PartialrpoBgene sequencing for identification ofLeptospiraspecies

Co-Infection by Leptospira montravelensis and Leptospira interrogans Serovar Pomona in Urine Samples of Donkeys and Pigs in Sardinia, Italy

Saprophytic leptospires are spirochetes enclosed within the non-pathogenic clade of the genus Leptospira, which in turn is subdivided into two subclades S1 and S2. To date, the microorganisms included in these subclades have been isolated from the environment in various parts of the world, and are believed to have no known animal reservoirs. After a case of Leptospira interrogans serovar Pomona was notified to the owner of a farm in Sardinia, all of the farm animals (11 pigs and 3 donkeys) were examined for the presence of Leptospira. Sera of all tested animals resulted positive for antibodies to Leptospira using a microscopic agglutination test (MAT). Moreover, nine (82%) kidney samples from pigs and three urine samples collected from donkeys (100%) tested positive for Leptospira DNA after qPCR. Results obtained after MLST analysis and sequencing of rrs, rpoB, and secY genes, performed on six Leptospira strains isolated in culture, revealed the presence of the genomospecies L. interrogans serovar Pomona in the kidney samples. Conversely, whole-genome sequencing combined with mean nucleotide identity revealed the presence of the saprophytic L. montravelensis in the urine samples. Our results report, for the first time, the isolation of a saprophytic species from mammalian urine, suggesting a new ecological specialization for these bacteria, with a possible transition from free-living to a symbiotic lifestyle. Further studies will have to be conducted to understand the evolution of virulence of these bacteria, potential infectivity, and possible public health implications.

Serological and Molecular Evidence of Pathogenic Leptospira spp. in Stray Dogs and Cats of Sicily (South Italy), 2017-2021

Leptospirosis is a zoonosis of public health concern. Its prevalence in stray animals in the South of Italy is unknown. This study aimed to investigate Leptospira spp. prevalence in 1009 stray animals. Out of them, 749 were alive animals, including 358 dogs (316 from Palermo and 42 from Ragusa) and 391 cats (359 from Palermo and 32 from Ragusa), and 260 were corpses (216 dogs and 44 cats) randomly collected in Sicily. Dogs and cats underwent a serological screening by Microscopic Agglutination Test and a molecular investigation by Real-Time PCR targeting lipL32. Corpses were subjected to Real-Time PCR. Serological analyses showed a prevalence of 1.12% (4/358) for dogs and 0.26% (1/391) for cats, with the only positive cat coming from Palermo. Serogroup Icterohaemorrhagiae serovar Icterohaemorrhagiae or Copenhageni, followed by Canicola and Bratislava, were the most spread among dogs, while the serological positive cat reacted with Hardjo serogroup. Two urine (2/32, 6.25%) and one blood (1/391, 0.26%) samples of cats, all from Ragusa, were positive at Real-Time PCR for pathogenic Leptospira spp. Sequencing analyses showed the presence of L. interrogans serogroup Icterohaemorrhagiae serovar Icterohaemorrhagiae or Copenhageni in one of the positive urine samples and in the positive blood sample. Analyses on corpses showed a prevalence of 1.85% (4/216) in Sicilian dog kidney samples, while all corpses of cats resulted in negative. Genotyping analysis showed a genetic relatedness between cat and human isolates. Results show Leptospira spp. circulation among Sicilian stray animals. The genetic relatedness between cat and human isolates suggests a possible common infection source.

Leptospira in Slaughtered Fattening Pigs in Southern Italy: Serological Survey and Molecular Typing

Simple Summary

In this study, serological and molecular assays in 55 pigs in Sicily were conducted in order to investigate Leptospira spp. prevalence and to carry out strain characterization. A seropositivity rate of 16.4% was determined; 3.64% of kidney samples tested positive for pathogenic Leptospiral DNA. Obtained data showed that Leptospira infection is common among pigs in southern Italy, confirming the importance of Leptospiral infection in pigs and reaffirming the potential role of these animals as a source of infection for humans (occupational risk) and other animals. Our study delivers a comprehensive overview based on up-to-date data to deepen the knowledge of swine leptospiral infections, characterize new potential emerging strains, and reinforce control measures able to reduce the infection risk in swine herds.

Abstract

Leptospirosis is a re-emerging zoonosis of worldwide significance; a wide spectrum of wild and domestic animal species act as natural or accidental hosts. Swine can act as maintenance or accidental hosts of pathogenic Leptospira spp. This study aimed at investigation of Leptospira spp. prevalence and diversity in slaughtered pigs in southern Italy (Sicily). In total, 55 samples of kidneys and blood were collected. Microscopic agglutination test and real-time PCR were performed to detect pathogenic and intermediately pathogenic Leptospira. Partial rpoB gene sequencing and multi-locus sequence typing (MLST) were performed to characterize Leptospira species. The analysis showed a seropositivity rate of 16.4%, with Australis representing the most frequently identified serogroup (63.64%); Pomona and Sejroe were detected with a prevalence of 27.27% and 9.09%, respectively. Pathogenic Leptospiral DNA was detected in 2 kidney samples (3.64%). Leptospira were identified through MLST as L. borgpetersenii serovar Tarassovi (serogroup Tarassovi). Obtained data confirmed the presence of Leptospira infection among pigs in southern Italy, suggesting that management of these animals may be considered an occupational risk for humans.

Microorganisms associated with the North African hedgehog Atelerix algirus and its parasitizing arthropods in Algeria

Hedgehogs are small mammals. They are potential reservoirs of various zoonotic agents. This study was conducted in Bouira, a north-central region of Algeria. A total of 21 Atelerix algirus corpses were picked up on roadsides and gardens. Hedgehog kidneys, spleens and ectoparasites were collected. Twelve hedgehogs were infested with ectoparasites, including Archaeopsylla erinacei, Rhipicephalus sanguineus s.l. and Haemaphysalis erinacei. Hedgehog organs and randomly selected arthropods were screened for microorganisms using molecular methods. Coxiella burnetii was detected in kidneys, spleens, A. erinacei, Hae. erinacei and Rh. sanguineus s.l. Leptospira interrogans was detected in kidneys. Rickettsia felis and Rickettsia massiliae were detected respectively in A. erinacei and in Rh. sanguineus s.l. DNA of an uncultivated Rickettsia spp. was found in Hae. erinacei. Wolbachia spp. DNA was detected in fleas. The DNA of potential new Bartonella and Ehrlichia species were found respectively in fleas and ticks. This study highlights the presence of DNA from a broad range of microorganisms in hedgehogs and their ectoparasites that may be responsible for zoonoses in Algeria.

An overview on the molecular diagnosis of animal leptospirosis

The most common presentation of animal leptospirosis is the subclinical and silent chronic form, that can lead to important reproductive disorders. The diagnosis of this chronic form remains a challenge. The aim of the present study is to gather and critically analyse the current information about molecular tools applied to animal leptospirosis diagnosis, particularly the silent chronic presentation of the infection. Regarding clinical specimens, samples from urinary tract were the most used (69/102, 67·7%), while few studies (12/102, 11·8%) investigated samples from reproductive tract. Concerning the molecular methods applied, the most used is still the conventional polymerase chain reaction (PCR) (46/102, 45%), followed by real-time PCR (38/102, 37·2%). The lipL32 gene is currently the most common target used for Leptospira detection, with 48% of studies applying this genetic marker. From all the studies, only few (21/102, 20·5%) performed gene sequencing. According to the majority of authors, current evidence suggests that lipL32-PCR is useful for an initial screening for Leptospira DNA detection in animal clinical samples. Posteriorly, if DNA sequencing could be performed on positive lipL32-PCR samples, we encourage the use of secY gene as a genetic marker. The molecular methods appear as the most important tools for the diagnosis of the chronic silent leptospirosis on domestic animals, reinforcing its evident impact not only on animal reproduction but also on a One Health context.

Leptospira interrogans serogroup Pomona strains isolated from river buffaloes

At present, little is known regarding the prevalence of buffalo leptospirosis worldwide, especially with respect to which Leptospira strains may infect this animal species. Furthermore, most investigations into this disease in buffaloes have only been performed with serological studies. In Brazil, particularly in the Amazon, buffalo production is growing and is just as important as cattle production, although few studies have been performed on buffalo compared to cattle. Thus, the aim of this study was to isolate and characterise Leptospira strains from river buffaloes raised in the Brazilian Amazon region. We collected 109 kidney samples from slaughtered buffaloes raised in the Amazon Delta region of Brazil. The samples were analysed by bacteriological culture for the isolation of leptospires, and the obtained isolates were serologically and molecularly characterised by microscopic agglutination test (MAT), DNA sequencing and multiple locus variable-number tandem repeat analysis (MLVA). Five isolates were obtained, and in serogrouping analyses, these isolates were only reactive for the Pomona serogroup, with an observed titre of 25,600. The DNA sequencing results revealed that all the isolates belonged to the species Leptospira interrogans, and the MLVA results showed that the VNTR loci 4, 7 and 10 profile of all the isolates was 4-1-10. In this study, we observed that Pomona serogroup strains circulate in buffaloes in the Amazon, showing that in Brazil, buffaloes can be affected by Leptospira strains other than the Sejroe group, which are adapted to cattle.

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.

Phylogenetic relationships and diversity of bat-associated Leptospira and the histopathological evaluation of these infections in bats from Grenada, West Indies

Bats can harbor zoonotic pathogens, but their status as reservoir hosts for Leptospira bacteria is unclear. During 2015-2017, kidneys from 47 of 173 bats captured in Grenada, West Indies, tested PCR-positive for Leptospira. Sequence analysis of the Leptospira rpoB gene from 31 of the positive samples showed 87-91% similarity to known Leptospira species. Pairwise and phylogenetic analysis of sequences indicate that bats from Grenada harbor as many as eight undescribed Leptospira genotypes that are most similar to known pathogenic Leptospira, including known zoonotic serovars. Warthin-Starry staining revealed leptospiral organisms colonizing the renal tubules in 70% of the PCR-positive bats examined. Mild inflammatory lesions in liver and kidney observed in some bats were not significantly correlated with renal Leptospira PCR-positivity. Our findings suggest that Grenada bats are asymptomatically infected with novel and diverse Leptospira genotypes phylogenetically related to known pathogenic strains, supporting the hypothesis that bats may be reservoirs for zoonotic Leptospira.

Evidence of Leptospiral Presence in the Cumberland Gap Region

BACKGROUND

Leptospirosis is a widespread zoonotic disease that causes reproductive losses and/or hepatorenal failure in a number of animal species. Wild reservoirs of the disease, such as rodents, harbor the causative bacterium, Leptospira spp., in their kidneys and contaminate the environment by excreting infected urine. In this study, we tested small wild mammals, environmental water, and livestock in the Cumberland Gap region of southeastern Appalachia for the presence of pathogenic Leptospira or leptospiral antibodies.

METHODS/RESULTS

Small wild mammals (n = 101) and environmental water samples (n = 89) were screened by a real time quantitative PCR that targets the pathogenic Leptospira-specific lipl32 gene. Kidneys from 63 small wild mammals (62.37%) and two water sources (2.25%) tested positive for leptospiral DNA. To identify the infecting leptospiral species in qPCR-positive water and kidney samples, a fragment of leptospiral rpoB gene was PCR amplified and sequenced. L. kirschneri and L. interrogans were the leptospiral species carried by small wild mammals. Furthermore, sera from livestock (n = 52; cattle and horses) were screened for leptospiral antibodies using microscopic agglutination test (MAT). Twenty sera (38.46%) from livestock had antibodies to one or more serovars of pathogenic Leptospira spp.

CONCLUSIONS

In conclusion, results from our study show exposure to leptospiral infection in farm animals and the presence of this zoonotic pathogen in the environmental water and kidneys of a significant number of small wild mammals. The public health implications of these findings remain to be assessed.

Molecular characterization and phylogenetic analysis of human pathogenic Leptospira species circulating in a tertiary care hospital of Western Uttar Pradesh in India

Leptospirosis is identified as an important reemerging zoonotic disease distributed worldwide, caused by Leptospira. This study was carried out to explore the genetic characterization and its phylogenetic analysis of circulating Leptospira species, among the Aligarh region of western Uttar Pradesh in India, utilizing secY gene-based nucleotide sequence. A total of 190 human samples were included in the study. Positive samples were identified by ELISA, MAT and PCR. MAT was carried out utilizing local circulating Leptospira serovars. Four positive samples including two MAT positive samples were subjected to DNA sequencing for further confirmation and phylogenetic tree was constructed. Out of the total of 190 samples, 24 patients were found positive by ELISA and 29 by PCR. Two samples were found reactive in MAT with L. interrogans serovars like hebdomadis and copenhageni. Phylogenetic analysis of four isolates based on partial secY gene nucleotide sequences revealed that species obtained from the Aligarh region clustered with the several published pathogenic Leptospira interrogans, while some of our isolates nucleotide sequences also clustered with the published sequence of intermediate and saprophytic Leptospira serovars like Leptospira inadai and Leptospira meyeri. This pilot study will help us to decipher the present scenario of circulating serovars of leptospira as well as to identify the nucleotide changes in secY gene, in this region.

An in silico approach towards identification of novel drug targets in pathogenic species of Leptospira

Leptospirosis is one of the leading zoonotic infections worldwide. As with other infectious diseases, report of antimicrobial resistance to existing therapeutic arsenal poses challenges in the management of disease. Hence, identification of novel drug targets for the pathogen deems essential. Present study used combined approach of comparative and subtractive genomics to identify putative drug targets. Crucial genes of 16 pathogenic Leptospira strains were filtered and subjected to homology search via target identification tool "TiD". Thereafter, comparative analysis was performed for non-homologous, essential genes to accomplish the broad-spectrum drug target. Consequently, 37 essential genes were found to be conserved in at least 10 strains of Leptospira. Further, prioritization of resultant set of genes revealed 18 were hubs in protein-protein interaction network. Sixteen putative targets among the hub genes were conserved in all strains of Leptospira. Out of sixteen, fourteen were enzymes while 8 were novel and 4 were involved in virulence mechanism. In addition, genome scale metabolic network reconstruction and choke point analysis revealed cobA (porphyrin and chlorophyll metabolism) and thiL (thiamine metabolism) as chokepoints in their respective metabolic pathways. The proposed hub genes could act as putative broad-spectrum drug targets for Leptospira species, however, these putative targets should be validated to ensure them as real one prior to utilizing them for target based lead discovery.

Association of rodent-borne Leptospira spp. with urban environments in Malaysian Borneo

Although leptospirosis is traditionally considered a disease of rural, agricultural and flooded environments, Leptospira spp. are found in a range of habitats and infect numerous host species, with rodents among the most significant reservoirs and vectors. To explore the local ecology of Leptospira spp. in a city experiencing rapid urbanization, we assessed Leptospira prevalence in rodents from three locations in Malaysian Borneo with differing levels of anthropogenic influence: 1) high but stable influence (urban); 2) moderate yet increasing (developing); and 3) low (rural). A total of 116 urban, 122 developing and 78 rural rodents were sampled, with the majority of individuals assigned to either the Rattus rattus lineage R3 (n = 165) or Sundamys muelleri (n = 100). Leptospira spp. DNA was detected in 31.6% of all rodents, with more urban rodents positive (44.8%), than developing (32.0%) or rural rodents (28.1%), and these differences were statistically significant. The majority of positive samples were identified by sequence comparison to belong to known human pathogens L. interrogans (n = 57) and L. borgpetersenii (n = 38). Statistical analyses revealed that both Leptospira species occurred more commonly at sites with higher anthropogenic influence, particularly those with a combination of commercial and residential activity, while L. interrogans infection was also associated with low forest cover, and L. borgpetersenii was more likely to be identified at sites without natural bodies of water. This study suggests that some features associated with urbanization may promote the circulation of Leptospira spp., resulting in a potential public health risk in cities that may be substantially underestimated.

Leptospirosis is a significant zoonotic disease that is found in a range of environments worldwide, most notably tropical regions prone to flooding. The bacterial agents of this disease, Leptospira spp., are most often associated with rodents, including species frequently found in urban areas. In cities, rodent populations are often larger and denser than those found in natural environments, which can lead to higher rates of contact with people and impact human disease risk. To investigate the impacts of urbanization on Leptospira spp., we sampled rodents at locations with differing levels of human influence, from highly urbanized to rural, surrounding a city in Malaysian Borneo. We found that 31.6% of all rodents were positive for Leptospira spp. DNA, and that two primary species were present, L. interrogans and L. borgpetersenii, both of which are known human pathogens. Statistical analyses revealed that infected animals were more common in areas with higher levels of human influence, and were more likely to occur at sites with limited forest cover, and mixed commercial and residential activity. Our study adds to a growing body of evidence suggesting that there is a significant yet underappreciated risk of leptospirosis for people living in urban environments.

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

Background

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

Methodology/principal findings

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

Conclusions/significance

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

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.

Characterization of multidrug-resistant strains isolated from medical intensive care units in Cali - Colombia

Introduction

The extensive use of antibiotics has led to the emergence of multi-resistant strains in some species of the genus Acinetobacter.

Objective

To investigate the molecular characteristics of multidrug-resistant of Acinetobacter ssp. strains isolated from 52 patients collected between March 2009 and July 2010 in medical intensive care units in Cali - Colombia.

Methods

The susceptibility to various classes of antibiotics was determined by disc diffusion method, and the determination of the genomic species was carried out using amplified ribosomal DNA restriction analysis (ARDRA) and by sequencing of the 16s rDNA gene. Also, the genes of beta-lactamases as well as, integrases IntI1 and IntI2 were analyzed by PCR method.

Results

The phenotypic identification showed that the isolates belong mainly to A. calcoaceticus- A. baumannii complex. All of them were multi-resistant to almost the whole antibiotics except to tigecycline and sulperazon, and they were grouped into five (I to V) different antibiotypes, being the antibiotype I the most common (50.0%). The percent of beta-lactamases detected was: blaTEM (17.3%), blaCTX-M (9.6%), blaVIM (21.2%), blaIMP (7.7%), blaOXA-58 (21.2%), and blaOXA-51 (21.2%). The phylogenetic tree analysis showed that the isolates were clustering to A. baumannii (74.1%), A. nosocomialis (11.1%) and A. calcoaceticus (7.4 %). Besides, the integron class 1 and class 2 were detected in 23.1% and 17.3% respectively.

Conclusion

The isolates were identified to species A. baumanii mainly, and they were multiresistant. The resistance to beta-lactams may be by for presence of beta-lactamases in the majority of the isolates.

Molecular detection and isolation of pathogenic Leptospira from asymptomatic humans, domestic animals and water sources in Nan province, a rural area of Thailand

Leptospirosis is an important zoonotic disease that is often associated with animal carriers and contamination of the environment via infected urine. This study aimed to assess pathogenic leptospiral carriage in Nan province, a rural area of Thailand where leptospirosis is endemic. Samples from 20 villages were obtained during the period 2013 to 2016, comprising urine samples collected from asymptomatic people (n=37) and domestic animals (n=342), and environmental water samples (n=14). Leptospira were cultured in Ellinghauson McCullough Johnson and Harris (EMJH) media. An rrs nested PCR identified 9.92% (95% confidence interval (CI) 6.96-12.88) of the urine and water samples as being positive for Leptospira spp., and phylogenetic analysis was conducted on the 443bp amplicons. Leptospira weilii, which has not previously been identified in Thailand, was recovered from 13 cattle, 9 pigs, 2 dogs, 2 water samples and 1 goat. L. interrogans was found in 4 dogs, 3 pigs, 3 cattle, 1 human and 1 water sample. Four leptospiral strains were isolated and multilocus sequence typing (MLST) analysis was performed on these. Three novel sequence types were identified, including two singletons of L. interrogans in ST26 and ST33, and one of L. weilii in ST94, with this having a close relationship to previous isolates from cases of human leptospirosis in Laos and China. Our results revealed that pathogenic Leptospira occur commonly in asymptomatic domestic animals, humans and environmental water samples in Nan Province, and emphasize the high potential for zoonotic transmission in the province.

The EbpA-RpoN Regulatory Pathway of the Pathogen Leptospira interrogans Is Essential for Survival in the Environment

Leptospira interrogans is the agent of leptospirosis, a reemerging zoonotic disease. It is transmitted to humans through environmental surface waters contaminated by the urine of mammals chronically infected by pathogenic strains able to survive in water for long periods. Little is known about the regulatory pathways underlying environmental sensing and host adaptation of L. interrogans during its enzootic cycle. This study identifies the EbpA-RpoN regulatory pathway in L. interrogans In this pathway, EbpA, a σ⁵⁴ activator and putative prokaryotic enhancer-binding protein (EBP), and the alternative sigma factor RpoN (σ⁵⁴) control expression of at least three genes, encoding AmtB (an ammonium transport protein) and two proteins of unknown function. Electrophoresis mobility shift assay demonstrated that recombinant RpoN and EbpA bind to the promoter region and upstream of these three identified genes, respectively. Genetic disruption of ebpA in L. interrogans serovar Manilae virtually abolished expression of the three genes, including amtB in two independent ebpA mutants. Complementation of the ebpA mutant restored expression of these genes. Intraperitoneal inoculation of gerbils with the ebpA mutant did not affect mortality. However, the ebpA mutant had decreased cell length in vitro and had a significantly lowered cell density at stationary phase when grown with l-alanine as the sole nitrogen source. Furthermore, the ebpA mutant has dramatically reduced long-term survival ability in water. Together, these studies identify a regulatory pathway, the EbpA-RpoN pathway, that plays an important role in the zoonotic cycle of L. interrogans IMPORTANCE: Leptospirosis is a reemerging disease with global importance. However, our understanding of gene regulation of the spirochetal pathogen Leptospira interrogans is still in its infancy, largely due to the lack of robust tools for genetic manipulation of this spirochete. Little is known about how the pathogen achieves its long-term survival in the aquatic environment. By utilizing bioinformatic, genetic, and biochemical methods, we discovered a regulatory pathway in L. interrogans, the EbpA-RpoN pathway, and demonstrated that this pathway plays an important role in environmental survival of this pathogen.

The salivary microbiome for differentiating individuals: proof of principle

Human identification has played a prominent role in forensic science for the past two decades. Identification based on unique genetic traits is driving the field. However, this may have limitations, for instance, for twins. Moreover, high-throughput sequencing techniques are now available and may provide a high amount of data likely useful in forensic science. This study investigates the potential for bacteria found in the salivary microbiome to be used to differentiate individuals. Two different targets (16S rRNA and rpoB) were chosen to maximise coverage of the salivary microbiome and when combined, they increase the power of differentiation (identification). Paired-end Illumina high-throughput sequencing was used to analyse the bacterial composition of saliva from two different people at four different time points (t = 0 and t = 28 days and then one year later at t = 0 and t = 28 days). Five major phyla dominate the samples: Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes and Fusobacteria. Streptococcus, a Firmicutes, is one of the most abundant aerobic genera found in saliva and targeting Streptococcus rpoB has enabled a deeper characterisation of the different streptococci species, which cannot be differentiated using 16S rRNA alone. We have observed that samples from the same person group together regardless of time of sampling. The results indicate that it is possible to distinguish two people using the bacterial microbiota present in their saliva.

Distribution of Leptospira interrogans by Multispacer Sequence Typing in Urban Norway Rats (Rattus norvegicus): A Survey in France in 2011-2013

BACKGROUND

Urban leptospirosis has increasingly been reported in both developing and developed countries. The control of the disease is limited because our understanding of basic aspects of the epidemiology, including the transmission routes of leptospires among rat populations, remains incomplete. Through the ability to distinguish among Leptospira strains in rats, multispacer sequence typing (MST) could provide a modern understanding of Leptospira epidemiology; however, to our knowledge, the distribution of Leptospira strains among urban rat colonies has not been investigated using MST.

AIMS AND METHODOLOGY

The objective of this study was to identify the Leptospira strains present in rats (Rattus norvegicus) in Lyon (France) using MST and to characterize their spatial distribution. Kidneys and urine were collected from rats trapped live in seven locations in the city and in one suburban location. Each location was considered to represent a rat colony. Bacterial cultures and quantitative polymerase chain reaction (qPCR) assays were performed, and the L. interrogans DNA identified was then genotyped using MST. The distributions of Leptospira strains were spatially described.

KEY RESULTS

Among 84 wild rats, MST profiles were obtained in 35 of 37 rats that had a positive result for L. interrogans by bacterial culture and/or qPCR analyses. All of the MST profiles were related to reference strains previously isolated from human patients that belong to the serogroup Icterohaemorrhagiae and the serovars [strain(s)] Copenhageni [Wijinberg or M20] (n = 26), Icterohaemorrhagiae [CHU Réunion] (n = 7), Icterohaemorrhagiae [R1] (n = 1) and Copenhageni [Shibaura 9] (n = 1). Each colony was infected with leptospires having the same MST profile.

MAJOR CONCLUSIONS

This study demonstrated that MST could be used for the purpose of field studies, either on culture isolates or on DNA extracted from kidneys and urine, to distinguish among L. interrogans isolates in rats. MST could thus be used to monitor their distributions in urban rats from the same city, thereby providing new knowledge that could be applied to explore the circulation of L. interrogans infection in rat colonies. Because the strains are related to those previously found in humans, this application of MST could aid in the source tracking of human leptospirosis, and the findings would be relevant for public health purposes according to the One Health principle.

The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota

Bacterial culture was the first method used to describe the human microbiota, but this method is considered outdated by many researchers. Metagenomics studies have since been applied to clinical microbiology; however, a "dark matter" of prokaryotes, which corresponds to a hole in our knowledge and includes minority bacterial populations, is not elucidated by these studies. By replicating the natural environment, environmental microbiologists were the first to reduce the "great plate count anomaly," which corresponds to the difference between microscopic and culture counts. The revolution in bacterial identification also allowed rapid progress. 16S rRNA bacterial identification allowed the accurate identification of new species. Mass spectrometry allowed the high-throughput identification of rare species and the detection of new species. By using these methods and by increasing the number of culture conditions, culturomics allowed the extension of the known human gut repertoire to levels equivalent to those of pyrosequencing. Finally, taxonogenomics strategies became an emerging method for describing new species, associating the genome sequence of the bacteria systematically. We provide a comprehensive review on these topics, demonstrating that both empirical and hypothesis-driven approaches will enable a rapid increase in the identification of the human prokaryote repertoire.

Identification of Leptospira serovars by RFLP of the RNA polymerase beta subunit gene (rpoB)

Leptospires are usually classified by methods based on DNA-DNA hybridization and the conventional cross-agglutination absorption test, which uses polyclonal antibodies against lipopolysaccharides. In this study, the amplification of the rpoB gene, which encodes the beta-subunit of RNA polymerase, was used as an alternative tool to identify Leptospira. DNA extracts from sixty-eight serovars were obtained, and the hypervariable region located between 1990 and 2500-bp in the rpoB gene was amplified by polymerase chain reaction (PCR). The 600-bp amplicons of the rpoB gene were digested with the restriction endonucleases TaqI, Tru1I, Sau3AI and MslI, and the restriction fragments were separated by 6% polyacrylamide gel electrophoresis. Thirty-five fragment patters were obtained from the combined data of restriction fragment length polymorphism (PCR-RFLP) analysis and used to infer the phylogenetic relationships among the Leptospira species and serovars. The species assignments obtained were in full agreement with the established taxonomic classifications. Twenty-two serovars were effectively identified based on differences in their molecular profiles. However, the other 46 serovars remained clustered in groups that included more than one serovar of different species. This study demonstrates the value of RFLP analysis of PCR-amplified rpoB as an initial method for identifying Leptospira species and serovars.

Molecular characterization of the first leptospires isolated from goats in Brazil

Two Leptospira sp. isolates were obtained by the first time from goats in Brazil and characterized by sequencing rrs, rpoB and secY genes, PFGE and typing with monoclonal antibodies. Both isolates are identical and belong to Leptospira santarosai. Analysis of the rrs and the rpoB genes sequences revealed 100% identity between the goat isolates and the Bananal reference strain. When secY sequences of the two isolates were compared to each other, it was observed that they had identical sequences. However, when compared to that of the Bananal reference strain, there were 15 mismatches along the 549 bp secY sequence. In conclusion, molecular methods are increasingly useful for the characterization of leptospires and allowed to identify those isolates of caprine origin as closely related but not identical to serovar Bananal, and constitute a new type named Carioca.

Evaluating the occurrence of Escherichia albertii in chicken carcass rinses by PCR, Vitek analysis, and sequencing of the rpoB gene

Escherichia albertii is a recently described species that has been associated with gastroenteritis in humans and with healthy and ill birds. Most recently, it has been identified as the causative agent in a food-borne outbreak in Japan. The distribution and clinical importance of E. albertii are not well studied because its importance is unclear. Culture methods for clinical isolation frequently miss E. albertii or incorrectly identify it as Shigella spp., Escherichia coli, or Hafnia alvei. This study was designed to determine if E. albertii could be recovered from chicken carcass rinses collected at slaughter during a 1-year period from November 2009 until October 2010. Colonies were isolated from chicken carcass rinses and tested by PCR for the presence or absence of clpX, lysP, mdh, intimin (eae), Shiga toxins 1 and 2 (stx1, stx2, and stx2f), heat-stable enterotoxin A (staA), and cytolethal distending toxins 1 and 2 (cdtB) genes. Sixty-five isolates were analyzed by sequencing a section of the rpoB gene. Analysis of the rpoB gene sequences revealed 14 fixed differences between E. albertii and other, closely related organisms. The fixed differences found in the rpoB gene could aid in future discrimination of E. albertii from closely related bacteria.

Interlaboratory and between-specimen comparisons of diagnostic tests for leptospirosis in sheep and cattle

A study was performed to investigate interlaboratory test agreement between a research and a commercial veterinary diagnostic laboratory on blood and urine samples, and to investigate test agreement between blood, urine, and kidney samples (research laboratory) for leptospirosis diagnosis. Samples were sourced from 399 sheep and 146 beef cattle from a local abattoir. Interlaboratory agreement for real-time quantitative polymerase chain reaction (qPCR) results on urine samples was almost perfect (kappa = 0.90), despite the use of different amplification targets (DNA gyrase subunit B gene vs. 16s ribosomal RNA gene), chemistries (SYTO9 vs. TaqMan probe), and pre-PCR processing. Interlaboratory agreement for microscopic agglutination test (MAT) positivity was almost perfect (kappa = 0.93) for Leptospira borgpetersenii serovar Hardjo subtype Hardjobovis (Hardjobovis) but moderate (kappa = 0.53) for Leptospira interrogans serovar Pomona (Pomona). Among animals that had different titers recorded, higher Hardjobovis and lower Pomona titers were reported by the commercial laboratory than by the research laboratory (P < 0.005). These interlaboratory comparisons can assist researchers and diagnosticians in interpreting the sometimes discrepant test results. Within the research laboratory, the comparison of qPCR results on urine and kidney showed almost perfect agreement (kappa = 0.84), suggesting that the qPCR on these 2 specimens can be used interchangeably. The agreement between MAT positivity and urine and kidney qPCR results was fair (kappa = 0.32 and kappa = 0.33, respectively). However, the prevalence ratio of urine and kidney qPCR positivity in Hardjobovis-seropositive versus Hardjobovis-seronegative sheep indicated that Hardjobovis seropositivity found in sheep may be able to predict shedding or renal carriage.

The characteristics of ubiquitous and unique Leptospira strains from the collection of Russian centre for leptospirosis

BACKGROUND AND AIM

Leptospira, the causal agent of leptospirosis, has been isolated from the environment, patients, and wide spectrum of animals in Russia. However, the genetic diversity of Leptospira in natural and anthropurgic foci was not clearly defined.

METHODS

The recent MLST scheme was used for the analysis of seven pathogenic species. 454 pyrosequencing technology was the base of the whole genome sequencing (WGS).

RESULTS

The most wide spread and prevalent Leptospira species in Russia were L. interrogans, L. kirschneri, and L. borgpetersenii. Five STs, common for Russian strains: 37, 17, 199, 110, and 146, were identified as having a longtime and ubiquitous distribution in various geographic areas. Unexpected properties were revealed for the environmental Leptospira strain Bairam-Ali. WGS of this strain genome suggested that it combined the features of the pathogenic and nonpathogenic strains and may be a reservoir of the natural resistance genes. Results of the comparative analysis of rrs and rpoB genes and MLST loci for different Leptospira species strains and phenotypic and serological properties of the strain Bairam-Ali suggested that it represented separate Leptospira species.

CONCLUSIONS

Thus, the natural and anthropurgic foci supported ubiquitous Leptospira species and the pool of genes important for bacterial adaptivity to various conditions.

Molecular characterization by LSSP-PCR and DNA sequencing of a pathogenic isolate of Leptospira interrogans from Brazil

We report the initial characterization of a leptospiral isolate, Leptospira interrogans, serogroup Sejroe, serovar Hardjo, genotype Hardjoprajitno, strain Norma, and its relatedness with L. interrogans, serogroup Sejroe, serovar Hardjo, genotype Hardjoprajitno, strain Hardjo and Leptospira borgpetersenii, serogroup Sejroe, serovar Hardjo, genotype Hardjobovis, strain Sponselee. The Norma strain singled out during a leptospirosis outbreak in cattle immunized with antigens from the reference strain Hardjoprajitno (OMS). By applying a microscopic agglutination serological test (MAT) to cattle (n = 2966) with symptoms of leptospirosis between 2003 and 2007, more than 50% of sera were found positive for one of the following serotypes: Hardjoprajitno (31-21%), Hardjo Norma (46-40%), Hardjo hardjobovis (18-10%), Mini (8-4%) and Wolffi (7-4%). In immunization trials using six isolates plus Norma isolate, the remission of MAT in these isolates was observed following 6 months of the initial vaccination. To provide molecular ground for the high MAT Norma frequency found in these isolates, a DNA polymorphic analysis was conducted by comparing the Norma isolate with reference strains Hardjoprajitno and Sponselee. The polymorphic analysis in secY showed five base changes in Norma relative to Hardjoprajitno strain, corresponding to 98% identity, while Sponselee displayed 49 polymorphic sites relative to the Hardjoprajitno strain, representing 80% identity. The alignment of secY translated sequences shows no differences between Hardjoprajitno and Norma, and eight polymorphisms between genotype hardjoprajttno and strain Sponselee. Three-dimensional modelling located these variations within the loop region connecting helices 7 and 8 from secY which is less conserved. DNA sequencing of 23S ribosomal conserved fragment revealed a single polymorphism between Hardjoprajitno and Norma, and 13 polymorphisms between strains Sponselee, Hardjoprajitno and Norma. The differences between Hardjo and Norma were confirmed by low stringency single-specific primer polymerase chain reaction (LSSP-PCR) signature experiments with the primer G2, using as template the 285 bp fragment initially amplified with G1/G2 primers.

Leptospira species and serovars identified by MALDI-TOF mass spectrometry after database implementation

Background

Leptospirosis, a spirochaetal zoonotic disease of worldwide distribution, endemic in Europe, has been recognized as an important emerging infectious disease, though yet it is mostly a neglected disease which imparts its greatest burden on impoverished populations from developing countries. Leptospirosis is caused by the infection with any of the more than 230 serovars of pathogenic Leptospira sp. In this study we aimed to implement the MALDI-TOF mass spectrometry (MS) database currently available in our laboratory with Leptospira reference pathogenic (L. interrogans, L. borgpetersenii, L. kirschneri, L. noguchii), intermediate (L. fainei) and saprophytic (L. biflexa) strains of our collection in order to evaluate its possible application to the diagnosis of leptospirosis and to the typing of strains. This was done with the goal of understanding whether this methodology could be used as a tool for the identification of Leptospira strains, not only at species level for diagnostic purposes, but also at serovar level for epidemiological purposes, overcoming the limits of serological and molecular conventional methods. Twenty Leptospira reference strains were analysed by MALDI-TOF MS. Statistical analysis of the protein spectra was performed by ClinProTools software.

Results

The spectra obtained by the analysis of the reference strains tested were grouped into 6 main classes corresponding to the species analysed, highlighting species-specific protein profiles. Moreover, the statistical analysis of the spectra identified discriminatory peaks to recognize Leptospira strains also at serovar level extending previously published data.

Conclusions

In conclusion, we confirmed that MALDI-TOF MS could be a powerful tool for research and diagnostic in the field of leptospirosis with broad applications ranging from the detection and identification of pathogenic leptospires for diagnostic purposes to the typing of pathogenic and non-pathogenic leptospires for epidemiological purposes in order to enrich our knowledge about the epidemiology of the infection in different areas and generate control strategies.

Pseudo-peptides as novel antileptospiral agents: synthesis and spectral characterization

In this paper, we describe the synthesis of novel class of pseudo-peptides derived by coupling an amino acid with a heterocyclic moiety containing free amine group using suitable coupling agents. The synthesized compounds were characterized using spectral ((1)H NMR, (13)C NMR and MS) techniques. Preliminary pharmacological assays for Leptospirosis were studied by test tube dilution (TDT) and micro dilution technique (MDT). In particular, all the analyses led to the conclusion that the synthesized compound inhibiting the Leptospira a causal organism of Leptospirosis.

rpoB gene as a novel molecular marker to infer phylogeny in Planctomycetales

The 16S rRNA gene has been used in the last decades as a gold standard for determining the phylogenetic position of bacteria and their taxonomy. It is a well conserved gene, with some variations, present in all bacteria and allows the reconstruction of genealogies of microorganisms. Nevertheless, this gene has its limitations when inferring phylogenetic relationships between closely related isolates. To overcome this problem, DNA-DNA hybridization appeared as a solution to clarify interspecies relationships when the sequence similarity of the 16S rRNA gene is above 97 %. However, this technique is time consuming, expensive and laborious and so, researchers developed other molecular markers such as sequencing of housekeeping or functional genes for accurate determination of bacterial phylogeny. One of these genes that have been used successfully, particularly in clinical microbiology, codes for the beta subunit of the RNA polymerase (rpoB). The rpoB gene is sufficiently conserved to be used as a molecular clock, it is present in all bacteria and it is a mono-copy gene. In this study, rpoB gene sequencing was applied to the phylum Planctomycetes. Based on the genomes of 19 planctomycetes it was possible to determine the correlation between the rpoB gene sequence and the phylogenetic position of the organisms at a 95-96 % sequence similarity threshold for a novel species. A 1200-bp fragment of the rpoB gene was amplified from several new planctomycetal isolates and their intra and inter-species relationships to other members of this group were determined based on a 96.3 % species border and 98.2 % for intraspecies resolution.

Characterization of leptospira isolates from animals and humans: phylogenetic analysis identifies the prevalence of intermediate species in India

In this study, 191 culture isolates were recovered from suspected samples of animals and humans in Ellinghausen McCullough Johnson and Harris (EMJH) medium and assessed for its morphological features by dark field microscopy. Extracted DNA from individual culture was subjected to different PCR assays for identification and characterization of leptospira. Out of 99 positive leptospira cultures, 52 pathogenic leptospira isolates were characterized at species level by using partial RNA polymerase β-subunit (rpoB) gene sequences. Phylogenetic analysis of the nucleotide sequences revealed that 30, 8, and 14 isolates belong to L. borgpetersenii / L. interrogans, L. kirschneri, and Leptospira intermediate species, respectively. Based on analysis of 99 leptospira isolates, the prevalent Leptospira species were L. borgpetersenii or L. interrogans (30.30%), L. kirschneri (8%) and Leptospira intermediate species (14.14%) in animals and humans. To the best of authors knowledge, this is the first study to use rpoB gene nucleotide sequence based phylogenetic analysis to identify/detect Leptospira intermediate species (L. wolffii) in animals and humans in India. Hence, the prevalence of this species will surely emphasize the importance of consideration of Leptospira intermediate species and formulate a way for further studies especially in understanding the newly emerging Leptospira in animals and humans and to combat the problem associated with the disease conditions.

Characterization of a virulent Leptospira interrogans strain isolated from an abandoned swimming pool

Pathogenic Leptospira spp. are the etiological agents of leptospirosis, an important disease of both humans and animals. In urban settings, L. interrogans serovars are the predominant cause of disease in humans. The purpose of this study was to characterize a novel Leptospira isolate recovered from an abandoned swimming pool. Molecular characterization through sequencing of the rpoB gene revealed 100% identity with L. interrogans and variable-number tandem-repeat (VNTR) analysis resulted in a banding pattern identical to L. interrogans serogroup Icterohaemorrhagiae, serovar Copenhageni or Icterohaemorrhagiae. The virulence of the strain was determined in a hamster model of lethal leptospirosis. The lethal dose 50% (LD50) was calculated to be two leptospires in female hamsters and a histopathological examination of infected animals found typical lesions associated with severe leptospirosis, including renal epithelium degeneration, hepatic karyomegaly, liver-plate disarray and lymphocyte infiltration. This highly virulent strain is now available for use in further studies, especially evaluation of vaccine candidates.

Molecular characterization of virulent Leptospira interrogans serogroup icterohaemorrhagiae isolated from Cavia aperea

Leptospirosis is a worldwide zoonotic infection caused by pathogenic Leptospira. Synanthropic rodents are recognized carriers of leptospires; however, the role of wild rodents in the epidemiology of the disease is still incipient. In this work, we describe Leptospira strain isolated from Cavia aperea (Brazilian guinea pig). The isolated strain was characterized by partial rpoB gene sequencing, variable-number tandem-repeats and histopathological analysis. The strain was identified as Leptospira interrogans, serogroup Icterohaemorrhagiae and caused clinical signs of leptospirosis in the hamster model, attesting to its virulence. In conclusion, these findings could be useful for elucidating the epidemiological role of C. aperea in leptospirosis.

Laboratory diagnosis of leptospirosis: a challenge

Leptospirosis is caused by pathogenic bacteria called leptospires that are transmitted directly or indirectly from animals to humans. It occurs worldwide but is most common in tropical and subtropical areas. It is a potentially serious but treatable disease. Its symptoms may mimic those of a number of other unrelated infections such as influenza, meningitis, hepatitis, dengue, or other viral hemorrhagic fevers. The spectrum of the disease is extremely wide, ranging from subclinical infection to a severe syndrome of multiorgan infection with high mortality. Laboratory diagnosis tests are not always available, especially in developing countries. Numerous tests have been developed, but availability of appropriate laboratory support is still a problem. Direct observation of leptospires by darkfield microscopy is unreliable and not recommended. Isolation of leptospires can take up to months and does not contribute to early diagnosis. Diagnosis is usually performed by serology; enzyme-linked immunosorbent assay and the microscopic agglutination tests are the laboratory methods generally used, rapid tests are also available. Limitation of serology is that antibodies are lacking at the acute phase of the disease. In recent years, several real-time polymerase chain reaction assays have been described. These can confirm the diagnosis in the early phase of the disease prior to antibody titers are at detectable levels, but molecular testing is not available in restricted resources areas.

Leptospira borgpetersenii from free-living white-eared opossum (Didelphis albiventris): first isolation in Brazil

Leptospirosis is a zoonotic disease that occurs all over the world, caused by bacteria of the genus Leptospira. Marsupial and didelphidae families are considered susceptible to infection caused by a wide range of Leptospira serovars for which they serve as reservoirs. Thirty-three free-living white-eared opossums (Didelphis albiventris) were captured in Southern Brazil and bodily fluids were collected. From the urine samples it was possible to obtain an isolate identified as Leptospira borgpetersenii by rpoB gene sequencing and belonging to serovar Castellonis by Multilocus Variable-Number Tandem-Repeat Analysis. This is the first report of the isolation of Leptospira spp. from the white-eared opossum in Brazil. In addition, the new strain was also virulent in the hamster model of lethal leptospirosis. The microscopic agglutination test (MAT) was used for detecting the presence of antibodies against Leptospira spp. in white-eared opossum, human, cattle and canine sera using a panel of 59 Leptospira strains that included the new isolate. The inclusion of the new strain in the MAT battery increased the MAT sensitivity for canine sera. These findings suggest that the white-eared opossum is an important reservoir of pathogenic Leptospira spp.

Classification of Leptospira genomospecies 1, 3, 4 and 5 as Leptospira alstonii sp. nov., Leptospira vanthielii sp. nov., Leptospira terpstrae sp. nov. and Leptospira yanagawae sp. nov., respectively

The genus Leptospira currently comprises 16 named species. In addition, four unnamed hybridization groups were designated Leptospira genomospecies 1, 3, 4 and 5. These groups represent valid species-level taxa, but were not assigned names in the original description by Brenner et al. [Int J Syst Bacteriol 49, 839-858 (1999)]. To rectify this situation, it is proposed that Leptospira genomospecies 1, genomospecies 3, genomospecies 4 and genomospecies 5 should be classified as Leptospira alstonii sp. nov., Leptospira vanthielii sp. nov., Leptospira terpstrae sp. nov. and Leptospira yanagawae sp. nov., respectively, with strains L. alstonii 79601(T) ( = ATCC BAA-2439(T)), L. vanthielii WaZ Holland(T) ( = ATCC 700522(T)), L. terpstrae LT 11-33(T) ( = ATCC 700639(T)) and L. yanagawae Sao Paulo(T) ( = ATCC 700523(T)) as the type strains. The type strains are also available from the culture collections of the WHO Collaborating Centres in Amsterdam, The Netherlands, and Brisbane, Australia.

Leptospira and rodents in Cambodia: environmental determinants of infection

We investigated infection of rodents and shrews by Leptospira spp. in two localities of Cambodia (Veal Renh, Kaev Seima) and in four types of habitat (forests, non-flooded lands, lowland rain-fed paddy fields, houses) during the wet and the dry seasons. Habitat preference was common, and rodent and shrew species were found only in houses or in rain-fed paddy fields or in forests. Among 649 small mammals trapped belonging to 12 rodent species and 1 shrew species, 71 of 642 animals tested were carriers of Leptospira according to the 16S ribosomal RNA marker used. Rodent infection was higher in low-slope locations, corresponding to rain-fed paddy fields, especially in the rainy season and in Kaev Seima. Rodents (Rattus exulans) and shrews (Suncus murinus) inhabiting households showed significantly low levels of infections, whereas rodents living in and near to forests (shrubby wasteland, orchards) showed high levels of infection.

Rapid MALDI-TOF mass spectrometry identification of Leptospira organisms

Leptospirosis is a worldwide deadly zoonotic disease. Accurate identification of the causative Leptospira spp. spirochetes ascertains the pathogenic status of the isolates, identifies potential source of infection and recognises outbreaks. Species identification is currently based on technically demanding, time and resources consuming serological and molecular methods. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) recently emerged as a first-line method for the accurate identification of bacteria, yet no data issued for Leptospira spp. We investigated the potential of MALDI-TOF-MS for the rapid identification of Leptospira isolates. Starting from a 10(5)organisms/mL suspension, MALDI-TOF-MS yielded an unique protein profile for each one of 19 Leptospira species reference isolates with a 100% reproducibility over 12 repeats, allowing to create a Leptopsira database. MALDI-TOF-MS further accurately identified 20/21 additional reference isolates representative of various serogroups at the species level as Leptospira interrogans (n=12), Leptospira kirschneri (n=5), Leptospira borgpetersenii (n=3), Leptospira noguchii (n=1) with identification score value of 2-2.5. Furthermore, six clinical isolates previously identified by rpoB sequencing, were correctly identified by MALDI-TOF-MS as L. interrogans (n=5) and L. borgpetersenii (n=1) with identification score value of 2-2.6. Identification was achieved in 40 min starting from the Leptospira suspension. MALDI-TOF-MS could complement serological and sequencing-based methods for the first line, rapid identification of Leptospira isolates in the clinical microbiology laboratory.

Leptospirosis in a French traveler returning from Mauritius

We report the first case of leptospirosis in a patient with a travel history to Mauritius, where the disease has very occasionally been reported in local populations. Following an initial dengue-like presentation, the patient suffered pancreatic involvement and trigeminal neuralgia, which are two unusual delayed features of leptospirosis.

Molecular detection and speciation of pathogenic Leptospira spp. in blood from patients with culture-negative leptospirosis

BACKGROUND

Pathogenic Leptospira spp. present in the blood of patients with leptospirosis during the first week of symptoms can be detected using culture or PCR. A proportion of patients who are positive by PCR are negative by culture. Leptospira spp. are fastidious bacteria, and we hypothesized that a false-negative culture result may represent infection with a distinct bacterial subset that fail to grow in standard culture medium.

METHODS

We evaluated our hypothesis during a prospective study of 418 consecutive patients presenting to a hospital in northeast Thailand with an acute febrile illness. Admission blood samples were taken for Leptospira culture and PCR. A single tube nested PCR that amplified a region of the rrs gene was developed and applied, amplicons sequenced and a phylogenetic tree reconstructed.

RESULTS

39/418 (9%) patients were culture-positive for Leptospira spp., and 81/418 (19%) patients were culture-negative but rrs PCR-positive. The species associated with culture-positive leptospirosis (37 L. interrogans and 2 L. borgpetersenii) were comparable to those associated with culture-negative, PCR-positive leptospirosis (76 L. interrogans, 4 L. borgpetersenii, 1 unidentified, possibly new species).

CONCLUSION

Molecular speciation failed to identify a unique bacterial subset in patients with culture-negative, PCR-positive leptospirosis. The rate of false-negative culture was high, and we speculate that antibiotic pre-treatment is the most likely explanation for this.

Comparison of two multilocus sequence based genotyping schemes for Leptospira species

BACKGROUND

Several sequence based genotyping schemes have been developed for Leptospira spp. The objective of this study was to genotype a collection of clinical and reference isolates using the two most commonly used schemes and compare and contrast the results.

METHODS AND FINDINGS

A total of 48 isolates consisting of L. interrogans (n = 40) and L. kirschneri (n = 8) were typed by the 7 locus MLST scheme described by Thaipadungpanit et al., and the 6 locus genotyping scheme described by Ahmed et al., (termed 7L and 6L, respectively). Two L. interrogans isolates were not typed using 6L because of a deletion of three nucleotides in lipL32. The remaining 46 isolates were resolved into 21 sequence types (STs) by 7L, and 30 genotypes by 6L. Overall nucleotide diversity (based on concatenated sequence) was 3.6% and 2.3% for 7L and 6L, respectively. The D value (discriminatory ability) of 7L and 6L were comparable, i.e. 92.0 (95% CI 87.5-96.5) vs. 93.5 (95% CI 88.6-98.4). The dN/dS ratios calculated for each locus indicated that none were under positive selection. Neighbor joining trees were reconstructed based on the concatenated sequences for each scheme. Both trees showed two distinct groups corresponding to L. interrogans and L. kirschneri, and both identified two clones containing 10 and 7 clinical isolates, respectively. There were six instances in which 6L split single STs as defined by 7L into closely related clusters. We noted two discrepancies between the trees in which the genetic relatedness between two pairs of strains were more closely related by 7L than by 6L.

CONCLUSIONS

This genetic analysis indicates that the two schemes are comparable. We discuss their practical advantages and disadvantages.

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

Background

Most of the current knowledge of leptospirosis epidemiology originates from serological results obtained with the reference Microscopic Agglutination Test (MAT). However, inconsistencies and weaknesses of this diagnostic technique are evident. A growing use of PCR has improved the early diagnosis of leptospirosis but a drawback is that it cannot provide information on the infecting Leptospira strain which provides important epidemiologic data. Our work is aimed at evaluating if the sequence polymorphism of diagnostic PCR products could be used to identify the infecting Leptospira strains in the New Caledonian environment.

Results

Both the lfb1 and secY diagnostic PCR products displayed a sequence polymorphism that could prove useful in presumptively identifying the infecting leptospire. Using both this polymorphism and MLST results with New Caledonian isolates and clinical samples, we confirmed the epidemiological relevance of the sequence-based identification of Leptospira strains. Additionally, we identified one cluster of L. interrogans that contained no reference strain and one cluster of L. borgpetersenii found only in the introduced Rusa deer Cervus timorensis russa that is its probable reservoir.

Conclusions

The sequence polymorphism of diagnostic PCR products proved useful in presumptively identifying the infecting Leptospira strains. This could contribute to a better understanding of leptospirosis epidemiology by providing epidemiological information that cannot be directly attained from the use of PCR as an early diagnostic test for leptospirosis.

Bioinformatics describes novel Loci for high resolution discrimination of leptospira isolates

Background

Leptospirosis is one of the most widespread zoonoses in the world and with over 260 pathogenic serovars there is an urgent need for a molecular system of classification. The development of multilocus sequence typing (MLST) schemes for Leptospira spp. is addressing this issue. The aim of this study was to identify loci with potential to enhance Leptospira strain discrimination by sequencing-based methods.

Methodology and Principal Findings

We used bioinformatics to evaluate pre-existing loci with the potential to increase the discrimination of outbreak strains. Previously deposited sequence data were evaluated by phylogenetic analyses using either single or concatenated sequences. We identified and evaluated the applicability of the ligB, secY, rpoB and lipL41 loci, individually and in combination, to discriminate between 38 pathogenic Leptospira strains and to cluster them according to the species they belonged to. Pairwise identity among the loci ranged from 82.0–92.0%, while interspecies identity was 97.7–98.5%. Using the ligB-secY-rpoB-lipL41 superlocus it was possible to discriminate 34/38 strains, which belong to six pathogenic Leptospira species. In addition, the sequences were concatenated with the superloci from 16 sequence types from a previous MLST scheme employed to study the association of a leptospiral clone with an outbreak of human leptospirosis in Thailand. Their use enhanced the discriminative power of the existing scheme. The lipL41 and rpoB loci raised the resolution from 81.0–100%, but the enhanced scheme still remains limited to the L. interrogans and L. kirschneri species.

Conclusions

As the first aim of our study, the ligB-secY-rpoB-lipL41 superlocus demonstrated a satisfactory level of discrimination among the strains evaluated. Second, the inclusion of the rpoB and lipL41 loci to a MLST scheme provided high resolution for discrimination of strains within L. interrogans and L. kirschneri and might be useful in future epidemiological studies.

A simple and rapid molecular method for Leptospira species identification

Serological and DNA-based classification systems only have little correlation. Currently serological and molecular methods for characterizing Leptospira are complex and costly restricting their world-wide distribution and use. Ligation mediated amplification combined with microarray analysis avoids many of these drawbacks. We demonstrated that this approach used in the Check-Points (CP) assay can successfully applied for the generic detection of Leptospira and can discriminate between saprophytic, intermediate and pathogenic species. In addition, the CP assay could unambiguously detect strains of seven pathogenic species and revealed discrepancies in previous speciation and culture collections. The method provides a valuable tool adding to the molecular study of leptospires and their local and global distribution.