Environmental DNA metabarcoding to detect pathogenic Leptospira and associated organisms in leptospirosis-endemic areas of Japan

Mizuyama, Masaru; Sato, Megumi; Minamoto, Toshifumi; Kimura, Ryosuke; Toma, Claudia

doi:10.1038/s41598-019-42978-1

Cited by 39 publications

(52 citation statements)

References 69 publications

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“…While most screening approaches for Leptospira prevalence in hosts only consider single infections, we chose a NGS approach to uncover potential mixed infection. To the best of our knowledge, NGS has been used for detection of multiple Leptospira species on environmental samples only (Sato et al 2019). Another approach to investigating mixed infections in animal hosts involves the implementation of a multiplex PCR targeting multiple Leptospira species, followed by sequencing of the amplicons.…”

Section: Discussionmentioning

confidence: 99%

Prevalence and risk factors of Leptospira infection in urban brown rats (Rattus norvegicus), Vienna, Austria

et al. 2020

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Leptospirosis is a worldwide bacterial zoonosis which incidence is expected to increase in conjunction with global change. In urban ecosystems, synanthropic rats are the key source of Leptospira infection in humans and other animals. Risk assessment and prediction of human leptospirosis require investigations of the environment associated with the bacteria and infection patterns in the reservoir hosts. The objective of this study was to address the prevalence of mixed Leptospira infection in the lungs and kidneys of brown rats captured in three sites of the city centre of Vienna, Austria, between 2016 and 2018. A total of 96 brown rats were examined for the presence of Leptospira using PCR. Occurrence of mixed Leptospira infections was explored through next-generation sequencing (NGS). A logistic regression model was built to predict the individual infection status using morphological and land-use data. Overall, the prevalence of Leptospira interrogans in the kidney was 25% but varied among sites (0-36%). We did not evidence any pulmonary nor mixed infections. Host body mass and sex were strong predictors of Leptospira carriage in the sampled rats (relative variable importance (RVI) = 0.98 and 0.89, respectively) while the presence of water affected it moderately (RVI = 0.44). Our findings demonstrate that NGS is an unbiased approach to the direct characterisation of mixed leptospiral infections that could provide further insights into the ecology of Leptospira. Future surveillance programmes should consider the use of rats as sentinels for the early detection of emerging pathogenic Leptospira in urban ecosystems.

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Section: Discussionmentioning

confidence: 99%

Prevalence and risk factors of Leptospira infection in urban brown rats (Rattus norvegicus), Vienna, Austria

et al. 2020

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“…Water and soils [47] Japan Soils [65] Philippines Soils [10] Brazil Soils [12] Soils apparently protect Leptospira from seawater toxicity Philippines Soils [10] Leptospira survive in wet soil on dry days and appear in surface water on rainy days Philippines, Japan Soils and water [11] Leptospira concentration in surface waters correlates with rainfall intensity Japan River water [127] suggest that disturbance of river sediments increase the Leptospira concentration in water https://doi.org/10.1371/journal.pone.0227055.t002…”

Section: Malaysiamentioning

confidence: 99%

“…More recently, a study used environmental DNA metabarcoding and ecological techniques targeting Leptospira spp. and Vertebrates in Japan, successfully evidencing Group I Leptospira in the environment and providing an unprecedented insight into animal / Leptospira / weather ecological associations in a very elegant One Health approach [127]. These technologies and the corresponding datasets offer unique opportunities to gain new knowledge on Leptospira habitat in the water and soil environments.…”

Section: Malaysiamentioning

confidence: 99%

A systematic review of Leptospira in water and soil environments

Bierque¹,

Thibeaux²,

Girault³

et al. 2020

PLoS ONE

152

151

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Background Leptospirosis, caused by pathogenic Leptospira, is a zoonosis of global distribution. This infectious disease is mainly transmitted by indirect exposure to urine of asymptomatic animals via the environment. As human cases generally occur after heavy rain, an emerging hypothesis suggests that rainfall re-suspend leptospires together with soil particles. Bacteria are then carried to surface water, where humans get exposed. It is currently assumed that pathogenic leptospires can survive in the environment but do not multiply. However, little is known on their capacity to survive in a soil and freshwater environment. Methods We conducted a systematic review on Leptospira and leptospirosis in the environment in order to collect current knowledge on the lifestyle of Leptospira in soil and water. In total, 86 scientific articles retrieved from online databases or institutional libraries were included in this study. Principals findings/significance This work identified evidence of survival of Leptospira in the environment but major gaps remain about the survival of virulent species associated with human and animal diseases. Studies providing quantitative data on Leptospira in soil and water are a very recent trend, but must be interpreted with caution because of the uncertainty in the species identification. Several studies mentioned the presence of Leptospira in soils more frequently than in waters, supporting the hypothesis of the soil habitat and dispersion of Leptospira with resuspended soil particles during heavy rain. In a near future, the growing use of high throughput sequencing will offer new opportunities to improve our understanding of the habitat of Leptospira in the environment. This better insight into the risk of leptospirosis will allow implementing efficient control measures and prevention for the human and animal populations exposed.

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“…Water samples were collected at ten locations in each region (K01−K10 and GK01−GK10 in Fig 1A) selected according to notified cases of leptospirosis informed by Public Health Inspectors of both Districts. In each location, irrigation water was manually collected at the agricultural or rice fields by wearing disposable gloves, using a clean plastic ladle, and 500 mL to 1,000 mL water was filtrated by the Sterivex filter with 0.45 μm pore size membrane (Merck Millipore, Milan, Italy), capable to capture leptospiral cells [24], using a 60 mL disposable syringe. After filtration, the filter unit was filled with 2 mL of DNAiso Reagent (Takara, Shiga, Japan) and tightly sealed by polypropylene luer-fitting caps (ISIS, Osaka, Japan) until DNA extraction was carried out at room temperature.…”

Section: Environmental Water Samplingmentioning

confidence: 99%

“…Environmental DNA (eDNA) in aquatic environments originates from various sources, including feces, urine, damaged tissue, and microorganisms, and has successfully been used to identify pathogenic Leptospira and associated organisms in rivers of leptospirosis endemic areas of Japan [24]. In paddy lands, irrigation water can be a reservoir and source of spreading urine-containing Leptospira.…”

Section: Introductionmentioning

confidence: 99%

Understanding leptospirosis eco-epidemiology by environmental DNA metabarcoding of irrigation water from two agro-ecological regions of Sri Lanka

et al. 2020

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Background Leptospirosis is one of the most significant zoonoses across the world not only because of its impact on human and animal health but also because of the economic and social impact on agrarian communities. Leptospirosis is endemic in Sri Lanka where paddy farming activities, the use of draught animals in agriculture, and peridomestic animals in urban and rural areas play important roles in maintaining the infection cycle of pathogenic Leptospira, especially concerning animals as a potential reservoir. In this study, an environmental DNA (eDNA) metabarcoding methodology was applied in two different agro-ecological regions of Sri Lanka to understand the eco-epidemiology of leptospirosis. Methodology/Principal findings Irrigation water samples were collected in Kandy District (wet zone mid-country region 2) and Girandurukotte, Badulla District (intermediate zone low-country region 2); and analysed for the presence of pathogenic Leptospira, associated microbiome and the potential reservoir animals. Briefly, we generated PCR products for high-throughput sequencing of multiple amplicons through next-generation sequencing. The analysis of eDNA showed different environmental microbiomes in both regions and a higher diversity of Leptospira species circulating in Kandy than in Girandurukotte. Moreover, the number of sequence reads of pathogenic Leptospira species associated with clinical cases such as L. interrogans was higher in Kandy than in Girandurukotte. Kandy also showed more animal species associated with pathogenic bacterial species than Girandurukotte. Finally, several pathogenic bacterial species including Arcobacter cryaerophilus, responsible for abortion in animals, was shown to be associated with pathogenic Leptospira.

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Environmental DNA metabarcoding to detect pathogenic Leptospira and associated organisms in leptospirosis-endemic areas of Japan

Cited by 39 publications

References 69 publications

Prevalence and risk factors of Leptospira infection in urban brown rats (Rattus norvegicus), Vienna, Austria

Prevalence and risk factors of Leptospira infection in urban brown rats (Rattus norvegicus), Vienna, Austria

A systematic review of Leptospira in water and soil environments

Understanding leptospirosis eco-epidemiology by environmental DNA metabarcoding of irrigation water from two agro-ecological regions of Sri Lanka

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