Salmonella surveillance data for Israeli poultry farms during 2017-2019

<strong>The Israeli Salmonella surveillance programme for pullet and layer farms during the study period </strong> Under the surveillance scheme for <em>Salmonella</em> that started in June 2017 and continued throughout the entire period of the dataset, layer farms were sampled every 15 weeks from the moment the flock reaches an age of 22 to 24 weeks. Pullet farms were sampled approximately one week prior to the distribution of pullets to layer farms. The general surveillance scheme aimed to include all pullet and layer farms. Samples were taken by inspectors from either the Israeli Veterinary Services (IVS) or the Egg and Poultry Board (EPB). On each sampling occasion, IVS inspectors usually took 2 pairs of drag swabs, 2 pairs of dust swabs from walls and equipment and one dust sample, while EPB inspectors usually took 2 pairs of drag swabs. If present, <em>Salmonella</em> serovars were identified to the group level according to the Kauffman-White scheme by the EPB laboratory. Isolates of groups B or D were further identified to the serovar level by the <em>Salmonella</em> National Reference Laboratory of the Israeli Ministry of Health. Farms testing positive for <em>Salmonella</em> serovars Enteritidis and/or Typhimurium were culled and thoroughly cleaned and disinfected. Repopulation of these farms was only allowed after drag swabs from the empty houses tested negative for all <em>Salmonella</em> serovars. <strong>Farm characteristics</strong> Hens were caged on the vast majority of layer farms (97.5%) and free-ranging on the remainder of farms. Farm size varied widely (less than 100 to 255,000), and the median size was around 2,900. The number of houses per farm varied from 1 to 6, but the vast majority of farms contained only one house (97.9%). <strong>Production cycle</strong> Production cycles on farms that did not test positive for the targeted Salmonella strains lasted on average 18.2 weeks for pullets and 95.4 weeks for layers. The number of houses per farm varied from 1 to 6, but the vast majority of farms contained only one house (97.9%). For farms that had several houses, the production cycle always started at the same date in all houses (same flock in all houses). <strong>Available data</strong> Sampling date were available for a total of 1,842 layer farms and 56 pullet farms during the period from early June 2017 to early April 2019. Three data files are available. All data fields in these files are described in the separate code book file, but here follows a summary of their content:- File “20230907 SamplingDate.txt” contains sampling data and includes a.o the following fields:· farm type· flock identifier· the sampling date· sample type· number of samples by type· date test result· test result- File “20230907 BetweenFarmDistanceMatrix.txt” contains information about the between-farm distance in kilometers.- File “20230907 FlockData.txt” describes the start and closing date of production cycles. These files can be linked via the farm and/o flock identifier fields. <strong>Data restrictions</strong><strong> </strong>The raw data in its original form could not be published, since it contains information that has been classified as sensitive by the Israeli government. Therefore, firstly, only the information required for the analyses in the Epi-Risk project could be published. Secondly, Instead of reporting farm locations, we therefore provide a matrix with the distance between anonymised farms in kilometers. Finally, we replaced the original farm, flock and sample identifiers by new anonymised ones.<strong> </strong>

**研究期间以色列针对青年鸡场与蛋鸡场的沙门氏菌监测计划**

本数据集依托2017年6月启动并贯穿全监测周期的沙门氏菌（Salmonella）监测方案开展工作：蛋鸡场于鸡群达到22~24周龄起，每15周采样一次；青年鸡场则于后备蛋鸡转运至蛋鸡场前约一周开展采样。该通用监测方案计划覆盖所有青年鸡场与蛋鸡场。采样工作由以色列兽医服务局（Israeli Veterinary Services, IVS）或鸡蛋与家禽委员会（Egg and Poultry Board, EPB）的执法人员完成。每次采样时，IVS执法人员通常采集2套拖拭棉拭子、2套墙面与设备积尘棉拭子及1份积尘样本；EPB执法人员通常采集2套拖拭棉拭子。若检出沙门氏菌血清型，EPB实验室将依据考夫曼-怀特（Kauffman-White）分型方案鉴定至菌群水平；对于B群或D群分离株，以色列卫生部沙门氏菌国家参考实验室将进一步鉴定至血清型水平。检出肠炎沙门氏菌（Salmonella Enteritidis）和/或鼠伤寒沙门氏菌（Salmonella Typhimurium）阳性的鸡场，将对场内鸡群实施扑杀并开展彻底清洁与消毒，仅当空置鸡舍的拖拭棉拭子检测所有沙门氏菌血清型均为阴性后，方可重新引入鸡群开展养殖。

**养殖场基本特征**
绝大多数蛋鸡场（97.5%）采用笼养模式，剩余养殖场采用散养模式。养殖场存栏规模差异悬殊（100只以下至255000只不等），存栏规模中位数约为2900只。单场鸡舍数量为1~6栋，但绝大多数养殖场仅设有1栋鸡舍（97.9%）。

**生产周期**
未检出目标沙门氏菌菌株的养殖场，其青年鸡生产周期平均为18.2周，蛋鸡生产周期平均为95.4周。单场鸡舍数量为1~6栋，但绝大多数养殖场仅设有1栋鸡舍（97.9%）。对于拥有多栋鸡舍的养殖场，所有鸡舍的生产周期均于同一日期启动（即各鸡舍饲养同一批次鸡群）。

**可用数据**
2017年6月初至2019年4月初期间，共获取1842家蛋鸡场及56家青年鸡场的采样记录。本次公开数据集包含3个数据文件，各文件内的所有数据字段均在独立的代码手册文件中详述，以下为内容概要：
- 文件「20230907 SamplingDate.txt」包含采样相关数据，字段涵盖养殖场类型、鸡群标识符、采样日期、样本类型、各类样本采集数量、检测结果出具日期、检测结果等。
- 文件「20230907 BetweenFarmDistanceMatrix.txt」包含养殖场间千米级距离信息。
- 文件「20230907 FlockData.txt」记载了生产周期的启动与结束日期。
上述文件可通过养殖场和/或鸡群标识符字段进行关联。

**数据使用限制**
原始数据因包含以色列政府认定为敏感的信息，无法以原貌公开。因此，其一，仅可公开Epi-Risk项目分析所需的必要信息；其二，我们未披露养殖场实际地理位置，取而代之的是一份包含匿名化养殖场间千米级距离的矩阵文件；最后，我们已将原始的养殖场、鸡群及样本标识符替换为全新的匿名化标识符。