Temporal Dynamics of Salmonella enterica subsp. enterica Serovar Agona Isolates From a Recurrent Multistate Outbreak.

Maria Hoffmann,David Melka,John Miller,Marc W Allard,James B Pettengill,Eric W Brown

doi:10.3389/fmicb.2020.00478

Abstract

The largest outbreak of Salmonella Agona in the United States occurred in 1998. It affected more than 400 patients and was linked to toasted oat cereal. Ten years later, a similar outbreak occurred with the same outbreak strain linked to the same production facility. In this study, whole-genome sequence (WGS) data from a set of 46 Salmonella Agona including five isolates associated with the 1998 outbreak and 25 isolates associated with the 2008 outbreak were analyzed. From each outbreak one isolate was sequenced on the Pacific Biosciences RS II Sequencer to determine the complete genome sequence. We reconstructed a phylogenetic hypothesis of the samples using a reference-based method for identifying variable sites. Using Single Nucleotide Polymorphism (SNP) analyses, we were able to distinguish and separate Salmonella Agona isolates from both outbreaks with only a mean of eight SNP differences between them. The phylogeny illustrates that the 2008 outbreak involves direct descendants from the 1998 outbreak rather than a second independent contamination event. Based on these results, there is evidence supporting the persistence of Salmonella over time in food processing facilities and highlights the need for consistent monitoring and control of organisms in the supply chain to minimize the risk of successive outbreaks.

Highlights

Salmonella enterica subsp. enterica is comprised of more than 1,500 serovars, including Salmonella enterica subsp. enterica serovar Agona (Salmonella Agona)
pulsed-field gel electrophoresis (PFGE) does not have the resolution to distinguish a transient strain from a resident strain (Pightling et al, 2018) and, at that time using this method officials from the state health department were able to correctly identify the source of an outbreak but were not able to determine if the 2008 Agona isolate is the same strain as the 1998 Agona isolate
The population and evolutionary dynamics associated with clonal bacterial populations can be investigated with much greater resolution afforded by generation sequencing (NGS) data

Summary

Introduction

Salmonella enterica subsp. enterica is comprised of more than 1,500 serovars, including Salmonella enterica subsp. enterica serovar Agona (Salmonella Agona). Enterica is comprised of more than 1,500 serovars, including Salmonella enterica subsp. Within the last several years, Salmonella Agona has been one of the top 20 most commonly reported serotypes causing human infections (CDC, 2014). It has been responsible for numerous human outbreaks associated with various dry food products such as dried milk, machacado, dried snacks, and cereal (Clark et al, 1973; Killalea et al, 1996; Taylor et al, 1998). In the United States, the largest known outbreak of Salmonella Agona infections occurred between April and May in 1998 (Russo et al, 2013). The Centers for Disease Control and Prevention (CDC) investigated a multistate (11 states) outbreak of WGS of a Recurrent Outbreak

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