Bartonella infections are prevalent in rodents despite efficient immune responses

Pathogens face strong selection from host immune responses, yet many host populations support pervasive pathogen populations. We investigated this puzzle in a model system of Bartonella and rodents from Israel’s northwestern Negev Desert. We chose to study this system because in this region, 75–100% of the rodents are infected with Bartonella at any given time, despite an efficient immunological response. In this region, Bartonella species circulate in three rodent species, and we tested the hypothesis that at least some of these hosts exhibit a waning immune response to Bartonella, which allows reinfections. To that end, we inoculated captive rodents from all three species with the same Bartonella strain, and we quantified the bacterial dynamics and Bartonella-specific IgG antibody kinetics through 139 days after the primary inoculation and then for 60 days following re-inoculation with the same strain. Contrary to our hypothesis, we found a strong, long-lasting IgG antibody response, ..., , , # Data from: Bartonella infections are prevalent in rodents despite efficient immune responses

This file contains: Descriptions of the data sets associated with the analyses presented in the paper.

code.R – R file containing all code necessary to analyze the data. A list of the required packages and is included. The analyses used R v4.1.3, but newer versions are also usable.

NOTE: for all files below \"NA\" values represent data that was not available for a specific animal on a specific day because that animal either died or was removed from the experiment.

bacterial_loads.csv – this is the data file containing information on bacterial dynamics. For the \"Negt.Ctr.\" samples, these are negative controls from each bacterial extraction session.

As such, there is no animal code, NA for species and dpi, as well as empty cells for the \"Infected\" column for these samples, as these data do not come from an experimental animal.

The following are explanations of the variables:

* animal.code ...,

病原体面临宿主免疫反应带来的强烈选择压力，但诸多宿主种群仍维持着广泛流行的病原体种群。我们以以色列西北内盖夫沙漠的巴尔通体（Bartonella）与啮齿动物为模型系统，对这一谜题展开研究。我们选择该系统开展实验的原因在于：尽管该区域啮齿动物具备高效的免疫应答能力，但任意时刻均有75%至100%的个体感染巴尔通体。该区域内，巴尔通体可在3种啮齿动物类群中循环传播，我们据此检验假说：这类宿主中至少部分个体对巴尔通体的免疫应答会出现衰减，从而允许重复感染。为此，我们用同一株巴尔通体对上述3种啮齿动物的圈养个体进行接种，并分别在初次接种后139天内、以及再次接种同一菌株后的60天内，定量检测了细菌动态与巴尔通体特异性IgG抗体的动力学变化。与我们的假说相悖的是，我们观测到了强烈且持久的IgG抗体应答……# 数据来源：尽管免疫应答高效，啮齿动物仍普遍存在巴尔通体感染

本文件包含：与本文所呈现的分析相关的数据集说明。

code.R——包含分析本数据集所需全部代码的R脚本文件，内含所需软件包清单。本分析基于R v4.1.3版本开展，较新的R版本亦可兼容使用。

注意：以下所有文件中的"NA"值代表某一动物在特定日期缺失的检测数据，原因是该动物已死亡或被移出实验。

bacterial_loads.csv——包含细菌动态相关信息的数据集文件。其中的"Negt.Ctr."样本为每次细菌提取流程对应的阴性对照。因此，此类样本无动物编码，物种（species）与dpi（感染后天数）字段均为"NA"，且"Infected"列单元格为空——因为这些数据并非来自实验动物。

以下为各变量的说明：* animal.code（动物编码）……