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

<p>This repository contains all data and code required to reproduce the growth curve-fitting analysis from the manuscript:</p>
<p>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 <em>Salmonella enterica</em> serovar Infantis. Journal of Food Protection, 100033. <a href="https://doi.org/10.1016/j.jfp.2022.100033">https://doi.org/10.1016/j.jfp.2022.100033</a></p>
<h3>Manuscript abstract</h3>
<p><em>Salmonella enterica</em> is a major cause of human foodborne illness and is often attributed to poultry food sources. <em>S. enterica</em> 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 <em>S.</em> ser. Infantis as a prevalent serovar in chicken and turkey meat product samples. </p>
<h3>Contents</h3>
<p>All necessary data are in a single comma-separated file, <code>Sal_Infantis_growth_curve_data_EAM.csv</code>. All R code is in a single RMarkdown document, <code>salmonella_growth_curve_fitting.Rmd</code>. 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.</p>
<p>Salmonella Infantis growth data: This is a comma-separated file containing data needed to reproduce the growth curve fitting analysis. Columns are:</p>
<ul>
<li>Strain: numerical ID of strain (see Table 1 in manuscript)</li>
<li>Colony_Forming_Units_per<em>mL</em>(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.</li>
<li>Media: whether nBPW or BPW was used in the growth medium</li>
<li>Time_hours: time in hours ranging from 0-6.</li>
</ul>
<p>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.</p>
<h3>Software versions</h3>
<p>This was run on Windows 10, R version 4.1.2. Models were fit using CmdStan version 2.28.2, with <strong>brms</strong> version 2.17.0, <strong>cmdstanr</strong> version 0.4.0, <strong>emmeans</strong> version 1.7.3, and <strong>tidybayes</strong> version 3.0.2.</p>
<h3>Program information</h3>
<p><strong>National Program</strong>: Food Safety (108)<br>
<strong>Project Plan Number</strong>: 6040-32000-085-000-D</p>
<div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Salmonella Infantis growth data.</p> <p>File Name: Sal_Infantis_growth_curve_data_EAM.csv</p></li><br><li><p>Resource Title: RMarkdown document with all analysis code.</p> <p>File Name: salmonella_growth_curve_fitting.Rmd</p></li></ul><p></p>

Tags: ars, data-gov, nbpw, np108, pesi, poultry, salmonella, salmonella-infantis
Organization: Department of Agriculture