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Philip N, Ahmed K. Leptospirosis in Malaysia: current status, insights, and future prospects. J Physiol Anthropol 2023; 42:30. [PMID: 38087323 PMCID: PMC10714552 DOI: 10.1186/s40101-023-00347-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/16/2023] [Indexed: 12/18/2023] Open
Abstract
Among zoonotic infections, leptospirosis has a worldwide distribution and high prevalence in tropical regions. It has a broad clinical presentation from mild to severe, life-threatening infection. Leptospires, the etiological agent of leptospirosis, are found in varied ecological niches and animal species, providing a significant source of human infection. This review aims to provide the current status of leptospirosis in Malaysia and the direction for future studies. The literature search for this review was performed using PubMed, Web of Sciences, and Google Scholar databases. The incidence of leptospirosis in Malaysia from 2004 to 2020 varied; however, a large number of cases occurred during floods. Leptospira has been isolated from wild and domestic animals as well as from the environment; among them, several novel species have been identified. In Malaysia, leptospirosis infection and death were mostly associated with recreational and non-recreational water activities. Despite the endemicity of leptospirosis, the public's knowledge, attitude, and practice level are relatively low in this country. More studies are needed in Malaysia to explore the extent of leptospirosis in different settings and locations.
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Affiliation(s)
- Noraini Philip
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | - Kamruddin Ahmed
- Department of Pathology and Microbiology, Faculty of Medicine and Health Sciences, University Malaysia Sabah, Kota Kinabalu, Malaysia.
- Borneo Medical and Health Research Centre, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Kota Kinabalu, Malaysia.
- Research Center for Global and Local Infectious Diseases, Oita University, Oita, Japan.
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Bradley EA, Lockaby G. Leptospirosis and the Environment: A Review and Future Directions. Pathogens 2023; 12:1167. [PMID: 37764975 PMCID: PMC10538202 DOI: 10.3390/pathogens12091167] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/31/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Leptospirosis is a zoonotic disease of global importance with significant morbidity and mortality. However, the disease is frequently overlooked and underdiagnosed, leading to uncertainty of the true scale and severity of the disease. A neglected tropical disease, leptospirosis disproportionately impacts disadvantaged socioeconomic communities most vulnerable to outbreaks of zoonotic disease, due to contact with infectious animals and contaminated soils and waters. With growing evidence that Leptospira survives, persists, and reproduces in the environment, this paper reviews the current understanding of the pathogen in the environment and highlights the unknowns that are most important for future study. Through a systematic Boolean review of the literature, our study finds that detailed field-based study of Leptospira prevalence, survival, and transmission in natural waters and soils is lacking from the current literature. This review identified a strong need for assessment of physical characteristics and biogeochemical processes that support long-term viability of Leptospira in the environment followed by epidemiological assessment of the transmission and movement of the same strains of Leptospira in the present wildlife and livestock as the first steps in improving our understanding of the environmental stage of the leptospirosis transmission cycle.
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Affiliation(s)
- Elizabeth A. Bradley
- College of Forestry, Wildlife, and Environment, Auburn University, Auburn, AL 36849, USA
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3
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Akaba Y, Kudo Y, Ket V, Ket V, Rin E, Masuzawa T. Identification of Leptospira Species in Environmental Soil of Urban Settlements in Cambodia. Vector Borne Zoonotic Dis 2023; 23:291-297. [PMID: 36927062 DOI: 10.1089/vbz.2022.0052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
Abstract
Background: Leptospirosis represents a major public health threat in Cambodia. To help establish preventive strategies for leptospirosis, we isolated and identified Leptospira from soil collected in Phnom Penh and its neighboring province during the dry and rainy seasons. Materials and Methods: Soil samples were collected from 15 sites in the Phnom Penh metropolitan area and Kandal Province in 2019 and 2020. A total of 120 soil samples were collected and analyzed after culturing. Cultured isolates were identified at the species level using 16S rRNA and gyrB gene sequencing analysis. Results: The positive culture rate for Leptospira was significantly higher for samples collected during the rainy season (31 out of 60 samples, 51.7%) than during the dry season (19 out of 60 samples; p < 0.05, chi-squared test). In terms of sampling area, 10 (35.7%) and 13 (46.9%) soil samples from Phnom Penh and 9 (28.1%) and 18 (56.3%) soil samples from Kandal Province were culture-positive when collected during the dry and rainy seasons, respectively. Three isolates from the Kandal samples collected during the dry season were categorized as pathogenic clade type P1 according to 16S rRNA and gyrB sequence analyses. In addition, samples collected during the rainy season from Phnom Penh and Kandal Province (three each) were categorized as clade type P1. The samples with isolates in clade type P1 were collected from riverbanks during both the dry and rainy seasons and from a hospital garden during the rainy season. Conclusions: This is the first report on the isolation of clade P1 Leptospira species in environmental soil samples from Cambodia. Environmental soil appears to be a reservoir for Leptospira in the capital city and surrounding areas of Cambodia. This study contributes to the understanding of Leptospira species distribution in Asian countries.
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Affiliation(s)
- Yuka Akaba
- Department of Clinical Laboratory, International University of Health and Welfare Narita Hospital, Chiba Prefecture, Japan
| | - Yoshiko Kudo
- International Exchange Center, Showa University, Tokyo, Japan
| | - Vansith Ket
- Samaki Medical Laboratory, Phnom Penh, Cambodia
| | - Vansen Ket
- Samaki Medical Laboratory, Phnom Penh, Cambodia
| | - En Rin
- Samaki Medical Laboratory, Phnom Penh, Cambodia
| | - Toshiyuki Masuzawa
- Faculty of Pharmaceutical Sciences, Chiba Institute of Science, Chiba Prefecture, Japan
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Fernandes LGV, Stone NE, Roe CC, Goris MGA, van der Linden H, Sahl JW, Wagner DM, Nally JE. Leptospira sanjuanensis sp. nov., a pathogenic species of the genus Leptospira isolated from soil in Puerto Rico. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two spirochetes (designated strains LGVF01 and LGVF02T) were isolated from soil samples in San Juan, Puerto Rico in HAN media after selection using a combination of ELISA, agar plating, and colony screening by Fluorescent Antibody Testing (FAT) and PCR for lipL32 and secY. Isolates were helix-shaped, aerobic, fast-growing, and highly motile. Genome sequence analysis indicated that both strains should be classified as members of a novel species within the pathogenic (P1) clade of the genus
Leptospira
. The average nucleotide identity between the two strains was 99.2 %, but below 93.2 % when compared to any previously described leptospiral species. Serotyping of strain LGVF02T indicates that it does not belong within any serogroup of
Leptospira
suggesting it also represents a new serovar. Collectively, strains LGVF01 and LGVF02T represent a new species of pathogenic leptospires for which the name Leptospira sanjuanensis sp. nov. is proposed. The type strain is LGVF02T (=NVSL-LGVF02T=KIT0302T).
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Affiliation(s)
- Luis G. V. Fernandes
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, São Paulo 05503-900, Brazil
- Infectious Bacterial Diseases Research Unit, ARS, United States Department of Agriculture, Ames, IA, USA
| | - Nathan E. Stone
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Chandler C. Roe
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Marga G. A. Goris
- Department of Medical Microbiology and Infection Prevention, OIE and National Collaborating Centre for Reference and Research on Leptospirosis, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Hans van der Linden
- Department of Medical Microbiology and Infection Prevention, OIE and National Collaborating Centre for Reference and Research on Leptospirosis, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Jason W. Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - David M. Wagner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Jarlath E. Nally
- Infectious Bacterial Diseases Research Unit, ARS, United States Department of Agriculture, Ames, IA, USA
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Gomard Y, Goodman SM, Soarimalala V, Turpin M, Lenclume G, Ah-Vane M, Golden CD, Tortosa P. Co-Radiation of Leptospira and Tenrecidae (Afrotheria) on Madagascar. Trop Med Infect Dis 2022; 7:tropicalmed7080193. [PMID: 36006285 PMCID: PMC9415048 DOI: 10.3390/tropicalmed7080193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/12/2022] [Accepted: 08/16/2022] [Indexed: 11/26/2022] Open
Abstract
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.
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Affiliation(s)
- Yann Gomard
- Unité Mixte de Recherche Processus Infectieux en Milieu Insulaire Tropical (UMR PIMIT), Université de La Réunion, CNRS 9192, INSERM 1187, IRD 249, Plateforme Technologique CYROI, 97490 Sainte-Clotilde, France
| | - Steven M. Goodman
- Association Vahatra, BP 3972, Antananarivo 101, Madagascar
- Field Museum of Natural History, Chicago, IL 60605, USA
| | | | - Magali Turpin
- Unité Mixte de Recherche Processus Infectieux en Milieu Insulaire Tropical (UMR PIMIT), Université de La Réunion, CNRS 9192, INSERM 1187, IRD 249, Plateforme Technologique CYROI, 97490 Sainte-Clotilde, France
| | - Guenaëlle Lenclume
- Unité Mixte de Recherche Processus Infectieux en Milieu Insulaire Tropical (UMR PIMIT), Université de La Réunion, CNRS 9192, INSERM 1187, IRD 249, Plateforme Technologique CYROI, 97490 Sainte-Clotilde, France
| | - Marion Ah-Vane
- Unité Mixte de Recherche Processus Infectieux en Milieu Insulaire Tropical (UMR PIMIT), Université de La Réunion, CNRS 9192, INSERM 1187, IRD 249, Plateforme Technologique CYROI, 97490 Sainte-Clotilde, France
| | - Christopher D. Golden
- Department of Nutrition, Harvard TH Chan School of Public Health, Boston, MA 02115, USA
- Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA 02115, USA
| | - Pablo Tortosa
- Unité Mixte de Recherche Processus Infectieux en Milieu Insulaire Tropical (UMR PIMIT), Université de La Réunion, CNRS 9192, INSERM 1187, IRD 249, Plateforme Technologique CYROI, 97490 Sainte-Clotilde, France
- Correspondence:
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Sato Y, Hermawan I, Kakita T, Okano S, Imai H, Nagai H, Kimura R, Yamashiro T, Kajita T, Toma C. Analysis of human clinical and environmental Leptospira to elucidate the eco-epidemiology of leptospirosis in Yaeyama, subtropical Japan. PLoS Negl Trop Dis 2022; 16:e0010234. [PMID: 35358181 PMCID: PMC8970387 DOI: 10.1371/journal.pntd.0010234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 02/05/2022] [Indexed: 01/10/2023] Open
Abstract
Background Leptospirosis, a zoonosis caused by species in the spirochete genus Leptospira, is endemic to the Yaeyama region in Okinawa, subtropical Japan. Species of the P1 subclade “virulent” group, within the genus Leptospira, are the main etiological agents of leptospirosis in Okinawa. However, their environmental persistence is poorly understood. This study used a combination of bacterial isolation and environmental DNA (eDNA) metabarcoding methods to understand the eco-epidemiology of leptospirosis in this endemic region. Findings Polymerase chain reaction (PCR) characterized twelve human clinical L. interrogans isolates belonging to the P1 subclade “virulent” subgroup and 11 environmental soil isolates of the P1subclade “low virulent” subgroup (genetically related to L. kmetyi, n = 1; L. alstonii, n = 4; L. barantonii, n = 6) from the Yaeyama region targeting four virulence-related genes (lipL32, ligA, ligB and lpxD1). Clinical isolates were PCR positive for at least three targeted genes, while all environmental isolates were positive only for lipL32. Analysis of infected renal epithelial cells with selected clinical and environmental strains, revealed the disassembly of cell-cell junctions for the Hebdomadis clinical strain serogroup. Comparison of leptospiral eDNA during winter and summer identified operational taxonomic units corresponding to the species isolated from soil samples (L. kmetyi and L. barantonii) and additional P2 subclade species (L. licerasiae, L. wolffii-related, among others) that were not detected by soil cultivation. Total Leptospira read counts were higher in summer than in winter and the analysis of leptospiral/animal eDNA relationship suggested Rattus spp. as a potential reservoir animal. Conclusion Our study demonstrated high environmental Leptospira diversity in the Yaeyama region, particularly during summer, when most of the leptospirosis cases are reported. In addition, several Leptospira species with pathogenic potential were identified that have not yet been reported in Yaeyama; however, the environmental persistence of P1 subclade species previously isolated from human clinical cases in this region was absent, suggesting the need of further methodology development and surveillance. Leptospirosis is a widespread bacterial zoonosis and one of the most important acute febrile infectious disease in tropical and subtropical regions, which is difficult to differentiate from other infectious diseases common in these regions. Leptospirosis is endemic to Okinawa prefecture, the southernmost prefecture of Japan, where the infection occurs mainly after recreational activities in rivers in the northern part of Okinawa Main Island and the Yaeyama region. This study combined several methods such as bacterial isolation from soil and environmental DNA metabarcoding from river water samples to understand the persistence of Leptospira outside the human host, leptospiral diversity in the environment, and their potential reservoir animals in the wild environment of the Yaeyama region. Although this study didn’t confirm the environmental persistence of Leptospira species previously isolated from clinical cases, several newly reported Leptospira species with pathogenic potential from the Yaeyama region suggested the need for continual surveillance to improve leptospirosis control and prevention in this region.
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Affiliation(s)
- Yukuto Sato
- Research Laboratory Center, Faculty of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan
- Center for Strategic Research Project, Organization for Research Promotion, University of the Ryukyus, Nishihara, Okinawa, Japan
- * E-mail: (YS); (CT)
| | - Idam Hermawan
- Department of Bacteriology, Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Tetsuya Kakita
- Department of Biological Sciences, Okinawa Prefectural Institute of Health and Environment, Uruma-shi, Okinawa, Japan
| | - Sho Okano
- Department of Biological Sciences, Okinawa Prefectural Institute of Health and Environment, Uruma-shi, Okinawa, Japan
| | - Hideyuki Imai
- Department of Chemistry, Biology and Marine Science; Faculty of Science, University of the Ryukyus, Nishihara, Japan
| | - Hiroto Nagai
- Department of Chemistry, Biology and Marine Science; Faculty of Science, University of the Ryukyus, Nishihara, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Tetsu Yamashiro
- Department of Bacteriology, Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Tadashi Kajita
- Iriomote Station, Tropical Biosphere Research Center, University of the Ryukyus, Taketomi, Okinawa, Japan
- United Graduate School of Agricultural Science, Kagoshima University, Kagoshima, Japan
| | - Claudia Toma
- Department of Bacteriology, Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan
- * E-mail: (YS); (CT)
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Nakao R, Masuzawa T, Nakamura S, Koizumi N. Complete Genome Sequence of Leptospira kobayashii Strain E30, Isolated from Soil in Japan. Microbiol Resour Announc 2021; 10:e0090721. [PMID: 34761960 PMCID: PMC8582313 DOI: 10.1128/mra.00907-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 10/22/2021] [Indexed: 11/20/2022] Open
Abstract
The spirochete bacterium Leptospira kobayashii is a recently designated species of the genus Leptospira. Here, we report the complete genome sequence of L. kobayashii strain E30, consisting of two circular chromosomes and two plasmids.
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Affiliation(s)
- Ryo Nakao
- Laboratory of Parasitology, Department of Disease Control, Graduate School of Infectious Diseases, Faculty of Veterinary Medicine, Hokkaido University, Hokkaido, Japan
| | - Toshiyuki Masuzawa
- Laboratory of Microbiology and Immunology, Faculty of Pharmaceutical Sciences, Chiba Institute of Science, Chiba, Japan
| | - Shuichi Nakamura
- Department of Applied Physics, Graduate School of Engineering, Tohoku University, Miyagi, Japan
| | - Nobuo Koizumi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
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Philip N, Jani J, Azhari NN, Sekawi Z, Neela VK. In vivo and in silico Virulence Analysis of Leptospira Species Isolated From Environments and Rodents in Leptospirosis Outbreak Areas in Malaysia. Front Microbiol 2021; 12:753328. [PMID: 34803975 PMCID: PMC8602918 DOI: 10.3389/fmicb.2021.753328] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/08/2021] [Indexed: 12/22/2022] Open
Abstract
The zoonotic disease leptospirosis is caused by pathogenic species of the genus Leptospira. With the advancement of studies in leptospirosis, several new species are being reported. It has always been a query, whether Leptospira species, serovars, and strains isolated from different geographical locations contribute to the difference in the disease presentations and severity. In an epidemiological surveillance study performed in Malaysia, we isolated seven novel intermediate and saprophytic species (Leptospira semungkisensis, Leptospira fletcheri, Leptospira langatensis, Leptospira selangorensis, Leptospira jelokensis, Leptospira perdikensis, Leptospira congkakensis) from environments and three pathogenic species from rodents (Leptospira borgpetersenii strain HP364, Leptospira weilii strain SC295, Leptospira interrogans strain HP358) trapped in human leptospirosis outbreak premises. To evaluate the pathogenic potential of these isolates, we performed an in vivo and in silico virulence analysis. Environmental isolates and strain HP364 did not induce any clinical manifestations in hamsters. Strain SC295 caused inactivity and weight loss with histopathological changes in kidneys, however, all hamsters survived until the end of the experiment. Strain HP358 showed a high virulent phenotype as all infected hamsters died or were moribund within 7 days postinfection. Lungs, liver, and kidneys showed pathological changes with hemorrhage as the main presentation. In silico analysis elucidated the genome size of strain HP358 to be larger than strains HP364 and SC295 and containing virulence genes reported in Leptospira species and a high number of specific putative virulence factors. In conclusion, L. interrogans strain HP358 was highly pathogenic with fatal outcome. The constituent of Leptospira genomes may determine the level of disease severity and that needs further investigations.
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Affiliation(s)
- Noraini Philip
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor, Malaysia
| | - Jaeyres Jani
- Borneo Medical and Health Research Center, Universiti Malaysia Sabah, Sabah, Malaysia
| | - Nurul Natasya Azhari
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor, Malaysia
| | - Zamberi Sekawi
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor, Malaysia
| | - Vasantha Kumari Neela
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor, Malaysia
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Chaiwattanarungruengpaisan S, Thepapichaikul W, Paungpin W, Ketchim K, Suwanpakdee S, Thongdee M. Potentially Pathogenic Leptospira in the Environment of an Elephant Camp in Thailand. Trop Med Infect Dis 2020; 5:tropicalmed5040183. [PMID: 33291225 PMCID: PMC7768412 DOI: 10.3390/tropicalmed5040183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 11/16/2022] Open
Abstract
Leptospira is the causative agent of leptospirosis, a globally emerging zoonotic disease. The infection is commonly acquired through contact with the contaminated environment. To extend the knowledge on environmental source of leptospirosis, we investigated the presence of Leptospira in an elephant camp setting where the interaction between humans, animals, and the shared environment occur particularly when engaging in recreational activities. In this study, a total of 24 environmental samples were collected from an elephant camp area in western Thailand. All samples were processed for Leptospira isolation using the EMJH medium. The identification of Leptospira species was carried out by partial 16S rRNA and secY gene sequencing. Of those 24 samples, 18 samples (75%) were culture-positive for Leptospira. The recovered leptospires were mostly derived from water and soil sampled from a river and a mud pond, the main areas for recreational activities. The majority of the isolates were classified into “Pathogens” clade (89%, 16/18) and more than half of the isolates (61%, 11/18) contained species of the “Saprophytes” clade. Notably, two soil isolates from the river beach sampling area were found to contain leptospiral DNA with high similarity to the pathogenic L. interrogans and L. santarosai. The evidence of diverse Leptospira species, particularly those belonging to the “Pathogens” clade, suggest that the shared environments of an elephant camp can serve as potential infection source and may pose a risk to the elephant camp tourists and workers.
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Affiliation(s)
- Somjit Chaiwattanarungruengpaisan
- The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Salaya, Nakhon Pathom 73170, Thailand; (S.C.); (W.P.); (K.K.); (S.S.)
| | - Wasinee Thepapichaikul
- Livestock and Wildlife Hospital, Faculty of Veterinary Science, Mahidol University, Sai Yok, Kanchanaburi 71150, Thailand;
| | - Weena Paungpin
- The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Salaya, Nakhon Pathom 73170, Thailand; (S.C.); (W.P.); (K.K.); (S.S.)
| | - Kanokwan Ketchim
- The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Salaya, Nakhon Pathom 73170, Thailand; (S.C.); (W.P.); (K.K.); (S.S.)
| | - Sarin Suwanpakdee
- The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Salaya, Nakhon Pathom 73170, Thailand; (S.C.); (W.P.); (K.K.); (S.S.)
- Department of Clinical Sciences and Public Health, Faculty of Veterinary Science, Mahidol University, Salaya, Nakhon Pathom 73170, Thailand
| | - Metawee Thongdee
- The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Salaya, Nakhon Pathom 73170, Thailand; (S.C.); (W.P.); (K.K.); (S.S.)
- Correspondence: ; Tel.: +66-2441-5236
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10
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Gamage CD, Sato Y, Kimura R, Yamashiro T, Toma C. Understanding leptospirosis eco-epidemiology by environmental DNA metabarcoding of irrigation water from two agro-ecological regions of Sri Lanka. PLoS Negl Trop Dis 2020; 14:e0008437. [PMID: 32701971 PMCID: PMC7377381 DOI: 10.1371/journal.pntd.0008437] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/01/2020] [Indexed: 02/06/2023] Open
Abstract
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. Conclusions/Significance Leptospirosis has been considered to be endemic in wet regions, consistently, leptospiral sequences were detected strongly in Kandy. The great Leptospira species diversity in Kandy observed in this study shows that the etiological agents of leptospirosis in Sri Lanka might be underestimated. Furthermore, our eDNA metabarcoding can be used to discriminate bacterial and animal species diversity in different regions and to explore environmental microbiomes to identify other associated bacterial pathogens in the environment. Leptospirosis is a widespread bacterial zoonosis with increasing importance due to its vast range of reservoir hosts. Early symptoms are shared by other infectious diseases common in tropical and sub-tropical regions, where the real burden and risk factors need to be known. In Sri Lanka, leptospirosis is mostly an occupational disease associated with freshwater or animal exposure in agriculture communities. Thus, there is a need for understanding the epidemiology of leptospirosis in agrarian regions of the country for developing better prevention and intervention strategies. In this study, we applied an environmental DNA metabarcoding methodology to understand the environmental microbiome, potential reservoir animals and the Leptospira species circulating in two different agro-ecological regions of Sri Lanka: Kandy (wet region mid-country region 2) and Girandurukotte (intermediate region low-country region 2). It is known that pathogenic Leptospira are excreted through the urine of reservoir animals in the environment, where they can persist in humid conditions. Congruently, this study showed a higher detection of pathogenic Leptospira in the environment of Kandy where the environmental microbiome showed a higher diversity than Girandurukotte. Potential animal reservoirs were also detected in samples positive for pathogenic Leptospira, suggesting that environmental DNA metabarcoding can provide important information for management and intervention strategies to control leptospirosis.
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Affiliation(s)
- Chandika D. Gamage
- Department of Microbiology, Faculty of Medicine, University of Peradeniya, Peradeniya, Kandy, Sri Lanka
| | - Yukuto Sato
- Center for Strategic Research Project, Organization for Research Promotion, University of the Ryukyus, Nishihara, Okinawa, Japan
- * E-mail: (YS); (CT)
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Tetsu Yamashiro
- Department of Bacteriology, Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Claudia Toma
- Department of Bacteriology, Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan
- * E-mail: (YS); (CT)
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Philip N, Bahtiar Affendy N, Ramli SNA, Arif M, Raja P, Nagandran E, Renganathan P, Taib NM, Masri SN, Yuhana MY, Than LTL, Seganathirajah M, Goarant C, Goris MGA, Sekawi Z, Neela VK. Leptospira interrogans and Leptospira kirschneri are the dominant Leptospira species causing human leptospirosis in Central Malaysia. PLoS Negl Trop Dis 2020; 14:e0008197. [PMID: 32203511 PMCID: PMC7117766 DOI: 10.1371/journal.pntd.0008197] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 04/02/2020] [Accepted: 03/03/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Leptospirosis, commonly known as rat-urine disease, is a global but endemic zoonotic disease in the tropics. Despite the historical report of leptospirosis in Malaysia, the information on human-infecting species is limited. Determining the circulating species is important to understand its epidemiology, thereby to strategize appropriate control measures through public health interventions, diagnostics, therapeutics and vaccine development. METHODOLOGY/PRINCIPLE FINDINGS We investigated the human-infecting Leptospira species in blood and serum samples collected from clinically suspected leptospirosis patients admitted to three tertiary care hospitals in Malaysia. From a total of 165 patients, 92 (56%) were confirmed cases of leptospirosis through Microscopic Agglutination Test (MAT) (n = 43; 47%), Polymerase Chain Reaction (PCR) (n = 63; 68%) or both MAT and PCR (n = 14; 15%). The infecting Leptospira spp., determined by partial 16S rDNA (rrs) gene sequencing revealed two pathogenic species namely Leptospira interrogans (n = 44, 70%) and Leptospira kirschneri (n = 17, 27%) and one intermediate species Leptospira wolffii (n = 2, 3%). Multilocus sequence typing (MLST) identified an isolate of L. interrogans as a novel sequence type (ST 265), suggesting that this human-infecting strain has a unique genetic profile different from similar species isolated from rodents so far. CONCLUSIONS/SIGNIFICANCE Leptospira interrogans and Leptospira kirschneri were identified as the dominant Leptospira species causing human leptospirosis in Central Malaysia. The existence of novel clinically important ST 265 (infecting human), that is different from rodent L. interrogans strains cautions reservoir(s) of these Leptospira lineages are yet to be identified.
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Affiliation(s)
- Noraini Philip
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Norliza Bahtiar Affendy
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Siti Nur Alia Ramli
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Muhamad Arif
- Center of Excellence in Life Sciences, Bharathidasan University, Tiruchirappalli, India
| | - Pappitha Raja
- School of Medicine, Dentistry and Biomedical Sciences, Queens University, Belfast, Northern Ireland, United Kingdom
| | - Elanngovan Nagandran
- Clinical Research Centre Unit, Tengku Ampuan Rahimah Hospital, Ministry of Health Malaysia, Klang, Selangor, Malaysia
| | - Pukunan Renganathan
- Clinical Research Centre Unit, Tengku Ampuan Rahimah Hospital, Ministry of Health Malaysia, Klang, Selangor, Malaysia
| | - Niazlin Mohd Taib
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Siti Norbaya Masri
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Muhamad Yazli Yuhana
- Infectious Diseases Unit, Internal Medicine Department, Universiti Teknologi MARA, Sungai Buloh, Selangor, Malaysia
| | - Leslie Thian Lung Than
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Mithra Seganathirajah
- General Medicine, Hospital Serdang, Ministry of Health Malaysia, Jalan Puchong, Kajang, Selangor, Malaysia
| | - Cyrille Goarant
- Institut Pasteur de Noume´a, Leptospirosis Research and Expertise Unit, Noume´a, New Caledonia
| | - Marga G. A. Goris
- OIE and National Collaborating Centre for Reference and Research on Leptospirosis Academic Medical Center, Department of Medical Microbiology, University of Amsterdam, Amsterdam, the Netherlands
| | - Zamberi Sekawi
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Vasantha Kumari Neela
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
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12
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Bierque E, Thibeaux R, Girault D, Soupé-Gilbert ME, Goarant C. A systematic review of Leptospira in water and soil environments. PLoS One 2020; 15:e0227055. [PMID: 31986154 PMCID: PMC6984726 DOI: 10.1371/journal.pone.0227055] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 12/10/2019] [Indexed: 01/02/2023] Open
Abstract
Background Leptospirosis, caused by pathogenic Leptospira, is a zoonosis of global distribution. This infectious disease is mainly transmitted by indirect exposure to urine of asymptomatic animals via the environment. As human cases generally occur after heavy rain, an emerging hypothesis suggests that rainfall re-suspend leptospires together with soil particles. Bacteria are then carried to surface water, where humans get exposed. It is currently assumed that pathogenic leptospires can survive in the environment but do not multiply. However, little is known on their capacity to survive in a soil and freshwater environment. Methods We conducted a systematic review on Leptospira and leptospirosis in the environment in order to collect current knowledge on the lifestyle of Leptospira in soil and water. In total, 86 scientific articles retrieved from online databases or institutional libraries were included in this study. Principals findings/significance This work identified evidence of survival of Leptospira in the environment but major gaps remain about the survival of virulent species associated with human and animal diseases. Studies providing quantitative data on Leptospira in soil and water are a very recent trend, but must be interpreted with caution because of the uncertainty in the species identification. Several studies mentioned the presence of Leptospira in soils more frequently than in waters, supporting the hypothesis of the soil habitat and dispersion of Leptospira with re-suspended soil particles during heavy rain. In a near future, the growing use of high throughput sequencing will offer new opportunities to improve our understanding of the habitat of Leptospira in the environment. This better insight into the risk of leptospirosis will allow implementing efficient control measures and prevention for the human and animal populations exposed.
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Affiliation(s)
- Emilie Bierque
- Leptospirosis Research and Expertise Unit, Institut Pasteur in New Caledonia, Institut Pasteur International Network, Noumea, New Caledonia
| | - Roman Thibeaux
- Leptospirosis Research and Expertise Unit, Institut Pasteur in New Caledonia, Institut Pasteur International Network, Noumea, New Caledonia
| | - Dominique Girault
- Leptospirosis Research and Expertise Unit, Institut Pasteur in New Caledonia, Institut Pasteur International Network, Noumea, New Caledonia
| | - Marie-Estelle Soupé-Gilbert
- Leptospirosis Research and Expertise Unit, Institut Pasteur in New Caledonia, Institut Pasteur International Network, Noumea, New Caledonia
| | - Cyrille Goarant
- Leptospirosis Research and Expertise Unit, Institut Pasteur in New Caledonia, Institut Pasteur International Network, Noumea, New Caledonia
- * E-mail:
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13
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Masuzawa T, Uno R, Matsuhashi N, Yamaguchi M, Xu J, Nakamura S. Comparison of Leptospira species isolated from environmental water and soil in Japan. Microbiol Immunol 2019; 63:469-473. [PMID: 31444810 DOI: 10.1111/1348-0421.12741] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 08/09/2019] [Accepted: 08/12/2019] [Indexed: 11/30/2022]
Abstract
Leptospira was isolated from environmental water in central Japan using selective medium comprising five antibiotics, namely sulfamethoxazole, trimethoprim, amphotericin B, fosfomycin, and 5-fluorouracil. Of 100 water samples 57 (57%) were culture-positive and 50 pure cultures were isolated. Of the 50 cultures isolated from water 48 were classified into a saprophytic clade on the basis of 16S ribosomal RNA gene sequences. However, it was previously reported that isolates from soil in Japan belonged to pathogenic, intermediate, and saprophytic clades, the current findings suggest less diversity of Leptospira species in environmental water than that in soil in Japan.
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Affiliation(s)
- Toshiyuki Masuzawa
- Laboratory of Microbiology and Immunology, Faculty of Pharmaceutical Sciences, Chiba Institute of Science (CIS), Choshi, Chiba, Japan
| | - Rurika Uno
- Laboratory of Microbiology and Immunology, Faculty of Pharmaceutical Sciences, Chiba Institute of Science (CIS), Choshi, Chiba, Japan
| | - Nana Matsuhashi
- Laboratory of Microbiology and Immunology, Faculty of Pharmaceutical Sciences, Chiba Institute of Science (CIS), Choshi, Chiba, Japan
| | - Masaya Yamaguchi
- Laboratory of Microbiology and Immunology, Faculty of Pharmaceutical Sciences, Chiba Institute of Science (CIS), Choshi, Chiba, Japan
| | - Jun Xu
- Department of Animal Microbiology, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, Japan
| | - Shuichi Nakamura
- Department of Applied Physics, Graduate School of Engineering, Tohoku University, Sendai, Miyagi, Japan
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14
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Revisiting the taxonomy and evolution of pathogenicity of the genus Leptospira through the prism of genomics. PLoS Negl Trop Dis 2019; 13:e0007270. [PMID: 31120895 PMCID: PMC6532842 DOI: 10.1371/journal.pntd.0007270] [Citation(s) in RCA: 267] [Impact Index Per Article: 53.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 02/28/2019] [Indexed: 12/11/2022] Open
Abstract
The causative agents of leptospirosis are responsible for an emerging zoonotic disease worldwide. One of the major routes of transmission for leptospirosis is the natural environment contaminated with the urine of a wide range of reservoir animals. Soils and surface waters also host a high diversity of non-pathogenic Leptospira and species for which the virulence status is not clearly established. The genus Leptospira is currently divided into 35 species classified into three phylogenetic clusters, which supposedly correlate with the virulence of the bacteria. In this study, a total of 90 Leptospira strains isolated from different environments worldwide including Japan, Malaysia, New Caledonia, Algeria, mainland France, and the island of Mayotte in the Indian Ocean were sequenced. A comparison of average nucleotide identity (ANI) values of genomes of the 90 isolates and representative genomes of known species revealed 30 new Leptospira species. These data also supported the existence of two clades and 4 subclades. To avoid classification that strongly implies assumption on the virulence status of the lineages, we called them P1, P2, S1, S2. One of these subclades has not yet been described and is composed of Leptospira idonii and 4 novel species that are phylogenetically related to the saprophytes. We then investigated genome diversity and evolutionary relationships among members of the genus Leptospira by studying the pangenome and core gene sets. Our data enable the identification of genome features, genes and domains that are important for each subclade, thereby laying the foundation for refining the classification of this complex bacterial genus. We also shed light on atypical genomic features of a group of species that includes the species often associated with human infection, suggesting a specific and ongoing evolution of this group of species that will require more attention. In conclusion, we have uncovered a massive species diversity and revealed a novel subclade in environmental samples collected worldwide and we have redefined the classification of species in the genus. The implication of several new potentially infectious Leptospira species for human and animal health remains to be determined but our data also provide new insights into the emergence of virulence in the pathogenic species.
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15
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Sato Y, Mizuyama M, Sato M, Minamoto T, Kimura R, Toma C. Environmental DNA metabarcoding to detect pathogenic Leptospira and associated organisms in leptospirosis-endemic areas of Japan. Sci Rep 2019; 9:6575. [PMID: 31024059 PMCID: PMC6484013 DOI: 10.1038/s41598-019-42978-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/11/2019] [Indexed: 02/06/2023] Open
Abstract
Leptospires, which cause the zoonotic disease leptospirosis, persist in soil and aqueous environments. Several factors, including rainfall, the presence of reservoir animals, and various abiotic and biotic components interact to influence leptospiral survival, persistence, and pathogenicity in the environment. However, how these factors modulate the risk of infection is poorly understood. Here we developed an approach using environmental DNA (eDNA) metabarcoding for detecting the microbiome, vertebrates, and pathogenic Leptospira in aquatic samples. Specifically, we combined 4 sets of primers to generate PCR products for high-throughput sequencing of multiple amplicons through next-generation sequencing. Using our method to analyze the eDNA of leptospirosis-endemic areas in northern Okinawa, Japan, we found that the microbiota in each river shifted over time. Operating taxonomic units corresponding to pathogenic L. alstonii, L. kmetyi, and L. interrogans were detected in association with 12 nonpathogenic bacterial species. In addition, the frequencies of 11 of these species correlated with the amount of rainfall. Furthermore, 10 vertebrate species, including Sus scrofa, Pteropus dasymallus, and Cynops ensicauda, showed high correlation with leptospiral eDNA detection. Our eDNA metabarcoding method is a powerful tool for understanding the environmental phase of Leptospira and predicting human infection risk.
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Affiliation(s)
- Yukuto Sato
- Center for Strategic Research Project, Organization for Research Promotion, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, 903-0213, Japan.
| | - Masaru Mizuyama
- Department of Bacteriology, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara, Okinawa, 903-0215, Japan.,Graduate School of Engineering and Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, 903-0213, Japan
| | - Megumi Sato
- Graduate School of Health Sciences, Niigata University, 2-746 Asahimachi-dori, Chuo-ku, Niigata, 951-8122, Japan
| | - Toshifumi Minamoto
- Graduate School of Human Development and Environment, Kobe University, 3-11 Tsurukabuto, Nada-ku, Kobe, 657-8501, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara, Okinawa, 903-0215, Japan
| | - Claudia Toma
- Department of Bacteriology, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara, Okinawa, 903-0215, Japan.
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Guglielmini J, Bourhy P, Schiettekatte O, Zinini F, Brisse S, Picardeau M. Genus-wide Leptospira core genome multilocus sequence typing for strain taxonomy and global surveillance. PLoS Negl Trop Dis 2019; 13:e0007374. [PMID: 31026256 PMCID: PMC6513109 DOI: 10.1371/journal.pntd.0007374] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 05/13/2019] [Accepted: 04/09/2019] [Indexed: 12/15/2022] Open
Abstract
Leptospira is a highly heterogeneous bacterial genus that can be divided into three evolutionary lineages and >300 serovars. The causative agents of leptospirosis are responsible of an emerging zoonotic disease worldwide. To advance our understanding of the biodiversity of Leptospira strains at the global level, we evaluated the performance of whole-genome sequencing (WGS) as a genus-wide strain classification and genotyping tool. Herein we propose a set of 545 highly conserved loci as a core genome MLST (cgMLST) genotyping scheme applicable to the entire Leptospira genus, including non-pathogenic species. Evaluation of cgMLST genotyping was undertaken with 509 genomes, including 327 newly sequenced genomes, from diverse species, sources and geographical locations. Phylogenetic analysis showed that cgMLST defines species, clades, subclades, clonal groups and cgMLST sequence types (cgST), with high precision and robustness to missing data. Novel Leptospira species, including a novel subclade named S2 (saprophytes 2), were identified. We defined clonal groups (CG) optimally using a single-linkage clustering threshold of 40 allelic mismatches. While some CGs such as L. interrogans CG6 (serogroup Icterohaemorrhagiae) are globally distributed, others are geographically restricted. cgMLST was congruent with classical MLST schemes, but had greatly improved resolution and broader applicability. Single nucleotide polymorphisms within single cgST groups was limited to <30 SNPs, underlining a potential role for cgMLST in epidemiological surveillance. Finally, cgMLST allowed identification of serogroups and closely related serovars. In conclusion, the proposed cgMLST strategy allows high-resolution genotyping of Leptospira isolates across the phylogenetic breadth of the genus. The unified genomic taxonomy of Leptospira strains, available publicly at http://bigsdb.pasteur.fr/leptospira, will facilitate global harmonization of Leptospira genotyping, strain emergence follow-up and novel collaborative studies of the epidemiology and evolution of this emerging pathogen.
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Affiliation(s)
- Julien Guglielmini
- Institut Pasteur, Bioinformatics and Biostatistics Hub, C3BI, USR 3756 IP CNRS, Paris, France
| | - Pascale Bourhy
- Institut Pasteur, Biology of Spirochetes unit, National Reference Center for Leptospirosis, Paris, France
| | - Olivier Schiettekatte
- Institut Pasteur, Biology of Spirochetes unit, National Reference Center for Leptospirosis, Paris, France
- Université Paris Diderot, Ecole Doctorale BioSPC, Paris, France
| | - Farida Zinini
- Institut Pasteur, Biology of Spirochetes unit, National Reference Center for Leptospirosis, Paris, France
| | - Sylvain Brisse
- Institut Pasteur, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Mathieu Picardeau
- Institut Pasteur, Biology of Spirochetes unit, National Reference Center for Leptospirosis, Paris, France
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Masuzawa T, Saito M, Nakao R, Nikaido Y, Matsumoto M, Ogawa M, Yokoyama M, Hidaka Y, Tomita J, Sakakibara K, Suzuki K, Yasuda S, Sato H, Yamaguchi M, Yoshida SI, Koizumi N, Kawamura Y. Molecular and phenotypic characterization of Leptospira johnsonii sp. nov., Leptospira ellinghausenii sp. nov. and Leptospira ryugenii sp. nov. isolated from soil and water in Japan. Microbiol Immunol 2019; 63:89-99. [PMID: 30817029 DOI: 10.1111/1348-0421.12671] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/07/2019] [Accepted: 02/20/2019] [Indexed: 11/27/2022]
Abstract
In a previous study, 50 of 132 soil samples collected throughout Japan were found to be Leptospira-positive. In the present study, three strains identified in the collected specimens, three, E8, E18 and YH101, were found to be divergent from previously described Leptospira species according to 16S ribosomal RNA gene sequence analysis. These three strains have a helical shape similar to that of typical Leptospira and were not re-isolated from experimental mice inoculated with the cultured strains. Upon 16S ribosomal RNA gene sequence analysis, E8 was found to belong to the intermediate Leptospira species clade and E18 and YH101 to belong to the saprophytic Leptospira species clade. Based on analyses of genome-to-genome distances and average nucleotide identity in silico using whole genome sequences and DNA-DNA hybridization in vitro, these isolates were found to be distinct from previously described Leptospira species. Therefore, these three isolates represent novel species of the genus Leptospira for which the names Leptospira johnsonii sp. nov., (type strain E8 T , = JCM 32515 T = CIP111620 T ), Leptospira ellinghausenii sp. nov., (type strain E18 T , = JCM 32516 T = CIP111618 T ) and Leptospira ryugenii sp. nov., (type strain YH101 T , = JCM 32518 T = CIP111617 T ) are proposed.
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Affiliation(s)
- Toshiyuki Masuzawa
- Laboratory of Microbiology and Immunology, Faculty of Pharmaceutical Sciences, Chiba Institute of Science (CIS), Choshi, Chiba
| | - Mitsumasa Saito
- Department of Microbiology, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Fukuoka
| | - Ryo Nakao
- Laboratory of Parasitology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido
| | - Yasuhiko Nikaido
- Department of Microbiology, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Fukuoka
| | - Masahiro Matsumoto
- Department of Microbiology, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Fukuoka
| | - Midori Ogawa
- Department of Microbiology, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Fukuoka
| | - Mitsuru Yokoyama
- Shared-Use Research Center, University of Occupational and Environmental Health, Kitakyushu, Fukuoka
| | - Yusuke Hidaka
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka
| | - Junko Tomita
- Department of Microbiology, School of Pharmacy, Aichi Gakuin University, Nagoya, Aichi
| | - Keiko Sakakibara
- Laboratory of Microbiology and Immunology, Faculty of Pharmaceutical Sciences, Chiba Institute of Science (CIS), Choshi, Chiba
| | - Kazushi Suzuki
- Laboratory of Microbiology and Immunology, Faculty of Pharmaceutical Sciences, Chiba Institute of Science (CIS), Choshi, Chiba
| | - Shima Yasuda
- Laboratory of Microbiology and Immunology, Faculty of Pharmaceutical Sciences, Chiba Institute of Science (CIS), Choshi, Chiba
| | - Hiroki Sato
- Laboratory of Microbiology and Immunology, Faculty of Pharmaceutical Sciences, Chiba Institute of Science (CIS), Choshi, Chiba
| | - Masaya Yamaguchi
- Laboratory of Microbiology and Immunology, Faculty of Pharmaceutical Sciences, Chiba Institute of Science (CIS), Choshi, Chiba
| | - Shin-Ichi Yoshida
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka
| | - Nobuo Koizumi
- Department of Bacteriology I, National Institute of Infectious Diseases, Toyama, Tokyo, Japan
| | - Yoshiaki Kawamura
- Department of Microbiology, School of Pharmacy, Aichi Gakuin University, Nagoya, Aichi
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