Data and code from: Buffered peptone water formulation does not influence growth of pESI positive Salmonella serovar Infantis

This repository contains all data and code required to reproduce the growth curve-fitting analysis from the manuscript:
McMillan, E. A., Berrang, M. E., Read, Q. D., Rasamsetti, S., Richards, A. K., Shariat, N. W., & Frye, J. G. (2022). Buffered peptone water formulation does not influence growth of pESI-positive Salmonella enterica serovar Infantis. Journal of Food Protection, 100033. https://doi.org/10.1016/j.jfp.2022.100033
Manuscript abstract
Salmonella enterica is a major cause of human foodborne illness and is often attributed to poultry food sources. S. enterica serovar Infantis, specifically those carrying the pESI plasmid, has become a frequently isolated serotype from poultry meat samples at processing and has caused numerous recent human infections. In 2016, the USDA Food Safety and Inspection Service changed the official sampling method for raw poultry products from BPW to using neutralizing BPW (nBPW) as the rinsing agent in order to prevent residual antimicrobial effects from acidifying and oxidizing processing aids. This change was contemporaneous to the emergence of pESI-positive ser. Infantis as a prevalent serovar in poultry, prompting some to question if nBPW could be selecting for this prevalent serovar. We performed two experiments: a comparison of ser. Infantis growth in BPW versus nBPW, and a simulation of regulatory sampling methods. We found that when inoculated into both broths, ser. Infantis initially grows slightly slower in nBPW than in BPW but little difference was seen in abundance after six hours of growth. Additionally, use of nBPW to simulate poultry rinse sample and overnight cold shipping to a regulatory lab did not affect survival or subsequent growth of ser. Infantis in BPW. We concluded that the change in USDA-FSIS methodology to include nBPW in sampling procedures has likely not affected the emergence of S. ser. Infantis as a prevalent serovar in chicken and turkey meat product samples.
Contents
All necessary data are in a single comma-separated file, Sal_Infantis_growth_curve_data_EAM.csv. All R code is in a single RMarkdown document, salmonella_growth_curve_fitting.Rmd. The RMarkdown contains code to read and process the data, produce exploratory plots, fit the model, do all hoc calculations with the posterior output, and produce figures and tables from the manuscript.
Salmonella Infantis growth data: This is a comma-separated file containing data needed to reproduce the growth curve fitting analysis. Columns are:

Strain: numerical ID of strain (see Table 1 in manuscript)
Colony_Forming_Units_permL(A, B, C): columns 2-4 are three replicate measurements of colony forming units per mL taken from the same sample at the same time.
Media: whether nBPW or BPW was used in the growth medium
Time_hours: time in hours ranging from 0-6.

RMarkdown document with all analysis code: This RMarkdown document contains code to read and process the data, produce exploratory plots, fit the model, do all hoc calculations with the posterior output, and produce figures and tables from the manuscript.
Software versions
This was run on Windows 10, R version 4.1.2. Models were fit using CmdStan version 2.28.2, with brms version 2.17.0, cmdstanr version 0.4.0, emmeans version 1.7.3, and tidybayes version 3.0.2.
Program information
National Program: Food Safety (108)
Project Plan Number: 6040-32000-085-000-D
Resources in this dataset:Resource Title: Salmonella Infantis growth data. File Name: Sal_Infantis_growth_curve_data_EAM.csvResource Title: RMarkdown document with all analysis code. File Name: salmonella_growth_curve_fitting.Rmd

本仓库包含了复现文献中生长曲线拟合分析所需的所有数据和代码：McMillan, E. A. 等.（2022）. 缓冲蛋白胨水配方对pESI阳性Salmonella enterica serovar Infantis生长的影响。食品保护杂志，100033。https://doi.org/10.1016/j.jfp.2022.100033

论文摘要
Salmonella enterica是导致人类食源性疾病的主要原因，常与家禽食品来源相关。特别是携带pESI质粒的S. enterica serovar Infantis，已成为在加工过程中从家禽肉样中频繁分离的血清型，并导致了近期多次人类感染。2016年，美国农业部食品安全检验局将未加工家禽产品的官方采样方法从BPW更改为使用中和BPW（nBPW）作为冲洗剂，以防止酸化和氧化加工助剂残留的抗菌作用。这一变更与pESI阳性血清型Infantis作为家禽中普遍的血清型同时出现，促使一些人质疑nBPW是否在选择性培育这种普遍的血清型。我们进行了两项实验：比较血清型Infantis在BPW与nBPW中的生长，以及模拟监管采样方法。我们发现，当接种到两种肉汤中时，血清型Infantis在nBPW中的初始生长速度略慢于BPW，但六小时后生长丰度差异不明显。此外，使用nBPW模拟家禽冲洗样本和过夜低温运输至监管实验室，并未影响血清型Infantis在BPW中的存活或后续生长。我们得出结论，美国农业部食品安全检验局采用包括nBPW在内的采样程序的方法变更，可能并未影响S. ser. Infantis作为鸡肉和火鸡肉产品样本中普遍的血清型的出现。

内容
所有必要的数据都存储在一个单独的逗号分隔文件中，名为Sal_Infantis_growth_curve_data_EAM.csv。所有R代码都存储在一个单独的RMarkdown文档中，即salmonella_growth_curve_fitting.Rmd。该RMarkdown文档包含读取和处理数据、生成探索性图、拟合模型、对后验输出进行所有假设计算以及从文献中生成图表和表格的代码。

Salmonella Infantis生长数据：这是一个逗号分隔文件，包含复现生长曲线拟合分析所需的数据。列包括：
菌株：菌株的数值ID（参见文献中的表1）；
形成菌落单位每毫升（A，B，C）：第2至4列是来自同一样本且在同一时间测量的每毫升形成菌落单位的三个重复测量值；
培养基：生长培养基中是否使用nBPW或BPW；
时间（小时）：从0到6小时的时间范围。

包含所有分析代码的RMarkdown文档：此RMarkdown文档包含读取和处理数据、生成探索性图、拟合模型、对后验输出进行所有假设计算以及从文献中生成图表和表格的代码。

软件版本：在Windows 10上运行，R版本4.1.2。模型使用CmdStan版本2.28.2、brms版本2.17.0、cmdstanr版本0.4.0、emmeans版本1.7.3和tidybayes版本3.0.2进行拟合。

项目信息：
国家项目：食品安全（108）；
项目计划编号：6040-32000-085-000-D；
本数据集中包含的资源：
资源标题：Salmonella Infantis生长数据。文件名：Sal_Infantis_growth_curve_data_EAM.csv；
资源标题：包含所有分析代码的RMarkdown文档。文件名：salmonella_growth_curve_fitting.Rmd。