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Comparative genomic analysis of Leptospira spp. isolated from Rattus norvegicus in Indonesia 收藏

钩端螺旋体属的比较基因组分析。从印度尼西亚的Rattus Norvegicus分离

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作者

作者单位

[a]aDepartment of Bacteriology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, JapanDepartment of Bacteriology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan[b]bIndonesian Research Center for Veterinary Science (BB Litvet), Jl. RE Martadinata No. 30, Bogor, West Java 16114, IndonesiaIndonesian Research Center for Veterinary Science (BB Litvet), Jl. RE Martadinata No. 30, Bogor, West Java 16114, Indonesia[c]cBogor Municipality Food Security and Agriculture Service, Jl. Cipaku No. 5, Bogor, IndonesiaBogor Municipality Food Security and Agriculture Service, Jl. Cipaku No. 5, Bogor, Indonesia[d]dBacterial Enteric and Emerging Diseases Laboratory, Center for Research, Diagnostics and Vaccine Development, Centers for Disease Control, Taiwan, No. 161 Kun-Yang Street, Taipei 11561, TaiwanBacterial 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[e]eSan Lazaro Hospital, Quiricada St Santa Cruz, Manila, Metro Manila 1003, PhilippinesSan Lazaro Hospital, Quiricada St Santa Cruz, Manila, Metro Manila 1003, Philippines[f]fDepartment of Microbiology, Faculty of Medicine, Oita University, 1-1 Idaigaoka, Hasamamachi, Yufu, Oita 879-5593, JapanDepartment of Microbiology, Faculty of Medicine, Oita University, 1-1 Idaigaoka, Hasamamachi, Yufu, Oita 879-5593, Japan[g]gSchool of Tropical Medicine and Global Health, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, Nagasaki 852-8523, JapanSchool of Tropical Medicine and Global Health, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, Nagasaki 852-8523, Japan[h]hDepartment of Clinical Tropical Medicine, Institute of Tropical Medicine, Nagasaki University Graduate School of Biomedical Science, 1-12-4 Sakamoto, Nagasaki, Nagasaki 852-8523, JapanDepartment of Clinical Tropical Medicine, Institute of Tropical Medicine, Nagasaki University Graduate School of Biomedical Science, 1-12-4 Sakamoto, Nagasaki, Nagasaki 852-8523, Japan[i]iDepartment of Bacteriology, National Institute of Hygiene and Epidemiology, Hanoi 10000, Viet NamDepartment of Bacteriology, National Institute of Hygiene and Epidemiology, Hanoi 10000, Vietnam[j]jGraduate School of Human Life Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka, Osaka 558-8585, JapanGraduate School of Human Life Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka, Osaka 558-8585, Japan[k]kDepartment of Veterinary Medical Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, JapanDepartment 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

关键词

Asia;Comparative genomics;Leptospira;Leptospirosis;Rattus norvegicus;Whole genome sequencing;

关键词译文

亚洲；比较基因组学；钩端螺旋体；钩端螺旋体病；诺维古斯氏菌；整个基因组测序；

发布日期

1 August 2022

DOI

10.1016/j.meegid.2022.105306

来源信息

Infection, Genetics and Evolution ISSN：1567-1348, 2022年, 102卷

摘要

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.

摘要译文

钩端螺旋体病是由钩端螺旋体属的致病性螺旋体引起的最普遍的人畜共患病之一。这种疾病已成为热带地区城市地区的公共卫生问题，在那里，大鼠是钩端螺旋体病的重要储层动物。在印度尼西亚，钩端螺旋体病的发生被低估了，有关诱发性钩端螺旋体基因型和血清型的信息受到限制。这项研究报告了钩端螺旋体属的分离。来自印度尼西亚博戈市区捕获的大鼠。对于分离株，确定了血清群和基因型，序列类型（STS）或使用11个基因座的多级别可变串联重复分析（MLVA）类型。此外，对其他亚洲国家的11个印尼分离株和24个分离株进行了整个基因组测序（WGS）。捕获了90个小型哺乳动物，包括80种Rattus Norvegicus和10个Suncus Murinus，以及25个leptospira spp。仅从R. norvegicus（31.3％）中分离出来。分离株被鉴定为具有ST 143（四个菌株）和链球菌的血清群和与来自其他亚洲国家的分离株相同的MLVA类型的Leptospira borgpetersenii javanica Javanica（19）；无法识别出具有ST252的两个L.杂物的血清群。基于基因组SNP的核心基因组的系统发育树显示，印尼分离株与Borgpetersenii血清群爪哇瘤菌株在亚洲国家广泛分布，但与其他菌株形成了不同的簇。来自印度尼西亚，菲律宾，台湾和越南的探究血清群的系统发育树表明，基于其地理位置将分离株分为五个簇。这项研究发现了较高的leptospira spp的运输速率。在印度尼西亚博戈的Norvegicus R. Norvegicus中，表明该地区有大鼠钩端螺旋体病的潜在风险。除了Borgpetersenii血清群Javanica之外，WGS上的WGS在L. extressogans serrogroup Bataviae上说明了Leptospira spp中遗传多样性的地理结构。

Nobuo Koizumi[a];Masatomo Morita[a];Harimurti Nuradji[b];Susan M. Noor[b];N.L.P. Indi Dharmayanti[b];Patriantariksina Randusari[c];Jung-Jung Mu[d];Rontgene M. Solante[e];Nobuo Saito[f][g];Koya Ariyoshi[g][h];Hoang Thi Thu Ha[i];Takayuki Wada[j];Yukihiro Akeda[a];Kozue Miura[k]. Comparative genomic analysis of Leptospira spp. isolated from Rattus norvegicus in Indonesia[J]. Infection, Genetics and Evolution, 2022,102