Understanding leptospirosis eco-epidemiology by environmental DNA metabarcoding of irrigation water from two agro-ecological regions of Sri Lanka
Understanding leptospirosis eco-epidemiology by environmental DNA metabarcoding of irrigation water from two agro-ecological regions of Sri Lanka
复制标题
DOI：
10.1371/journal.pntd.0008437
复制
发表时间：
2020-07-01
影响因子：
3.8
通讯作者：
Toma, Claudia
中科院分区：
文献类型：
--
作者：
Gamage, Chandika D.;Sato, Yukuto;Toma, Claudia
钩端螺旋体病是一种广泛存在的细菌性人畜共患病，由于其广泛的储存宿主，其重要性日益增加。热带和亚热带地区常见的其他传染病也有早期症状，需要了解这些地区的真实的负担和风险因素。在斯里兰卡，钩端螺旋体病主要是一种与农业社区接触淡水或动物有关的职业病。因此，有必要了解该国农业地区钩端螺旋体病的流行病学，以制定更好的预防和干预战略。在这项研究中，我们应用环境DNA元条形码编码方法来了解环境微生物组，潜在的水库动物和在斯里兰卡的两个不同的农业生态区域循环的钩端螺旋体物种：康提（湿区中部地区2）和Girandurukotte（中部地区低地地区2）。已知致病性钩端螺旋体通过环境中宿主动物的尿液排泄，在潮湿条件下可持续存在。相应地，该研究显示，在康提环境中检出的致病性钩端螺旋体较高，其中环境微生物组显示出比Girandurukotte更高的多样性。在病原性钩端螺旋体阳性的样本中还检测到潜在的动物宿主，这表明环境DNA元条形码可以为控制钩端螺旋体病的管理和干预策略提供重要信息。背景钩端螺旋体病是世界上最重要的人畜共患疾病之一，不仅因为它对人类和动物健康的影响，还因为它对农业社区的经济和社会影响。钩端螺旋体病是斯里兰卡的地方病，其中水稻种植活动，农业中使用的耕畜，以及城市和农村地区的围产期动物在维持病原性钩端螺旋体的感染循环中发挥重要作用，特别是关于作为潜在宿主的动物。在这项研究中，环境DNA（eDNA）元条码编码方法应用于斯里兰卡的两个不同的农业生态区域，以了解钩端螺旋体病的生态流行病学。方法/主要发现在康提区（湿润区中部地区2）和Girandurukotte，Badulla区（中间区低地地区2）采集灌溉水样本;并分析是否存在致病性钩端螺旋体、相关微生物组和潜在的水库动物。简而言之，我们通过下一代测序产生了用于多个扩增子的高通量测序的PCR产物。eDNA分析显示两个地区的环境微生物组不同，康提的钩端螺旋体物种多样性高于吉兰杜鲁科特。此外，康提与临床病例相关的致病性钩端螺旋体物种（如问号钩端螺旋体）的序列读段数高于Girandurukotte。康提也显示出更多的动物物种与致病细菌物种比Girandurukotte。最后，包括嗜冷弓形杆菌在内的几种致病性细菌，与致病性钩端螺旋体有关，这些致病性细菌可导致动物流产。结论/意义钩端螺旋体病已被认为是潮湿地区的地方病，一致地，钩端螺旋体序列在康提检测到强烈。本研究中观察到的康提钩端螺旋体物种多样性表明，斯里兰卡钩端螺旋体病的病原体可能被低估。此外，我们的eDNA元条形码可用于区分不同地区的细菌和动物物种多样性，并探索环境微生物组，以识别环境中其他相关的细菌病原体。
Author summary 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 theLeptospiraspecies 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 pathogenicLeptospiraare 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 pathogenicLeptospirain the environment of Kandy where the environmental microbiome showed a higher diversity than Girandurukotte. Potential animal reservoirs were also detected in samples positive for pathogenicLeptospira, suggesting that environmental DNA metabarcoding can provide important information for management and intervention strategies to control leptospirosis.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 pathogenicLeptospira, 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 pathogenicLeptospira, 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 ofLeptospiraspecies circulating in Kandy than in Girandurukotte. Moreover, the number of sequence reads of pathogenicLeptospiraspecies associated with clinical cases such asL.interroganswas higher in Kandy than in Girandurukotte. Kandy also showed more animal species associated with pathogenic bacterial species than Girandurukotte. Finally, several pathogenic bacterial species includingArcobacter cryaerophilus, responsible for abortion in animals, was shown to be associated with pathogenicLeptospira. Conclusions/Significance Leptospirosis has been considered to be endemic in wet regions, consistently, leptospiral sequences were detected strongly in Kandy. The greatLeptospiraspecies 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.