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., M. E. Berrang, Q. D. Read, S. Ramasetti, A. K. Richards, N. W. Shariat, and J. G. Frye. Buffered peptone water formulation does not influence growth of pESI positive Salmonella serovar Infantis. Journal of Food Protection, accepted.
citation will be updated upon publication
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.
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