase plasma, serum, and urine samples obtained from study participants with serologically confirmed leptospirosis and participants who had died with febrile illness. Leptospira blood culture was also performed. In positive specimens, we performed species-specific PCR and compared participant Leptospira secY sequences with Leptospira reference sequences and sequences previously obtained from animals in Tanzania. We detected Leptospira DNA in four (3.6%) of 111 participant blood samples. We detected Leptospira borgpetersenii (one participant, 25.0%), Leptospira interrogans (one participant, 25.0%), and Leptospira kirschneri (one participant, 25.0%) (one [25%] undetermined). Phylogenetic comparison of secY sequence from the L. borgpetersenii and L. kirschneri genotypes detected from participants was closely related to but distinct from genotypes detected among local livestock species. Our results indicate that a diverse range of Leptospira species is causing human infection. Although our analysis suggests a close relationship between Leptospira genotypes found in people and livestock, continued efforts are needed to obtain more Leptospira genetic material from human leptospirosis cases to help prioritize Leptospira species and genotypes for control.

Genetic relatedness of Leptospira interrogans serogroup Autumnalis isolated from humans, dogs, and mice in Japan

OBJECTIVE

Leptospirosis is a zoonotic disease caused by pathogenic spirochetes of Leptospira spp., and peridomiciliary rodents are the most important reservoir animals for human infection. Dogs are known to be the reservoir animal of L. interrogans serovar Canicola, but the importance of dogs in zoonotic transmission of other Leptospira serotypes/genotypes remains unclear. This study reports the isolation of L. interrogans serogroup Autumnalis from two human patients in Japan and describes the genetic comparison between canine and mouse isolates using multiple-locus variable-number tandem repeat analysis (MLVA).

RESULTS

MLVA revealed that 8 out of the 11 loci compared were identical between the two human isolates. The human isolates clustered with the dog but not the mouse isolates. Moreover, the profile of one of the human isolates was identical to that of one of the dog isolates.

Serological evidence of Leptospira sp. in humans from Fernando de Noronha Island, Brazil

The prevalence of leptospirosis in humans is highly variable, being influenced by climatic factors, the presence of reservoirs, occupational exposure, recreational activity, and socioeconomic conditions. The objective of this study was to estimate the prevalence of Leptospira sp. and identify the predominant human serovars on the island of Fernando de Noronha, Brazil, based on a microscopic agglutination test. The prevalence of anti-Leptospira antibodies was 1.17% (4/341; I.C. 0.46%-2.98%), with the predominance of serovars Icterohaemorrhagiae, Javanica, Mini and Louisiana. This is the first study on the occurrence of antibodies against Leptospira sp. in humans in Fernando de Noronha and highlights the need to implement control and prevention strategies in this island environment.

Pathogenic Leptospira and their animal reservoirs: testing host specificity through experimental infection

Leptospirosis is caused by pathogenic Leptospira transmitted through contact with contaminated environments. Most mammalian species are infectable by Leptospira but only few act as efficient reservoir being capable of establishing long term kidney colonization and shedding Leptospira in urine. In Madagascar, a large diversity of pathogenic Leptospira display a tight specificity towards their endemic volant or terrestrial mammalian hosts. The basis of this specificity is unknown: it may indicate some genetically determined compatibility between host cells and bacteria or only reflect ecological constraints preventing contacts between specific hosts. In this study, Rattus norvegicus was experimentally infected with either Leptospira interrogans, Leptospira borgpetersenii or Leptospira mayottensis isolated from rats, bats or tenrecs, respectively. Leptospira borgpetersenii and L. mayottensis do not support renal colonization as featured by no shedding of live bacteria in urine and low level and sporadic detection of Leptospira DNA in kidneys. In contrast 2 out of the 7 R. norvegicus challenged with L. interrogans developed renal colonization and intense Leptospira shedding in urine throughout the 3 months of experimental infection. These data suggest that host-Leptospira specificity in this biodiversity hotspot is driven at least in part by genetic determinants likely resulting from long-term co-diversification processes.

Feral cats do not play a major role in leptospirosis epidemiology on Reunion Island

Although previous studies have reported Leptospira carriage in kidneys and urine of cats, the role of these animals in leptospirosis epidemiology remains poorly understood. Using molecular methods, we investigated Leptospira renal carriage in 172 feral cats from Reunion Island, an oceanic geographically isolated island located in the South West Indian Ocean. Only one out of the 172 analysed specimens tested positive for Leptospira DNA through quantitative real-time polymerase chain reaction. Using this positive sample, we could obtain sequences at three Leptospira loci (rrs2, lipL32 and lipL41) allowing to report for the first time Leptospira borgpetersenii naturally infecting cats. Comparisons with bacterial sequences from both acute human cases and animal reservoirs revealed similarities with Leptospira sequences previously reported on Reunion Island. However, the low prevalence (0.6%) reported herein does not support any major role of feral cats in leptospirosis epidemiology on Reunion Island, contrasting with results recently reported on another Indian Ocean Island, Christmas Island. The significance of these discrepancies is discussed.

Leptospiral shedding and seropositivity in shelter dogs in the Cumberland Gap Region of Southeastern Appalachia

BACKGROUND

Leptospirosis, caused by pathogenic Leptospira spp., is a zoonotic infection that affects humans, dogs and many other mammalian species. Virtually any mammalian species can act as asymptomatic reservoir, characterized by chronic renal carriage and shedding of a host-adapted leptospiral serovar. Environmental contamination by chronic shedders results in acquisition of infection by humans and susceptible animals.

METHODS

In this study, we investigated if clinically normal shelter dogs and cats harbor leptospires in their kidneys by screening urine samples for the presence of leptospiral DNA by a TaqMan based-quantitative PCR (qPCR) that targets pathogen-associated lipl32 gene. To identify the infecting leptospiral species, a fragment of leptospiral rpoB gene was PCR amplified and sequenced. Additionally, we measured Leptospira-specific serum antibodies using the microscopic agglutination test (MAT), a gold standard in leptospiral serology.

RESULTS

A total of 269 shelter animals (219 dogs and 50 cats) from seven shelters located in the tri-state area of western Virginia, eastern Tennessee, and southeastern Kentucky were included in this study. All cats tested negative by both qPCR and MAT. Of the 219 dogs tested in the study, 26/198 (13.1%, 95% CI: 8.4-17.8%) were positive for leptospiral DNA in urine by qPCR and 38/211 (18.0%, 95% CI: 12.8-23.2%) were seropositive by MAT. Twelve dogs were positive for both qPCR and MAT. Fourteen dogs were positive by qPCR but not by MAT. Additionally, leptospiral rpoB gene sequencing from a sub-set of qPCR-positive urine samples (n = 21) revealed L. interrogans to be the leptospiral species shed by dogs.

CONCLUSIONS

These findings have significant implications regarding animal and public health in the Cumberland Gap Region and possibly outside where these animals may be adopted.

High Prevalence of Leptospira spp. in Rodents in an Urban Setting in Madagascar

Leptospirosis is a neglected zoonotic bacterial disease caused by pathogenic Leptospira spp. Only limited studies have been conducted on the presence of Leptospira spp. in rats in Antananarivo, the capital city of Madagascar. We assessed Leptospira prevalence in small mammals in urban areas of Antananarivo where sanitation is inadequate and there is risk of flooding during the rainy season. We captured rodents and shrews at two sites and examined kidney samples from 114 animals using culture and a real-time polymerase chain reaction (PCR) assay specific to pathogenic Leptospira spp. We identified 23 positive samples containing Leptospira interrogans and Leptospira borgpetersenii, with a high prevalence in Rattus norvegicus (44.9%). Our results indicate that small mammals, in particular R. norvegicus, present a major public health risk for acquiring leptospirosis in Antananarivo.

Genetic diversity of pathogenic leptospires from wild, domestic and captive host species in Portugal

Leptospirosis is a neglected zoonotic disease of worldwide distribution with a significant veterinary and public health impact. It is caused by pathogenic bacteria of the genus Leptospira. The availability of effective tools to accurately identify and type leptospires is of utmost importance for the diagnosis of the disease and for assessing its epidemiology. Several multi-locus sequence typing (MLST) approaches were described for the typing of worldwide isolates of Leptospira but an extensive agreement towards the adoption of a unique consensus scheme for this agent is still lacking. Most genotyped strains originate from Asian and South American countries, with a minority originating from Europe (being most countries represented only by one or a few isolates). The knowledge of the diversity of circulating leptospires is the key to understanding the disease transmission and its zoonotic implications. In this study, we revisited the taxonomy of several isolates of pathogenic Leptospira obtained from domestic, wild and captive animals in Portugal, between 1990 and 2012. A selection of these isolates was genotyped using two previously published MLST schemes. A total of seven distinct sequence types (STs) were detected among the Portuguese isolates with two STs representing L. borgpetersenii (ST149 and ST152), two STs representing L. kirschneri (ST117 and ST100) and three STs representing L. interrogans (ST17, ST24 and ST140). Global widespread (and maybe more virulent) Leptospira genotypes seem to circulate in Portugal, particularly the L. interrogans ST17 isolates which are associated with several outbreaks of leptospirosis among humans and animals in different regions of the world. This study contributes to the enrichment of the global MLST databases with a new set of allele and sequence type information also providing novel data on circulating Leptospira serovars in Portugal.

Leptospira in livestock in Madagascar: uncultured strains, mixed infections and small mammal-livestock transmission highlight challenges in controlling and diagnosing leptospirosis in the developing world

In developing countries, estimates of the prevalence and diversity of Leptospira infections in livestock, an important but neglected zoonotic pathogen and cause of livestock productivity loss, are lacking. In Madagascar, abattoir sampling of cattle and pigs demonstrated a prevalence of infection of 20% in cattle and 5% in pigs by real-time PCR. In cattle, amplification and sequencing of the Leptospira-specific lfb1 gene revealed novel genotypes, mixed infections of two or more Leptospira species and evidence for potential transmission between small mammals and cattle. Sequencing of the secY gene demonstrated genetic similarities between Leptospira detected in Madagascar and, as yet, uncultured Leptospira strains identified in Tanzania, Reunion and Brazil. Detection of Leptospira DNA in the same animal was more likely in urine samples or pooled samples from four kidney lobes relative to samples collected from a single kidney lobe, suggesting an effect of sampling method on detection. In pigs, no molecular typing of positive samples was possible. Further research into the epidemiology of livestock leptospirosis in developing countries is needed to inform efforts to reduce human infections and to improve livestock productivity.

Pathogenic Leptospira in Commensal Small Mammals from the Extensively Urbanized Coastal Benin

Leptospirosis is caused by spirochete bacteria of the genus Leptospira that affect one million and kill 60,000 persons annually in the world, who get infected through environmental mammal-excreted (notably rodent) pathogens. Using qPCR and DNA sequencing approaches, we here examine Leptospira occurrence and diversity in 971 commensal small mammals in urban and peri-urban habitats from south Benin, where socio-environmental conditions are favorable for human contamination. Prevalence reached 12.9% on average, but showed very important variations in both space and time, thus pointing toward a role of local processes in the maintenance and circulation of rodent-borne leptospires in the area. Prevalence peaks may occur during or one month after moderate (100–200 mm) monthly rainfall, suggesting that rodent-borne leptospires may be more prevalent when standing waters are present, but not at their highest levels (i.e., floods). However, this pattern will have to be confirmed through proper diachronic analysis. Finally, an incomplete but significant host-specificity was observed, with L. kirschneri retrieved only in African shrews, and the invasive Rattus norvegicus and the native Mastomys natalensis preferentially infected by L. interrogans and L. borgpeterseni, respectively. Our study highlights the urgent need for investigations on human leptospirosis in the extensively urbanized Abidjan–Lagos corridor.

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.

Genetic characteristics of pathogenic Leptospira in wild small animals and livestock in Jiangxi Province, China, 2002-2015

Background

Leptospirosis is one of the most important neglected tropical bacterial diseases worldwide. However, there is limited information on the genetic diversity and host selectivity of pathogenic Leptospira in wild small mammal populations.

Methodology/Principal findings

Jiangxi Province, located in southern China, is a region highly endemic for leptospirosis. In this study, among a total of 3,531 trapped rodents dominated by Apodemus agrarius (59.7%), 330 Leptospira strains were successfully isolated from six different sites in Jiangxi between 2002 and 2015. Adding 71 local strains from humans, various kinds of livestock and wild animals in Jiangxi, a total of 401 epidemic strains were characterized using 16S rRNA gene senquencing, multilocus sequence typing (MLST) and the microscopic agglutination test (MAT). Among them, the most prevalent serogroup was Icterohaemorrhagiae (61.10%), followed by Javanica (19.20%) and Australis (9.73%); the remaining five serogroups, Canicola, Autumnalis, Grippotyphosa, Hebdomadis and Pomona, accounted for 9.97%. Species identification revealed that 325 were L. interrogans and 76 were L. borgpetersenii. Moreover, L. interrogans was the only pathogenic species in Fuliang and Shanggao and was predominant in Shangrao (95.0%); L. borgpetersenii was the most common in the remaining three sites. Twenty-one sequence types (STs) were identified. Similarly, ST1 and serogroup Icterohaemorrhagiae were most prevalent in Shangrao (86.0% and 86.4%) and Fuliang (90.4% and 90.4%), ST143 and serogroup Javanica in Shangyou (88.5% and 90.4%) and Longnan (73.1% and 73.1%), and ST105 and serogroup Australis in Shanggao (46.3% and 56.1%). Serogroup Icterohaemorhagiae primarily linked to A. agrarius (86.9%), serogroup Canicola to dogs (83.3%). There were significant differences in the distribution of leptospiral species/serogroups/STs prevalence across host species/collected locations among the 394 animal-associated strains (Fisher’s exact test, p<0.001).

Conclusions/Significance

Our study demonstrated high genetic diversity of pathogenic Leptospira strains from wild small animals in Jiangxi from 2002 to 2015. A. agrarius was the most abundantly trapped animal reservoir, and serogroup Icterohaemorrhagiae and ST1 were the most dominant in Jiangxi. Significant geographic variation and host diversity in the distribution of dominant species, STs and serogroups were observed. Moreover, rat-to-human transmission might play a crucial role in the circulation of Leptospirosis in Jiangxi. Details of the serological and molecular characteristics circulating in this region will be essential in implementing prevention and intervention measures to reduce the risk of disease transmission in China. However, phylogenetic analysis of more Leptospira isolates should explore the impact of ecological change on leptospirosis transmission dynamics and investigate how such new knowledge might better impact environmental monitoring for disease control and prevention at a public health level.

Leptospirosis, caused by pathogenic Leptospira spp, is one of the most widespread zoonoses. In recent years, human leptospirosis with occasionally fatal infections has been frequently reported in Jiangxi Province, a highly endemic region located in the south of China. However, there is a lack of information on circulating Leptospira strains in this province. To identify the etiological characteristics, 401 Leptospira from Jiangxi were characterized using serological and molecular typing methods. Serological typing revealed that 61.10% of the isolates belonged to serogroup Icterohaemorrhagiae. Two species, L. interrogans and L. borgpetersenii, were identified using 16S rRNA gene sequencing. A. agrarius may be the main carrier of leptospirosis in this endemic region. Furthermore, the diversity of leptospiral isolates was demonstrated using MLST analysis. ST1, as the most prevalent ST of pathogenic leptospires, was widely dispersed in China. Significant geographic variation and host diversity in the distribution of dominant species, serogroups and STs were found in Jiangxi. This study is the first to demonstrate the distribution of Leptospira in domestic and wildlife animals in Jiangxi. This retrospective study represents the longest and largest field epidemiological investigation on the etiological characteristics and genetic diversity of pathogenic Leptospira among large wild animal reservoirs and human populations in Jiangxi. A better understanding of the circulating etiological agents and epidemiology of leptospirosis will provide a good starting point for efforts to control and prevent this disease.

Systematic Review of Important Bacterial Zoonoses in Africa in the Last Decade in Light of the 'One Health' Concept

Zoonoses present a major public health threat and are estimated to account for a substantial part of the infectious disease burden in low-income countries. The severity of zoonotic diseases is compounded by factors such as poverty, living in close contact with livestock and wildlife, immunosuppression as well as coinfection with other diseases. The interconnections between humans, animals and the environment are essential to understand the spread and subsequent containment of zoonoses. We searched three scientific databases for articles relevant to the epidemiology of bacterial zoonoses/zoonotic bacterial pathogens, including disease prevalence and control measures in humans and multiple animal species, in various African countries within the period from 2008 to 2018. The review identified 1966 articles, of which 58 studies in 29 countries met the quality criteria for data extraction. The prevalence of brucellosis, leptospirosis, Q fever ranged from 0–40%, 1.1–24% and 0.9–28.2%, respectively, depending on geographical location and even higher in suspected outbreak cases. Risk factors for human zoonotic infection included exposure to livestock and animal slaughters. Dietary factors linked with seropositivity were found to include consumption of raw milk and locally fermented milk products. It was found that zoonoses such as leptospirosis, brucellosis, Q fever and rickettsiosis among others are frequently under/misdiagnosed in febrile patients seeking treatment at healthcare centres, leading to overdiagnoses of more familiar febrile conditions such as malaria and typhoid fever. The interactions at the human–animal interface contribute substantially to zoonotic infections. Seroprevalence of the various zoonoses varies by geographic location and species. There is a need to build laboratory capacity and effective surveillance processes for timely and effective detection and control of zoonoses in Africa. A multifaceted ‘One Health’ approach to tackle zoonoses is critical in the fight against zoonotic diseases. The impacts of zoonoses include: (1) Humans are always in contact with animals including livestock and zoonoses are causing serious life-threatening infections in humans. Almost 75% of the recent major global disease outbreaks have a zoonotic origin. (2) Zoonoses are a global health challenge represented either by well-known or newly emerging zoonotic diseases. (3) Zoonoses are caused by all-known cellular (bacteria, fungi and parasites) and noncellular (viruses or prions) pathogens. (4) There are limited data on zoonotic diseases from Africa. The fact that human health and animal health are inextricably linked, global coordinated and well-established interdisciplinary research efforts are essential to successfully fight and reduce the health burden due to zoonoses. This critically requires integrated data from both humans and animals on zoonotic diseases.

Mixed Leptospira Infections in a Diverse Reservoir Host Community, Madagascar, 2013-2015

We identified mixed infections of pathogenic Leptospira in small mammals across a landscape-scale study area in Madagascar by using primers targeting different Leptospira spp. Using targeted primers increased prevalence estimates and evidence for transmission between endemic and invasive hosts. Future studies should assess rodentborne transmission of Leptospira to humans.

Epidemiology of Leptospira infection in livestock species in Saint Kitts

This pilot study describes the prevalence of Leptospira infection and exposure in livestock species, cattle, pig, sheep, and goats in Saint Kitts in the Caribbean region. Serum and kidney samples were collected from cattle, pigs, sheep, and goats at a local abattoir between September 2016 and March 2017. Cattle had the highest seroprevalence (79.8%) followed by pigs (64.8%), sheep (39.4%), and goats (24.8%). Highest seroprevalence was observed to serovars, Mankarso in cattle, Bratislava in pigs, Hardjo in sheep, and goats. Leptospira DNA was amplified from kidney samples of 18/99 cattle (18.2%), 11/106 pigs (10.4%), 4/106 sheep (3.8%), and 2/105 goats (1.9%). Our findings warrant further studies to assess leptospirosis associated economic burden to subsistence farmers and public health impact.

Three Leptospira Strains From Western Indian Ocean Wildlife Show Highly Distinct Virulence Phenotypes Through Hamster Experimental Infection

Leptospirosis is one of the most widespread zoonoses worldwide, with highest incidence reported on tropical islands. Recent investigations carried out in a One-Health framework have revealed a wide diversity of pathogenic Leptospira lineages on the different islands of Western Indian Ocean carried out by a large diversity of mammal reservoirs, including domestic and wild fauna. Using golden Syrian hamsters as a model of acute infection, we studied the virulence of Leptospira interrogans, L. mayottensis, and L. borgpetersenii isolates obtained from rats, tenrecs, and bats, respectively. Hamsters were inoculated with 2.10⁸ bacterial cells and monitored for 1 month. The L. interrogans isolate proved to be the most pathogenic while L. mayottensis and L. borgpetersenii isolates induced no clinical symptoms in the infected hamsters. High leptospiral DNA amounts were also detected in the urine and organs of hamsters infected with the L. interrogans isolate while L. mayottensis and L. borgpetersenii isolates mostly failed to disseminate into the organism. In addition, histological damage was more pronounced in the kidneys and lungs of hamsters infected with the L. interrogans isolate. Altogether, these data support that Leptospira strains shed by mammals endemic to this insular ecosystem (L. mayottensis and L. borgpetersenii isolates) are less pathogenic than the L. interrogans rat-borne isolate. These results may provide a relevant framework for understanding the contrasting epidemiology of human leptospirosis observed among Western Indian Ocean islands.

Circulating Leptospira species identified in cattle of the Brazilian Amazon

The present study aimed to detect the most prevalent serogroups and circulating Leptospira species in cows from Brazilian Amazon. Samples of blood serum, urine and kidney of 208 animals were collected at a municipal slaughterhouse in the Baixo Tocantins region of Pará State, Northern Brazil. The tests used were microscopic agglutination test (MAT), bacteriological isolation, polymerase chain reaction (PCR) and DNA sequencing. The frequency of MAT-reactive cows was 46.6% (97/208) with titers ranging from 100 to 3200, being Sejroe serogroup the most prevalent. There was no Leptospira isolation, but the DNA of bacterium was detected in 5.8% (12/208) of the kidney and in 14.9% (31/208) of the urine samples. DNA sequencing was performed directly from PCR products of 30 samples (3 kidneys and 27 urines), with identification of four different species: L. borgpetersenii with 56.7% (17/30), followed by L. kirschneri with 13.3% (4/30), L. interrogans with 6.7% (2/30), L. santarosai with 3.3% (1/30), and 20.0% (6/30) of samples were identified only at the genus level. These results reveal a diversity and peculiarity for bovine leptospirosis in the Amazon region, mainly due to the low frequency of L. santarosai and more surprising, the presence of L. kirschneri, differently of what is observed in other regions of Brazil.

Phylogeography of freshwater planorbid snails reveals diversification patterns in Eurasian continental islands

Background

Islands have traditionally been the centre of evolutionary biological research, but the dynamics of immigration and differentiation at continental islands have not been well studied. Therefore, we focused on the Japanese archipelago, the continental islands located at the eastern end of the Eurasian continent. While the Japanese archipelago is characterised by high biodiversity and rich freshwater habitats, the origin and formation mechanisms of its freshwater organisms are not clear. In order to clarify the history of the planorbid gastropod fauna, we conducted phylogenetic analysis, divergence time estimation, ancestral state reconstruction, and lineage diversity estimations.

Results

Our analyses revealed the formation process of the planorbid fauna in the Japanese archipelago. Most lineages in the Japanese archipelago have closely related lineages on the continent, and the divergence within the Japanese lineages presumably occurred after the late Pliocene. In addition, each lineage is characterised by different phylogeographical patterns, suggesting that immigration routes from the continent to the Japanese archipelago differ among lineages. Furthermore, a regional lineage diversity plot showed that the present diversity in the Japanese archipelago potentially reflects the differentiation of lineages within the islands after the development of the Japanese archipelago.

Conclusions

Although additional taxon sampling and genetic analysis focused on each lineage are needed, our results suggest that immigration from multiple routes just prior to the development of the Japanese archipelago and subsequent diversification within the islands are major causes of the present-day diversity of the Japanese planorbid fauna.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1273-3) contains supplementary material, which is available to authorized users.

Complete Genome Sequences of Three Leptospira mayottensis Strains from Tenrecs That Are Endemic in the Malagasy Region

Leptospirosis is a zoonosis caused by Leptospira, a diversified genus containing more than 10 pathogenic species. Tenrecs are small terrestrial mammals endemic in the Malagasy region and are known to be reservoirs of the recently described species Leptospira mayottensis.

Leptospirosis is a zoonosis caused by Leptospira, a diversified genus containing more than 10 pathogenic species. Tenrecs are small terrestrial mammals endemic in the Malagasy region and are known to be reservoirs of the recently described species Leptospira mayottensis. We report the complete genome sequences of three L. mayottensis strains isolated from two tenrec species.

Assessment of animal hosts of pathogenic Leptospira in northern Tanzania

Leptospirosis is a zoonotic bacterial disease that affects more than one million people worldwide each year. Human infection is acquired through direct or indirect contact with the urine of an infected animal. A wide range of animals including rodents and livestock may shed Leptospira bacteria and act as a source of infection for people. In the Kilimanjaro Region of northern Tanzania, leptospirosis is an important cause of acute febrile illness, yet relatively little is known about animal hosts of Leptospira infection in this area. The roles of rodents and ruminant livestock in the epidemiology of leptospirosis were evaluated through two linked studies. A cross-sectional study of peri-domestic rodents performed in two districts with a high reported incidence of human leptospirosis found no evidence of Leptospira infection among rodent species trapped in and around randomly selected households. In contrast, pathogenic Leptospira infection was detected in 7.08% cattle (n = 452 [5.1-9.8%]), 1.20% goats (n = 167 [0.3-4.3%]) and 1.12% sheep (n = 89 [0.1-60.0%]) sampled in local slaughterhouses. Four Leptospira genotypes were detected in livestock. Two distinct clades of L. borgpetersenii were identified in cattle as well as a clade of novel secY sequences that showed only 95% identity to known Leptospira sequences. Identical L. kirschneri sequences were obtained from qPCR-positive kidney samples from cattle, sheep and goats. These results indicate that ruminant livestock are important hosts of Leptospira in northern Tanzania. Infected livestock may act as a source of Leptospira infection for people. Additional work is needed to understand the role of livestock in the maintenance and transmission of Leptospira infection in this region and to examine linkages between human and livestock infections.

Biogeography of Leptospira in wild animal communities inhabiting the insular ecosystem of the western Indian Ocean islands and neighboring Africa

Understanding the processes driving parasite assemblages is particularly important in the context of zoonotic infectious diseases. Leptospirosis is a widespread zoonotic bacterial infection caused by pathogenic species of the genus Leptospira. Despite a wide range of animal hosts, information is still lacking on the factors shaping Leptospira diversity in wild animal communities, especially in regions, such as tropical insular ecosystems, with high host species richness and complex biogeographical patterns. Using a large dataset (34 mammal species) and a multilocus approach at a regional scale, we analyzed the role of both host species diversity and geography in Leptospira genetic diversity in terrestrial small mammals (rodents, tenrecs, and shrews) and bats from 10 different islands/countries in the western Indian Ocean (WIO) and neighboring Africa. At least four Leptospira spp. (L. interrogans, L. borgpetersenii, L. kirschneri, and L. mayottensis) and several yet-unidentified genetic clades contributed to a remarkable regional Leptospira diversity, which was generally related to the local occurrence of the host species rather than the geography. In addition, the genetic structure patterns varied between Leptospira spp., suggesting different evolutionary histories in the region, which might reflect both in situ diversification of native mammals (for L. borgpetersenii) and the more recent introduction of non-native host species (for L. interrogans). Our data also suggested that host shifts occurred between bats and rodents, but further investigations are needed to determine how host ecology may influence these events.

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.

Detection of pathogenic Leptospira species associated with phyllostomid bats (Mammalia: Chiroptera) from Veracruz, Mexico

The genus Leptospira encompass 22 species of spirochaetes, with ten pathogenic species that have been recorded in more than 160 mammals worldwide. In the last two decades, the numbers of records of these agents associated with bats have increased exponentially, particularly in America. Although order Chiroptera represents the second most diverse order of mammals in Mexico, and leptospirosis represents a human and veterinary problem in the country, few studies have been conducted to identify potential wildlife reservoirs. The aim of this study was to detect the presence and diversity of Leptospira sp. in communities of bats in an endemic state of leptospirosis in Mexico. During January to September 2016, 81 bats of ten species from three localities of Veracruz, Mexico, were collected with mist nets. Kidney samples were obtained from all specimens. For the detection of Leptospira sp., we amplified several genes using specific primers. Amplicons of the expected size were submitted to sequencing, and sequences recovered were compared with those of reference deposited in GenBank using the BLAST tool. To identify their phylogenetic position, we realized a reconstruction using maximum-likelihood (ML) method. Twenty-five samples from three bat species (Artibeus lituratus, Choeroniscus godmani and Desmodus rotundus) showed the presence of Leptospira DNA. Sequences recovered were close to Leptospira noguchii, Leptospira weilii and Leptospira interrogans. Our results include the first record of Leptospira in bats from Mexico and exhibit a high diversity of these pathogens circulating in the state. Due to the finding of a large number of positive wild animals, it is necessary to implement a surveillance system in populations of the positive bats as well as in related species, in order to understand their role as carriers of this bacterial genus.

Deciphering the unexplored Leptospira diversity from soils uncovers genomic evolution to virulence

Despite recent advances in our understanding of the genomics of members of the genus Leptospira, little is known on how virulence has emerged in this heterogeneous bacterial genus as well as on the lifestyle of pathogenic members of the genus Leptospira outside animal hosts. Here, we isolated 12 novel species of the genus Leptospira from tropical soils, significantly increasing the number of known species to 35 and finding evidence of highly unexplored biodiversity in the genus. Extended comparative phylogenomics and pan-genome analyses at the genus level by incorporating 26 novel genomes, revealed that, the traditional leptospiral ‘pathogens’ cluster, as defined by their phylogenetic position, can be split in two groups with distinct virulence potential and accessory gene patterns. These genomic distinctions are strongly linked to the ability to cause or not severe infections in animal models and humans. Our results not only provide new insights into virulence evolution in the members of the genus Leptospira, but also lay the foundations for refining the classification of the pathogenic species.

Presence of Borrelia spp. DNA in ticks, but absence of Borrelia spp. and of Leptospira spp. DNA in blood of fever patients in Madagascar

The occurrence of tick-borne relapsing fever and leptospirosis in humans in Madagascar remains unclear despite the presence of their potential vectors and reservoir hosts. We screened 255 Amblyomma variegatum ticks and 148 Rhipicephalus microplus ticks from Zebu cattle in Madagascar for Borrelia-specific DNA. Borrelia spp. DNA was detected in 21 Amblyomma variegatum ticks and 2 Rhipicephalus microplus ticks. One Borrelia found in one Rhipicephalus microplus showed close relationship to Borrelia theileri based on genetic distance and phylogenetic analyses on 16S rRNA and flaB sequences. The borreliae from Amblyomma variegatum could not be identified due to very low quantities of present DNA reflected by high cycle threshold values in real-time-PCR. It is uncertain whether these low numbers of Borrelia spp. are sufficient for transmission of infection from ticks to humans. In order to determine whether spirochaete infections are relevant in humans, blood samples of 1009 patients from the highlands of Madagascar with fever of unknown origin were screened for Borrelia spp. - and in addition for Leptospira spp. - by real-time PCR. No target DNA was detected, indicating a limited relevance of these pathogens for humans in the highlands of Madagascar.

Renal carriage of Leptospira species in rodents from Mediterranean Chile: The Norway rat (Rattus norvegicus) as a relevant host in agricultural lands

We evaluated the renal carriage of Leptospira species in rodent communities from Mediterranean Chile using a PCR technique. We found that animals inhabiting agricultural areas were almost three times more infected than in wild areas (14.4% vs. 4.4%). The Norwegian rat (Rattus norvegicus), an invasive murid ubiquitous in the country, was the most infected species (38.1%).

Human leptospirosis in Seychelles: A prospective study confirms the heavy burden of the disease but suggests that rats are not the main reservoir

Background

Leptospirosis is a bacterial zoonosis caused by pathogenic Leptospira for which rats are considered as the main reservoir. Disease incidence is higher in tropical countries, especially in insular ecosystems. Our objectives were to determine the current burden of leptospirosis in Seychelles, a country ranking first worldwide according to historical data, to establish epidemiological links between animal reservoirs and human disease, and to identify drivers of transmission.

Methods

A total of 223 patients with acute febrile symptoms of unknown origin were enrolled in a 12-months prospective study and tested for leptospirosis through real-time PCR, IgM ELISA and MAT. In addition, 739 rats trapped throughout the main island were investigated for Leptospira renal carriage. All molecularly confirmed positive samples were further genotyped.

Results

A total of 51 patients fulfilled the biological criteria of acute leptospirosis, corresponding to an annual incidence of 54.6 (95% CI 40.7–71.8) per 100,000 inhabitants. Leptospira carriage in Rattus spp. was overall low (7.7%) but dramatically higher in Rattus norvegicus (52.9%) than in Rattus rattus (4.4%). Leptospira interrogans was the only detected species in both humans and rats, and was represented by three distinct Sequence Types (STs). Two were novel STs identified in two thirds of acute human cases while noteworthily absent from rats.

Conclusions

This study shows that human leptospirosis still represents a heavy disease burden in Seychelles. Genotype data suggests that rats are actually not the main reservoir for human disease. We highlight a rather limited efficacy of preventive measures so far implemented in Seychelles. This could result from ineffective control measures of excreting animal populations, possibly due to a misidentification of the main contaminating reservoir(s). Altogether, presented data stimulate the exploration of alternative reservoir animal hosts.

Leptospirosis is an emerging environmental infectious disease caused by corkscrew shaped bacteria called Leptospira. Humans usually get infected during recreational or work-related outdoor activities through contact with urine excreted by animal reservoirs. As a zoonotic disease, leptospirosis is a good example of the One Health concept for it links humans, animals and ecosystems in a web of pathogen maintenance and transmission. This zoonosis is highly prevalent in the tropics and especially in tropical islands. Seychelles archipelago has been reported as the country with highest human incidence worldwide, although figures are based on dated studies and/or poorly specific tests. The presented investigation aimed at providing an updated information on human leptospirosis burden in Seychelles and exploring the transmission chains in their environmental aspects. Presented data confirms that the disease still heavily impacts the country. Genotyping of pathogenic Leptospira in human acute cases reveals that three distinct Sequence Types (STs) are involved in the disease. However, rats typically considered as the main reservoir in Seychelles, harbor only one of these STs, found only in a minority of human cases. Hence, it appears that rats are likely not the main reservoir of leptospirosis in Seychelles, which has important consequences in terms of preventive measures to be implemented for a better control of human leptospirosis.

Evidence of infection with Leptospira interrogans and spotted fever group rickettsiae among rodents in an urban area of Osaka City, Japan

We examined 33 rodents captured in an urban area of Osaka City, Japan for IgG antibodies against Seoul virus, severe fever with thrombocytopenia syndrome virus, hepatitis E virus, Leptospira interrogans, Yersinia pestis, spotted fever, typhus and scrub typhus group rickettsiae. We found that 3 (9.1%) and 1 (3.0%) of the 33 rodents had antibodies against L. interrogans and spotted fever group rickettsiae, respectively. DNAs of leptospires were detected from 2 of the 3 seropositive rodents, but DNA of rickettsia was not detected. Phylogenetic analysis and multiple locus sequence typing revealed that the 2 leptospires were L. interrogans belonging to a novel sequence type. There is a potential risk for acquiring rodent-borne zoonotic pathogens even in cities in developed countries.

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.

Comparison of the Estimated Incidence of Acute Leptospirosis in the Kilimanjaro Region of Tanzania between 2007-08 and 2012-14

Background

The sole report of annual leptospirosis incidence in continental Africa of 75–102 cases per 100,000 population is from a study performed in August 2007 through September 2008 in the Kilimanjaro Region of Tanzania. To evaluate the stability of this estimate over time, we estimated the incidence of acute leptospirosis in Kilimanjaro Region, northern Tanzania for the time period 2012–2014.

Methodology and Principal Findings

Leptospirosis cases were identified among febrile patients at two sentinel hospitals in the Kilimanjaro Region. Leptospirosis was diagnosed by serum microscopic agglutination testing using a panel of 20 Leptospira serovars belonging to 17 separate serogroups. Serum was taken at enrolment and patients were asked to return 4–6 weeks later to provide convalescent serum. Confirmed cases required a 4-fold rise in titre and probable cases required a single titre of ≥800. Findings from a healthcare utilisation survey were used to estimate multipliers to adjust for cases not seen at sentinel hospitals. We identified 19 (1.7%) confirmed or probable cases among 1,115 patients who presented with a febrile illness. Of cases, the predominant reactive serogroups were Australis 8 (42.1%), Sejroe 3 (15.8%), Grippotyphosa 2 (10.5%), Icterohaemorrhagiae 2 (10.5%), Pyrogenes 2 (10.5%), Djasiman 1 (5.3%), Tarassovi 1 (5.3%). We estimated that the annual incidence of leptospirosis was 11–18 cases per 100,000 population. This was a significantly lower incidence than 2007–08 (p<0.001).

Conclusions

We estimated a much lower incidence of acute leptospirosis than previously, with a notable absence of cases due to the previously predominant serogroup Mini. Our findings indicate a dynamic epidemiology of leptospirosis in this area and highlight the value of multi-year surveillance to understand leptospirosis epidemiology.

Leptospirosis is an infectious disease that causes a fever. It can be severe or fatal. Understanding how many people get leptospirosis helps to determine priorities in allocating resources for disease diagnosis, treatment, and prevention. There are few data about leptospirosis incidence in sub-Saharan African countries. The only mainland estimate is from northern Tanzania for the years 2007–08. To see if leptospirosis incidence had changed since 2007–08, we measured leptospirosis incidence in the same location in 2012–2014. To do this, we systematically approached people at two hospitals in the Kilimanjaro Region and tested them for leptospirosis. We adjusted the number of identified cases of leptospirosis found at the hospitals to account for people with fever who did not come to hospital for testing and care. We also adjusted for imperfect testing methods. We found that the number of people who developed leptospirosis annually had dropped from 75–102 cases per 100,000 people during 2007–08 to 11–18 cases per 100,000 people during 2012–14. Also, the subtype of leptospirosis responsible for the most cases during 2007–08 was not present during 2012–14. The number of people developing leptospirosis was not stable, highlighting the value of measuring how commonly leptospirosis occurs over several years.

Molecular epidemiology of pathogenic Leptospira spp. among large ruminants in the Philippines

The extent of Leptospira infection in large ruminants resulting to economic problems in livestock industry in a leptospirosis-endemic country like the Philippines has not been extensively explored. Therefore, we determined the prevalence and carrier status of leptospirosis in large ruminants using molecular techniques and assessed the risk factors of acquiring leptospirosis in these animals. Water buffalo and cattle urine samples (n=831) collected from 21 farms during 2013-2015 were subjected to flaB-nested PCR to detect pathogenic Leptospira spp. Leptospiral flaB was detected in both species with a detection rate of 16.1%. Leptospiral DNA was detected only in samples from animals managed in communal farms. Sequence analysis of Leptospira flaB in large ruminants revealed the formation of three major clusters with L. borgpetersenii or L. kirschneri. One farm contained Leptospira flaB sequences from all clusters identified in this study, suggesting this farm was the main source of leptospires for other farms. This study suggested that these large ruminants are infected with various pathogenic Leptospira species causing possible major economic loss in the livestock industry as well as potential Leptospira reservoirs that can transmit infection to humans and other animals in the Philippines.

Identification of Tenrec ecaudatus, a Wild Mammal Introduced to Mayotte Island, as a Reservoir of the Newly Identified Human Pathogenic Leptospira mayottensis

Leptospirosis is a bacterial zoonosis of major concern on tropical islands. Human populations on western Indian Ocean islands are strongly affected by the disease although each archipelago shows contrasting epidemiology. For instance, Mayotte, part of the Comoros Archipelago, differs from the other neighbouring islands by a high diversity of Leptospira species infecting humans that includes Leptospira mayottensis, a species thought to be unique to this island. Using bacterial culture, molecular detection and typing, the present study explored the wild and domestic local mammalian fauna for renal carriage of leptospires and addressed the genetic relationships of the infecting strains with local isolates obtained from acute human cases and with Leptospira strains hosted by mammal species endemic to nearby Madagascar. Tenrec (Tenrec ecaudatus, Family Tenrecidae), a terrestrial mammal introduced from Madagascar, is identified as a reservoir of L. mayottensis. All isolated L. mayottensis sequence types form a monophyletic clade that includes Leptospira strains infecting humans and tenrecs on Mayotte, as well as two other Malagasy endemic tenrecid species of the genus Microgale. The lower diversity of L. mayottensis in tenrecs from Mayotte, compared to that occurring in Madagascar, suggests that L. mayottensis has indeed a Malagasy origin. This study also showed that introduced rats (Rattus rattus) and dogs are probably the main reservoirs of Leptospira borgpetersenii and Leptospira kirschneri, both bacteria being prevalent in local clinical cases. Data emphasize the epidemiological link between the two neighbouring islands and the role of introduced small mammals in shaping the local epidemiology of leptospirosis.

Islands are exceptionally prone to species introduction, including pathogens with detrimental public health consequences for which the invasive alien species could act as reservoirs. Our study shows how the local non-native mammal fauna of Mayotte Island is associated with the introduction and epidemiology of human leptospirosis, a zoonosis strongly affecting tropical islands. Data presented herein identify Tenrec ecaudatus (Family Tenrecidae), an omnivorous species introduced from neighbouring Madagascar, as a reservoir of the recently named Leptospira mayottensis. Further, we suggest a Malagasy origin of L. mayottensis, which occurs naturally within the Tenrecidae radiation endemic to Madagascar. Finally, we provide evidence that dogs and rats are reservoirs for other Leptospira lineages of medical importance on Mayotte. Altogether, our study highlights the impact of species introduction on human health and further suggests that the biogeography of microorganisms in insular ecosystems, including pathogenic endemic lineages, should be considered from evolutionary and medical perspectives.

Serological Evidence of Lyssaviruses among Bats on Southwestern Indian Ocean Islands

We provide serological evidence of lyssavirus circulation among bats on southwestern Indian Ocean (SWIO) islands. A total of 572 bats belonging to 22 species were collected on Anjouan, Mayotte, La Réunion, Mauritius, Mahé and Madagascar and screened by the Rapid Fluorescent Focus Inhibition Test for the presence of neutralising antibodies against the two main rabies related lyssaviruses circulating on the African continent: Duvenhage lyssavirus (DUVV) and Lagos bat lyssavirus (LBV), representing phylogroups I and II, respectively. A total of 97 and 42 sera were able to neutralise DUVV and LBV, respectively. No serum neutralised both DUVV and LBV but most DUVV-seropositive bats (n = 32/220) also neutralised European bat lyssavirus 1 (EBLV-1) but not Rabies lyssavirus (RABV), the prototypic lyssavirus of phylogroup I. These results highlight that lyssaviruses belonging to phylogroups I and II circulate in regional bat populations and that the putative phylogroup I lyssavirus is antigenically closer to DUVV and EBLV-1 than to RABV. Variation between bat species, roost sites and bioclimatic regions were observed. All brain samples tested by RT-PCR specific for lyssavirus RNA were negative.

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.