Data from: Groundwater surveillance of endemic swine pathogens on forty Iowa swine farms via dead-end ultrafiltration

Groundwater samples were collected in an observational study design by dead-end ultrafiltration from private wells on 40 Iowa swine farms and analyzed by quantitative polymerase chain reaction (qPCR) to assess contamination by endemic swine pathogens and swine manure markers. These data facilitate investigation of groundwater as a biosecurity risk on swine farms. Each farm was sampled one time. Twenty farms were sampled in spring of 2024 (4/15/2024 – 5/29/2024) and twenty farms were sampled in fall of 2024 (9/16/2024 – 10/29/2024). Sample volumes were 639–853 L (mean = 759). Control samples were collected in the field for each field sample, and control samples were tested for all organisms if the corresponding field sample tested positive for any organism. Samples were shipped on ice to the laboratory where they were backflushed, underwent secondary concentration, and archived at -80 degrees Celsius. Secondary concentrates were subsampled for nucleic acid extraction using the QIAGEN QIAcube Connect system, and each nucleic acid extract was analyzed in duplicate by qPCR using a Roche LightCycler 480 II for the following microorganisms: <i>Cryptosporidium</i> spp., enteropathogenic <i>Escherichia coli</i>, porcine circovirus type 2, porcine epidemic diarrhea virus, porcine reproductive and respiratory syndrome virus, rotavirus group C, <i>Salmonella</i> spp., swine <i>Bacteroidales</i> (2 qPCR assays), and swine influenza virus. Negative and positive controls were included at lab steps for concentration, nucleic acid extraction, reverse transcription, and qPCR. PCR inhibition was assessed in each nucleic acid extract and mitigated by dilution if necessary. Data are expressed as genomic copies per liter of groundwater sampled unless otherwise indicated. Dataset consists of 1 spreadsheet file: Dataset 01102025_V4.csv. Variables in this file are described in the included data dictionary.

本数据集源自一项观察性研究：研究人员采用死端超滤法，从艾奥瓦州40家生猪养殖场的私人水井中采集地下水样本，并通过定量聚合酶链反应（qPCR）开展分析，以评估水样受地方性生猪病原体及猪粪源标志物的污染情况。该数据集可用于探究生猪养殖场地下水作为生物安全风险因子的相关问题。

所有养殖场均仅采样一次。其中20家养殖场于2024年春季（2024年4月15日—2024年5月29日）完成采样，剩余20家于2024年秋季（2024年9月16日—2024年10月29日）完成采样。单份样本的采集体积为639~853升（平均值为759升）。

针对每一份现场样本，均同步采集现场对照样本；若对应现场样本检出任意一种病原体，则对所有对照样本开展检测。

样本全程冰藏运输至实验室，经反冲处理、二次浓缩后，于-80℃条件下存档保存。

使用凯杰（QIAGEN）QIAcube Connect系统对二次浓缩产物进行分样后开展核酸提取，每份核酸提取物采用罗氏LightCycler 480 II型实时荧光定量PCR仪进行平行双份检测，检测对象包括以下微生物：隐孢子虫属（Cryptosporidium spp.）、肠致病性大肠埃希菌（enteropathogenic Escherichia coli）、猪圆环病毒2型、猪流行性腹泻病毒、猪繁殖与呼吸综合征病毒、C群轮状病毒、沙门氏菌属（Salmonella spp.）、猪拟杆菌（swine Bacteroidales，共包含2项qPCR检测方法）以及猪流感病毒。

在浓缩、核酸提取、逆转录及qPCR各实验步骤中均设置阴性与阳性对照。针对每份核酸提取物均开展PCR抑制性检测，必要时通过稀释方式解除抑制作用。

除特别说明外，所有数据均以每升采集地下水中的基因组拷贝数为单位进行表述。

本数据集包含1个电子表格文件：Dataset 01102025_V4.csv。文件内的变量说明详见附带的数据字典。