Data_Sheet_1_Disentangling the influence of reservoir abundance and pathogen shedding on zoonotic spillover of the Leptospira agent in urban informal settlements.docx

Rats are major reservoirs for pathogenic Leptospira, the bacteria causing leptospirosis, particularly in urban informal settlements. However, the impact of variation in rat abundance and pathogen shedding rates on spillover transmission to humans remains unclear. This study aimed to investigate how spatial variation in reservoir abundance and pathogen pressure affect Leptospira spillover transmission to humans in a Brazilian urban informal settlement. A longitudinal eco-epidemiological study was conducted from 2013 to 2014 to characterize the spatial distribution of rat abundance and Leptospira shedding rates in rats and determine the association with human infection risk in a cohort of 2,206 community residents. Tracking plates and live-trapping were used to measure rat abundance and quantify rat shedding status and load. In parallel, four sequential biannual serosurveys were used to identify human Leptospira infections. To evaluate the role of shedding on human risk, we built three statistical models for: (1) the relative abundance of rats, (2) the shedding rate by individual rats, and (3) human Leptospira infection, in which “total shedding”, obtained by multiplying the predictions from those two models, was used as a risk factor. We found that Leptospira shedding was associated with older and sexually mature rats and varied spatially and temporally—higher at valley bottoms and with seasonal rainfall (December to March). The point estimate for “total shedding” by rat populations was positive, i.e., Leptospira infection risk increased with total shedding, but the association was not significant [odds ratio (OR) = 1.1; 95% confidence interval (CI): 0.9, 1.4]. This positive trend was mainly driven by rat abundance, rather than individual rat shedding (OR = 1.8; 95% CI: 0.6, 5.4 vs. OR = 1.0; 95% CI: 0.7, 1.4]. Infection risk was higher in areas with more vegetative land cover (OR = 2.4; 95% CI: 1.2, 4.8), and when floodwater entered the house (OR = 2.4; 95% CI: 1.6, 3.4). Our findings indicate that environmental and hydrological factors play a more significant role in Leptospira spillover than rat associated factors. Furthermore, we developed a novel approach combining several models to elucidate complex links between animal reservoir abundance, pathogen shedding and environmental factors on zoonotic spillover in humans that can be extended to other environmentally transmitted diseases.

大鼠是致病性钩端螺旋体（Leptospira）的主要储存宿主，该病原体可引发钩端螺旋体病（leptospirosis），在城市非正式定居点中这一现象尤为突出。然而，大鼠种群丰度与病原体排出率的变异对病原体向人类的溢出传播的影响仍不明确。本研究旨在探究储存宿主丰度与病原体压力的空间变异，如何影响巴西某城市非正式定居点内钩端螺旋体向人类的溢出传播。本研究于2013年至2014年间开展一项纵向生态流行病学研究，以刻画大鼠丰度与大鼠钩端螺旋体排出率的空间分布特征，并明确其与2206名社区居民队列的人类感染风险之间的关联。研究采用活动追踪板与活捕法对大鼠丰度进行测算，并量化大鼠的病原体排出状态与载量。同时，开展4次连续的每半年一次的血清学调查，以识别人类钩端螺旋体感染病例。为评估病原体排出对人类感染风险的作用，我们构建了三类统计模型：（1）大鼠相对丰度模型，（2）单只大鼠的病原体排出率模型，（3）人类钩端螺旋体感染风险模型；其中将通过前两个模型的预测值相乘得到的"总排出量"作为风险因子纳入分析。研究发现，钩端螺旋体排出与年龄更大、性成熟的大鼠相关，且存在空间与时间上的变异——在谷底与12月至3月的降雨季节排出率更高。大鼠种群的"总排出量"点估计值为正，即钩端螺旋体感染风险随总排出量升高而上升，但该关联未达到统计学显著性[优势比（OR）=1.1；95%置信区间（CI）：0.9, 1.4]。这一正向趋势主要由大鼠丰度驱动，而非单只大鼠的病原体排出率（OR=1.8；95%CI：0.6, 5.4 vs. OR=1.0；95%CI：0.7, 1.4）。感染风险在植被覆盖度更高的区域更高（OR=2.4；95%CI：1.2, 4.8），且当洪水进入住宅时风险也会升高（OR=2.4；95%CI：1.6, 3.4）。我们的研究结果表明，环境与水文因素在钩端螺旋体的溢出传播中发挥的作用，较与大鼠相关的因素更为显著。此外，我们开发了一种全新的联合多模型分析方法，用以阐明动物储存宿主丰度、病原体排出量与环境因素之间的复杂关联，以及其对人类人畜共患病溢出传播的影响，该方法可推广应用于其他经环境传播的疾病研究。