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Koizumi N, Morita M, Nuradji H, Noor SM, Dharmayanti NLPI, Randusari P, Mu JJ, Solante RM, Saito N, Ariyoshi K, Ha HTT, Wada T, Akeda Y, Miura K. Comparative genomic analysis of Leptospira spp. isolated from Rattus norvegicus in Indonesia. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 102:105306. [PMID: 35618255 DOI: 10.1016/j.meegid.2022.105306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 05/11/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
Leptospirosis is one of the most prevalent zoonotic diseases caused by pathogenic spirochetes of Leptospira spp. The disease has become a public health concern in urban localities in the tropics, where rats serve as significant reservoir animals for leptospirosis transmission. In Indonesia, the occurrence of leptospirosis is underestimated, and information on the causative Leptospira genotypes and serotypes is limited. This study reports the isolation of Leptospira spp. from rats captured in urban areas of Bogor, Indonesia. Serogroups and genotypes, sequence types (STs), or multiple-locus variable-number tandem repeat analysis (MLVA) types using 11 loci, were determined for the isolates. Furthermore, whole genome sequencing (WGS) was performed on 11 Indonesian isolates and 24 isolates from other Asian countries. Ninety small mammals, including 80 Rattus norvegicus and ten Suncus murinus, were captured and, 25 Leptospira spp. were isolated solely from R. norvegicus (31.3%). The isolates were identified as Leptospira borgpetersenii serogroup Javanica with ST 143 (four strains) and Leptospira interrogans serogroup Bataviae with the same MLVA type as isolates from other Asian countries (19); the serogroup of the two L. interrogans with ST252 could not be identified. The core genome SNP-based phylogenetic tree revealed that Indonesian isolates were genetically related to L. borgpetersenii serogroup Javanica strains widely distributed in Asian countries but formed a different cluster from other strains. The phylogenetic tree of L. interrogans serogroup Bataviae isolates from Indonesia, the Philippines, Taiwan, and Vietnam revealed that isolates were grouped into five clusters based on their geographic locations. This study discovered a high carriage rate of Leptospira spp. among R. norvegicus in Bogor, Indonesia, indicating a potential risk of rat-borne leptospirosis in the area. Besides L. borgpetersenii serogroup Javanica, WGS on L. interrogans serogroup Bataviae illustrated the geographical structuring of genetic diversity in Leptospira spp.
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Affiliation(s)
- Nobuo Koizumi
- Department of Bacteriology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan.
| | - Masatomo Morita
- Department of Bacteriology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Harimurti Nuradji
- Indonesian Research Center for Veterinary Science (BB Litvet), Jl. RE Martadinata No. 30, Bogor, West Java 16114, Indonesia
| | - Susan M Noor
- Indonesian Research Center for Veterinary Science (BB Litvet), Jl. RE Martadinata No. 30, Bogor, West Java 16114, Indonesia
| | - N L P Indi Dharmayanti
- Indonesian Research Center for Veterinary Science (BB Litvet), Jl. RE Martadinata No. 30, Bogor, West Java 16114, Indonesia
| | | | - Jung-Jung Mu
- Bacterial Enteric and Emerging Diseases Laboratory, Center for Research, Diagnostics and Vaccine Development, Centers for Disease Control, Taiwan, No. 161 Kun-Yang Street, Taipei 11561, Taiwan
| | - Rontgene M Solante
- San Lazaro Hospital, Quiricada St Santa Cruz, Manila, Metro Manila 1003, Philippines
| | - Nobuo Saito
- Department of Microbiology, Faculty of Medicine, Oita University, 1-1 Idaigaoka, Hasamamachi, Yufu, Oita 879-5593, Japan; School of Tropical Medicine and Global Health, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, Nagasaki 852-8523, Japan
| | - Koya Ariyoshi
- School of Tropical Medicine and Global Health, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, Nagasaki 852-8523, Japan; Department of Clinical Tropical Medicine, Institute of Tropical Medicine, Nagasaki University Graduate School of Biomedical Science, 1-12-4 Sakamoto, Nagasaki, Nagasaki 852-8523, Japan
| | - Hoang Thi Thu Ha
- Department of Bacteriology, National Institute of Hygiene and Epidemiology, Hanoi 10000, Viet Nam
| | - Takayuki Wada
- Graduate School of Human Life Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka, Osaka 558-8585, Japan
| | - Yukihiro Akeda
- Department of Bacteriology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Kozue Miura
- Department of Veterinary Medical Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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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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Molecular and serological epidemiology of Leptospira infection in cats in Okinawa Island, Japan. Sci Rep 2021; 11:10365. [PMID: 33990653 PMCID: PMC8121857 DOI: 10.1038/s41598-021-89872-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 04/26/2021] [Indexed: 12/03/2022] Open
Abstract
Leptospirosis is a zoonosis caused by pathogenic Leptospira spp. Cats have been reported to be infected with Leptospira spp. and shed the bacteria in the urine. However, the importance of cats as an infection source for humans remains unclear. In this study, Leptospira infection in cats in Okinawa Prefecture, Japan, where leptospirosis is endemic, was investigated by leptospiral antibody and DNA detection using microscopic agglutination test and nested PCR, respectively. Moreover, multilocus sequence typing (MLST) and whole genome sequencing (WGS) were conducted on the Leptospira borgpetersenii serogroup Javanica isolated from cats, black rats, a mongoose, and humans. Anti-Leptospira antibodies were detected in 16.6% (40/241) of the cats tested, and the predominant reactive serogroup was Javanica. The leptospiral flaB gene was detected in 7.1% (3/42) of cat urine samples, and their sequences were identical and identified as L. borgpetersenii. MLST and WGS revealed the genetic relatedness of L. borgpetersenii serogroup Javanica isolates. This study indicated that most seropositive cats had antibodies against the serogroup Javanica and that cats excreted L. borgpetersenii in the urine after infection. Further, genetic relatedness between cat and human isolates suggests that cats may be a maintenance host for L. borgpetersenii serogroup Javanica and a source for human infection.
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Shinya S, Muraoka Y, Negishi D, Koizumi N. Molecular epidemiology of Leptospira spp. among wild mammals and a dog in Amami Oshima Island, Japan. PLoS One 2021; 16:e0249987. [PMID: 33886632 PMCID: PMC8061989 DOI: 10.1371/journal.pone.0249987] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 03/30/2021] [Indexed: 11/23/2022] Open
Abstract
Leptospirosis is a worldwide zoonosis caused by the pathogenic Leptospira spp. Canine and human leptospirosis sometimes occur on Amami Oshima Island, located in the Nansei Archipelago, southwestern Japan; however, information on the causative Leptospira spp. on this island is quite limited. This study aimed to investigate the molecular and serological characteristics of Leptospira spp. isolated from wild animals and a dog in Amami Oshima Island. We obtained seven Leptospira strains by culturing kidney tissues of wild animals, such as black rats (2), wild boars (3), and rabbit (1) as well as blood from a symptomatic dog. Using flaB sequencing and microscopic agglutination test with antisera for 18 serovars, the isolates were identified as Leptospira borgpetersenii serogroups Javanica (black rat), L. interrogans serogroup Australis (black rat and dog), and L. interrogans serogroup Hebdomadis (wild boar and rabbit). The sequence type (ST) of L. borgpetersenii serogroup Javanica was determined to be ST143 via multilocus sequence typing (MLST) using seven housekeeping genes. For L. interrogans, MLST and multiple-locus variable-tandem repeat analysis (MLVA) revealed identical ST and MLVA types in rat and canine isolates, whereas two STs and MLVA types were identified in wild boar isolates. The STs and MLVA types of rabbit and one of the wild boars were identical. Bacterial culture and flaB-nested polymerase chain reaction demonstrated a high rate of Leptospira infection in wild boars (58.3%, 7/12), whereas Leptospira spp. were detected in 4.8% of black rats (2/42). This study revealed diverse Leptospira genotype and serotype maintenance in wild mammals on Amami Oshima Island. MLST and MLVA indicated that black rats were a source of canine infection. Wild boars carry L. interrogans and are considered an important maintenance host because antibodies against serogroup Hebdomadis were detected in human and canine leptospirosis patients on this island.
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Affiliation(s)
- So Shinya
- Yuinoshima Animal Clinic, Amami-City, Kagoshima, Japan
- * E-mail: (SS); (NK)
| | | | - Daigo Negishi
- Yuinoshima Animal Clinic, Amami-City, Kagoshima, Japan
| | - Nobuo Koizumi
- Department of Bacteriology I, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
- * E-mail: (SS); (NK)
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Koizumi N, Morita M, Pheng V, Wann C, Masuoka H, Higa Y, Wada T, Hirayama K, Ohnishi M, Miura K. Rat trade and leptospirosis: Molecular epidemiology of Leptospira species in rats exported from Cambodia to Vietnam. Transbound Emerg Dis 2021; 69:1641-1648. [PMID: 33735490 DOI: 10.1111/tbed.14077] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/09/2021] [Accepted: 03/15/2021] [Indexed: 01/12/2023]
Abstract
Rats are an important maintenance host of Leptospira spp., the causative agents of leptospirosis, a zoonotic disease with worldwide distribution. Rats are traded as food in the Mekong Delta, where Cambodia exports tons of rats to Vietnam. Handling wild rats is a potential health risk, but the information on Leptospira spp. carried by rats traded in the region remains limited. In this study, we investigated the carriage of Leptospira spp. in rats exported from Cambodia to Vietnam using bacterial culture, nested PCR and DNA sequencing. Isolates were then assessed using serological analysis and whole-genome sequencing (WGS), and Leptospira DNA detected in rat kidney tissues was also analysed by multilocus sequence typing (MLST). Seventy-two rats (2 Bandicota indica, 57 Rattus argentiventer, 11 R. losea, 1 R. norvegicus and 1 R. rattus) were subjected to bacterial culture, and three L. borgpetersenii serogroup Javanica isolates were obtained from R. argentiventer (5.3%). WGS revealed that although Cambodian isolates were genetically related to L. borgpetersenii serogroup Javanica strains widely distributed in East and South-East Asian countries, they formed a different cluster from other strains. In addition to the three L. borgpetersenii sequences, the flaB sequence of L. interrogans was detected in 18 R. argentiventer and 7 R. losea kidney tissue samples (38.9%) using nested PCR followed by DNA sequencing. The L. interrogans flaB-positive samples were further analysed by MLST, revealing that seven housekeeping genes (glmU, pntA, sucA, tpiA, pfkB, mreA and caiB) contained novel sequences with distinct lineages from other sequence types. This study revealed a high prevalence of Leptospira spp. among rats exported from Cambodia to Vietnam, indicating a potential risk to people engaging in rat trade and demonstrating that a fastidious L. interrogans strain circulates among Cambodian rats.
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Affiliation(s)
- Nobuo Koizumi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masatomo Morita
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Vutha Pheng
- Prek Leap National Institute of Agriculture, Phnom Penh, Cambodia
| | - Chinda Wann
- Prek Leap National Institute of Agriculture, Phnom Penh, Cambodia
| | - Hiroaki Masuoka
- Department of Veterinary Medical Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yukiko Higa
- Department of Medical Entomology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takayuki Wada
- Graduate School of Human Life Science, Osaka City University, Osaka, Japan
| | - Kazuhiro Hirayama
- Department of Veterinary Medical Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kozue Miura
- Department of Veterinary Medical Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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